Percolation of Monte Carlo clusters

International Nuclear Information System (INIS)

Wanzeller, W.G.; Krein, G.; Cucchieri, A.; Mendes, T.

2004-01-01

Percolation theory is of interest in problems of phase transitions in condensed matter physics, and in biology and chemistry. More recently, concepts of percolation theory have been invoked in studies of color deconfinement at high temperatures in Quantum Chromodynamics. In the present paper we briefly review the basic concept of percolation theory, exemplify its application to the Ising model, and present the arguments for a possible relevance of percolation theory to the problem of color deconfinement. (author)

Integral hierarchies and percolation

International Nuclear Information System (INIS)

Klein, W.; Stell, G.

1985-01-01

For a variation of the Potts model which has been shown to describe continuum percolation, we derive a hierarchy of integral equations of Kirkwood-Salsburg type. The distribution functions which are the solutions of this hierarchy can be simply related to the connectedness functions in continuum percolation. From this hierarchy a second set of equations is derived from which the connectedness functions can be obtained directly. This approach is extremely useful when investigating properties of systems far from the percolation transition. These hierarchies are solved exactly in the mean-field (Kac-Baker) limit and possible implications for cluster growth are discussed. The relation between the Potts model for continuum percolation and the Widom-Rowlinson model is also noted

Motif analysis unveils the possible co-regulation of chloroplast genes and nuclear genes encoding chloroplast proteins.

Science.gov (United States)

Wang, Ying; Ding, Jun; Daniell, Henry; Hu, Haiyan; Li, Xiaoman

2012-09-01

Chloroplasts play critical roles in land plant cells. Despite their importance and the availability of at least 200 sequenced chloroplast genomes, the number of known DNA regulatory sequences in chloroplast genomes are limited. In this paper, we designed computational methods to systematically study putative DNA regulatory sequences in intergenic regions near chloroplast genes in seven plant species and in promoter sequences of nuclear genes in Arabidopsis and rice. We found that -35/-10 elements alone cannot explain the transcriptional regulation of chloroplast genes. We also concluded that there are unlikely motifs shared by intergenic sequences of most of chloroplast genes, indicating that these genes are regulated differently. Finally and surprisingly, we found five conserved motifs, each of which occurs in no more than six chloroplast intergenic sequences, are significantly shared by promoters of nuclear-genes encoding chloroplast proteins. By integrating information from gene function annotation, protein subcellular localization analyses, protein-protein interaction data, and gene expression data, we further showed support of the functionality of these conserved motifs. Our study implies the existence of unknown nuclear-encoded transcription factors that regulate both chloroplast genes and nuclear genes encoding chloroplast protein, which sheds light on the understanding of the transcriptional regulation of chloroplast genes.

Group percolation in interdependent networks

Science.gov (United States)

Wang, Zexun; Zhou, Dong; Hu, Yanqing

2018-03-01

In many real network systems, nodes usually cooperate with each other and form groups to enhance their robustness to risks. This motivates us to study an alternative type of percolation, group percolation, in interdependent networks under attack. In this model, nodes belonging to the same group survive or fail together. We develop a theoretical framework for this group percolation and find that the formation of groups can improve the resilience of interdependent networks significantly. However, the percolation transition is always of first order, regardless of the distribution of group sizes. As an application, we map the interdependent networks with intersimilarity structures, which have attracted much attention recently, onto the group percolation and confirm the nonexistence of continuous phase transitions.

PERCOLATION TRANSITION AND TOPOLOGY

Directory of Open Access Journals (Sweden)

Patricia Jouannot-Chesney

2017-06-01

Full Text Available A number of bidimensional random structures with increasing densities are simulated to explore possible links between Euler-Poincaré characteristic (EPC, or connectivity, and percolation threshold. For each structure model, the percolation threshold is compared with a number of typical points (extrema, zero crossings... of the EPC curve. From these exercises, it can be concluded that the percolation threshold cannot be generally predicted using the evolution of the EPC.

Analyses of charophyte chloroplast genomes help characterize the ancestral chloroplast genome of land plants.

Science.gov (United States)

Civaň, Peter; Foster, Peter G; Embley, Martin T; Séneca, Ana; Cox, Cymon J

2014-04-01

Despite the significance of the relationships between embryophytes and their charophyte algal ancestors in deciphering the origin and evolutionary success of land plants, few chloroplast genomes of the charophyte algae have been reconstructed to date. Here, we present new data for three chloroplast genomes of the freshwater charophytes Klebsormidium flaccidum (Klebsormidiophyceae), Mesotaenium endlicherianum (Zygnematophyceae), and Roya anglica (Zygnematophyceae). The chloroplast genome of Klebsormidium has a quadripartite organization with exceptionally large inverted repeat (IR) regions and, uniquely among streptophytes, has lost the rrn5 and rrn4.5 genes from the ribosomal RNA (rRNA) gene cluster operon. The chloroplast genome of Roya differs from other zygnematophycean chloroplasts, including the newly sequenced Mesotaenium, by having a quadripartite structure that is typical of other streptophytes. On the basis of the improbability of the novel gain of IR regions, we infer that the quadripartite structure has likely been lost independently in at least three zygnematophycean lineages, although the absence of the usual rRNA operonic synteny in the IR regions of Roya may indicate their de novo origin. Significantly, all zygnematophycean chloroplast genomes have undergone substantial genomic rearrangement, which may be the result of ancient retroelement activity evidenced by the presence of integrase-like and reverse transcriptase-like elements in the Roya chloroplast genome. Our results corroborate the close phylogenetic relationship between Zygnematophyceae and land plants and identify 89 protein-coding genes and 22 introns present in the chloroplast genome at the time of the evolutionary transition of plants to land, all of which can be found in the chloroplast genomes of extant charophytes.

Target-Searching on Percolation

International Nuclear Information System (INIS)

Yang Shijie

2005-01-01

We study target-searching processes on a percolation, on which a hunter tracks a target by smelling odors it emits. The odor intensity is supposed to be inversely proportional to the distance it propagates. The Monte Carlo simulation is performed on a 2-dimensional bond-percolation above the threshold. Having no idea of the location of the target, the hunter determines its moves only by random attempts in each direction. For lager percolation connectivity p ∼> 0.90, it reveals a scaling law for the searching time versus the distance to the position of the target. The scaling exponent is dependent on the sensitivity of the hunter. For smaller p, the scaling law is broken and the probability of finding out the target significantly reduces. The hunter seems trapped in the cluster of the percolation and can hardly reach the goal.

AT_CHLORO, a comprehensive chloroplast proteome database with subplastidial localization and curated information on envelope proteins.

Science.gov (United States)

Ferro, Myriam; Brugière, Sabine; Salvi, Daniel; Seigneurin-Berny, Daphné; Court, Magali; Moyet, Lucas; Ramus, Claire; Miras, Stéphane; Mellal, Mourad; Le Gall, Sophie; Kieffer-Jaquinod, Sylvie; Bruley, Christophe; Garin, Jérôme; Joyard, Jacques; Masselon, Christophe; Rolland, Norbert

2010-06-01

Recent advances in the proteomics field have allowed a series of high throughput experiments to be conducted on chloroplast samples, and the data are available in several public databases. However, the accurate localization of many chloroplast proteins often remains hypothetical. This is especially true for envelope proteins. We went a step further into the knowledge of the chloroplast proteome by focusing, in the same set of experiments, on the localization of proteins in the stroma, the thylakoids, and envelope membranes. LC-MS/MS-based analyses first allowed building the AT_CHLORO database (http://www.grenoble.prabi.fr/protehome/grenoble-plant-proteomics/), a comprehensive repertoire of the 1323 proteins, identified by 10,654 unique peptide sequences, present in highly purified chloroplasts and their subfractions prepared from Arabidopsis thaliana leaves. This database also provides extensive proteomics information (peptide sequences and molecular weight, chromatographic retention times, MS/MS spectra, and spectral count) for a unique chloroplast protein accurate mass and time tag database gathering identified peptides with their respective and precise analytical coordinates, molecular weight, and retention time. We assessed the partitioning of each protein in the three chloroplast compartments by using a semiquantitative proteomics approach (spectral count). These data together with an in-depth investigation of the literature were compiled to provide accurate subplastidial localization of previously known and newly identified proteins. A unique knowledge base containing extensive information on the proteins identified in envelope fractions was thus obtained, allowing new insights into this membrane system to be revealed. Altogether, the data we obtained provide unexpected information about plastidial or subplastidial localization of some proteins that were not suspected to be associated to this membrane system. The spectral counting-based strategy was further

Euglena mitochondria and chloroplasts form tyrosine-O-sulfate

Energy Technology Data Exchange (ETDEWEB)

Saidha, T.; Hanfstingl, U.; Schiff, J.A. (Brandeis Univ., Waltham, MA (USA))

1989-04-01

Mitochondria from light-grown wild-type Euglena gracilis var. bacillaris Cori or dark-grown mutant W{sub 10}BSmL incubated with {sup 35}SO{sub 4}{sup 2{minus}} and ATP, or with {sup 14}C-tyrosine, non-radioactive sulfate and ATP accumulate a labeled compound in the medium. Since this compound shows exact coelectrophoresis with tyrosine-O-sulfate (TOS) at pH 2.0, 5.8 or 8.0., yields sulfate and tyrosine on acid hydrolysis, and treatment with aryl sulfatase from Aerobacter aerogenes yields sulfate and tyrosine but no tyrosine methyl ester, it is identified as TOS. No TOS is found outside purified developing chloroplasts incubated with {sup 35}SO{sub 4}{sup 2{minus}} and ATP, but both chloroplasts and mitochondria form to {sup 35}S externally when incubated with adenosine 3{prime} phosphate 5{prime}phospho({sup 35}S) sulfate (PAP{sup 35}S). Since no tyrosine need be added, tyrosine is provided from endogenous sources. Although TOS is found in the free pool of Euglena cells it cannot be detected in proteins of cells or mucus ruling our sulfation of tyrosine of protein or incorporation of TOS into proteins. The system forming TOS is membrane-bound and may be involved in tyrosine transport.

The internal percolation problem

International Nuclear Information System (INIS)

Bezsudnov, I.V.; Snarskii, A.A.

2010-01-01

The internal percolation problem (IP) as a new type of the percolation problem is introduced and investigated. In spite of the usual (or external) percolation problem (EP) when the percolation current flows from the top to the bottom of the system, in IP case the voltage is applied through bars which are present in the hole located within the system. The EP problem has two major parameters: M-size of the system and a 0 -size of inclusions, bond size, etc. The IP problem holds one parameter more: size of the hole L. Numerical simulation shows that the critical indexes of conductance for the IP problem are very close to those in the EP problem. On the contrary, the indexes of the relative spectral noise density of 1/f noise and higher moments differ from those in the EP problem. The basics of these facts is discussed.

Percolation technique for galaxy clustering

Science.gov (United States)

Klypin, Anatoly; Shandarin, Sergei F.

1993-01-01

We study percolation in mass and galaxy distributions obtained in 3D simulations of the CDM, C + HDM, and the power law (n = -1) models in the Omega = 1 universe. Percolation statistics is used here as a quantitative measure of the degree to which a mass or galaxy distribution is of a filamentary or cellular type. The very fast code used calculates the statistics of clusters along with the direct detection of percolation. We found that the two parameters mu(infinity), characterizing the size of the largest cluster, and mu-squared, characterizing the weighted mean size of all clusters excluding the largest one, are extremely useful for evaluating the percolation threshold. An advantage of using these parameters is their low sensitivity to boundary effects. We show that both the CDM and the C + HDM models are extremely filamentary both in mass and galaxy distribution. The percolation thresholds for the mass distributions are determined.

Transient foreign gene expression in chloroplasts of cultured tobacco cells after biolistic delivery of chloroplast vectors.

Science.gov (United States)

Daniell, H; Vivekananda, J; Nielsen, B L; Ye, G N; Tewari, K K; Sanford, J C

1990-01-01

Expression of chloramphenicol acetyltransferase (cat) by suitable vectors in chloroplasts of cultured tobacco cells, delivered by high-velocity microprojectiles, is reported here. Several chloroplast expression vectors containing bacterial cat genes, placed under the control of either psbA promoter region from pea (pHD series) or rbcL promoter region from maize (pAC series) have been used in this study. In addition, chloroplast expression vectors containing replicon fragments from pea, tobacco, or maize chloroplast DNA have also been tested for efficiency and duration of cat expression in chloroplasts of tobacco cells. Cultured NT1 tobacco cells collected on filter papers were bombarded with tungsten particles coated with pUC118 (negative control), 35S-CAT (nuclear expression vector), pHD312 (repliconless chloroplast expression vector), and pHD407, pACp18, and pACp19 (chloroplast expression vectors with replicon). Sonic extracts of cells bombarded with pUC118 showed no detectable cat activity in the autoradiograms. Nuclear expression of cat reached two-thirds of the maximal 48 hr after bombardment and the maximal at 72 hr. Cells bombarded with chloroplast expression vectors showed a low level of expression until 48 hr of incubation. A dramatic increase in the expression of cat was observed 24 hr after the addition of fresh medium to cultured cells in samples bombarded with pHD407; the repliconless vector pHD312 showed about 50% of this maximal activity. The expression of nuclear cat and the repliconless chloroplast vector decreased after 72 hr, but a high level of chloroplast cat expression was maintained in cells bombarded with pHD407. Organelle-specific expression of cat in appropriate compartments was checked by introducing various plasmid constructions into tobacco protoplasts by electroporation. Although the nuclear expression vector 35S-CAT showed expression of cat, no activity was observed with any chloroplast vectors.

Disorder-induced quantum bond percolation

International Nuclear Information System (INIS)

Nishino, Shinya; Katsuno, Shuji; Goda, Masaki

2009-01-01

We investigate the effects of off-diagonal disorder on localization properties in quantum bond percolation networks on cubic lattices, motivated by the finding that the off-diagonal disorder does not always enhance the quantum localization of wavefunctions. We numerically construct a diagram of the 'percolation threshold', distinguishing extended states from localized states as a function of two degrees of disorder, by using the level statistics and finite-size scaling. The percolation threshold increases in a characteristic way on increasing the disorder in the connected bonds, while it gradually decreases on increasing the disorder in the disconnected bonds. Furthermore, the exchange of connected and disconnected bonds induced by the disorder causes a dramatic change of the percolation threshold.

Reversible first-order transition in Pauli percolation

Science.gov (United States)

Maksymenko, Mykola; Moessner, Roderich; Shtengel, Kirill

2015-06-01

Percolation plays an important role in fields and phenomena as diverse as the study of social networks, the dynamics of epidemics, the robustness of electricity grids, conduction in disordered media, and geometric properties in statistical physics. We analyze a new percolation problem in which the first-order nature of an equilibrium percolation transition can be established analytically and verified numerically. The rules for this site percolation model are physical and very simple, requiring only the introduction of a weight W (n )=n +1 for a cluster of size n . This establishes that a discontinuous percolation transition can occur with qualitatively more local interactions than in all currently considered examples of explosive percolation; and that, unlike these, it can be reversible. This greatly extends both the applicability of such percolation models in principle and their reach in practice.

Dimensional crossover in directed percolation

International Nuclear Information System (INIS)

Chame, A.M.N.; Queiroz, S.L.A. de; Santos, Raimundo R. dos.

1984-04-01

We study the dimensional crossover in directed percolation in three dimensions. Bonds are allowed to have different concentrations along the three cartesian axes of the lattice. Through a Position Space Renormalization Group we obtain the phase-diagrama where non-percolating, 1-D, 2-D and 3-D percolating phases are present. We find that the isotropic fixed points are unstable with respect to anisotropy, thus driving the system into a different universality class. (author) [pt

Attacks and infections in percolation processes

International Nuclear Information System (INIS)

Janssen, Hans-Karl; Stenull, Olaf

2017-01-01

We discuss attacks and infections at propagating fronts of percolation processes based on the extended general epidemic process. The scaling behavior of the number of the attacked and infected sites in the long time limit at the ordinary and tricritical percolation transitions is governed by specific composite operators of the field-theoretic representation of this process. We calculate corresponding critical exponents for tricritical percolation in mean-field theory and for ordinary percolation to 1-loop order. Our results agree well with the available numerical data. (paper)

Percolator: Scalable Pattern Discovery in Dynamic Graphs

Energy Technology Data Exchange (ETDEWEB)

Choudhury, Sutanay; Purohit, Sumit; Lin, Peng; Wu, Yinghui; Holder, Lawrence B.; Agarwal, Khushbu

2018-02-06

We demonstrate Percolator, a distributed system for graph pattern discovery in dynamic graphs. In contrast to conventional mining systems, Percolator advocates efficient pattern mining schemes that (1) support pattern detection with keywords; (2) integrate incremental and parallel pattern mining; and (3) support analytical queries such as trend analysis. The core idea of Percolator is to dynamically decide and verify a small fraction of patterns and their in- stances that must be inspected in response to buffered updates in dynamic graphs, with a total mining cost independent of graph size. We demonstrate a) the feasibility of incremental pattern mining by walking through each component of Percolator, b) the efficiency and scalability of Percolator over the sheer size of real-world dynamic graphs, and c) how the user-friendly GUI of Percolator inter- acts with users to support keyword-based queries that detect, browse and inspect trending patterns. We also demonstrate two user cases of Percolator, in social media trend analysis and academic collaboration analysis, respectively.

Social percolation models

Science.gov (United States)

Solomon, Sorin; Weisbuch, Gerard; de Arcangelis, Lucilla; Jan, Naeem; Stauffer, Dietrich

2000-03-01

We here relate the occurrence of extreme market shares, close to either 0 or 100%, in the media industry to a percolation phenomenon across the social network of customers. We further discuss the possibility of observing self-organized criticality when customers and cinema producers adjust their preferences and the quality of the produced films according to previous experience. Comprehensive computer simulations on square lattices do indeed exhibit self-organized criticality towards the usual percolation threshold and related scaling behaviour.

Anisotropic Percolation Analysis of Discharge

Science.gov (United States)

Matsumoto, Shogo; Odagaki, Takashi

2014-03-01

Exploiting a nonlinear resistor network on a square lattice in two dimensions, we investigate discharge when two opposite sides of the lattice are subjected to a constant voltage difference. Each site is ionized randomly with a probability in proportion to the square of the strength of the electric field, and the resistivity between two ionized sites is assumed to be 10-6 times smaller than the original resistivity. Using Monte Carlo simulation, we obtain the current and distribution of clusters of ionized sites as functions of the fraction of ionized sites. It is found that a wall of potential drop is formed as the fraction approaches a critical value, which is followed by discharge. The critical value is much smaller than the critical percolation probability of the standard site percolation on the square lattice. We also find that a singular behavior of the cluster distribution is expected at a critical fraction differently from that for the current, and that the critical exponents characterizing the cluster distribution satisfy the scaling relation known for two-dimensional percolation, while the critical exponent of the percolation probability is close to the value reported for a directed percolation.

REDUCED CHLOROPLAST COVERAGE genes from Arabidopsis thaliana help to establish the size of the chloroplast compartment.

Science.gov (United States)

Larkin, Robert M; Stefano, Giovanni; Ruckle, Michael E; Stavoe, Andrea K; Sinkler, Christopher A; Brandizzi, Federica; Malmstrom, Carolyn M; Osteryoung, Katherine W

2016-02-23

Eukaryotic cells require mechanisms to establish the proportion of cellular volume devoted to particular organelles. These mechanisms are poorly understood. From a screen for plastid-to-nucleus signaling mutants in Arabidopsis thaliana, we cloned a mutant allele of a gene that encodes a protein of unknown function that is homologous to two other Arabidopsis genes of unknown function and to FRIENDLY, which was previously shown to promote the normal distribution of mitochondria in Arabidopsis. In contrast to FRIENDLY, these three homologs of FRIENDLY are found only in photosynthetic organisms. Based on these data, we proposed that FRIENDLY expanded into a small gene family to help regulate the energy metabolism of cells that contain both mitochondria and chloroplasts. Indeed, we found that knocking out these genes caused a number of chloroplast phenotypes, including a reduction in the proportion of cellular volume devoted to chloroplasts to 50% of wild type. Thus, we refer to these genes as REDUCED CHLOROPLAST COVERAGE (REC). The size of the chloroplast compartment was reduced most in rec1 mutants. The REC1 protein accumulated in the cytosol and the nucleus. REC1 was excluded from the nucleus when plants were treated with amitrole, which inhibits cell expansion and chloroplast function. We conclude that REC1 is an extraplastidic protein that helps to establish the size of the chloroplast compartment, and that signals derived from cell expansion or chloroplasts may regulate REC1.

Percolation in real multiplex networks

Science.gov (United States)

Bianconi, Ginestra; Radicchi, Filippo

2016-12-01

We present an exact mathematical framework able to describe site-percolation transitions in real multiplex networks. Specifically, we consider the average percolation diagram valid over an infinite number of random configurations where nodes are present in the system with given probability. The approach relies on the locally treelike ansatz, so that it is expected to accurately reproduce the true percolation diagram of sparse multiplex networks with negligible number of short loops. The performance of our theory is tested in social, biological, and transportation multiplex graphs. When compared against previously introduced methods, we observe improvements in the prediction of the percolation diagrams in all networks analyzed. Results from our method confirm previous claims about the robustness of real multiplex networks, in the sense that the average connectedness of the system does not exhibit any significant abrupt change as its individual components are randomly destroyed.

Arabidopsis thaliana AMY3 Is a Unique Redox-regulated Chloroplastic α-Amylase

DEFF Research Database (Denmark)

Seung, David; Thalmann, Matthias; Sparla, Francesca

2013-01-01

α-Amylases are glucan hydrolases that cleave α-1,4-glucosidic bonds in starch. In vascular plants, α-amylases can be classified into three subfamilies. Arabidopsis has one member of each subfamily. Among them, only AtAMY3 is localized in the chloroplast. We expressed and purified AtAMY3 from...... to be dependent on a conserved aspartic acid residue (Asp666), identified as the catalytic nucleophile in other plant α-amylases such as the barley AMY1. AtAMY3 released small linear and branched glucans from Arabidopsis starch granules, and the proportion of branched glucans increased after the predigestion...

Recent advances in percolation theory and its applications

Energy Technology Data Exchange (ETDEWEB)

Saberi, Abbas Ali, E-mail: ab.saberi@ut.ac.ir

2015-05-24

Percolation is the simplest fundamental model in statistical mechanics that exhibits phase transitions signaled by the emergence of a giant connected component. Despite its very simple rules, percolation theory has successfully been applied to describe a large variety of natural, technological and social systems. Percolation models serve as important universality classes in critical phenomena characterized by a set of critical exponents which correspond to a rich fractal and scaling structure of their geometric features. We will first outline the basic features of the ordinary model. Over the years a variety of percolation models has been introduced some of which with completely different scaling and universal properties from the original model with either continuous or discontinuous transitions depending on the control parameter, dimensionality and the type of the underlying rules and networks. We will try to take a glimpse at a number of selective variations including Achlioptas process, half-restricted process and spanning cluster-avoiding process as examples of the so-called explosive percolation. We will also introduce non-self-averaging percolation and discuss correlated percolation and bootstrap percolation with special emphasis on their recent progress. Directed percolation process will be also discussed as a prototype of systems displaying a nonequilibrium phase transition into an absorbing state. In the past decade, after the invention of stochastic Löwner evolution (SLE) by Oded Schramm, two-dimensional (2D) percolation has become a central problem in probability theory leading to the two recent Fields medals. After a short review on SLE, we will provide an overview on existence of the scaling limit and conformal invariance of the critical percolation. We will also establish a connection with the magnetic models based on the percolation properties of the Fortuin–Kasteleyn and geometric spin clusters. As an application we will discuss how percolation

Recent advances in percolation theory and its applications

Science.gov (United States)

Saberi, Abbas Ali

2015-05-01

Percolation is the simplest fundamental model in statistical mechanics that exhibits phase transitions signaled by the emergence of a giant connected component. Despite its very simple rules, percolation theory has successfully been applied to describe a large variety of natural, technological and social systems. Percolation models serve as important universality classes in critical phenomena characterized by a set of critical exponents which correspond to a rich fractal and scaling structure of their geometric features. We will first outline the basic features of the ordinary model. Over the years a variety of percolation models has been introduced some of which with completely different scaling and universal properties from the original model with either continuous or discontinuous transitions depending on the control parameter, dimensionality and the type of the underlying rules and networks. We will try to take a glimpse at a number of selective variations including Achlioptas process, half-restricted process and spanning cluster-avoiding process as examples of the so-called explosive percolation. We will also introduce non-self-averaging percolation and discuss correlated percolation and bootstrap percolation with special emphasis on their recent progress. Directed percolation process will be also discussed as a prototype of systems displaying a nonequilibrium phase transition into an absorbing state. In the past decade, after the invention of stochastic Löwner evolution (SLE) by Oded Schramm, two-dimensional (2D) percolation has become a central problem in probability theory leading to the two recent Fields medals. After a short review on SLE, we will provide an overview on existence of the scaling limit and conformal invariance of the critical percolation. We will also establish a connection with the magnetic models based on the percolation properties of the Fortuin-Kasteleyn and geometric spin clusters. As an application we will discuss how percolation

Recent advances in percolation theory and its applications

International Nuclear Information System (INIS)

Saberi, Abbas Ali

2015-01-01

Percolation is the simplest fundamental model in statistical mechanics that exhibits phase transitions signaled by the emergence of a giant connected component. Despite its very simple rules, percolation theory has successfully been applied to describe a large variety of natural, technological and social systems. Percolation models serve as important universality classes in critical phenomena characterized by a set of critical exponents which correspond to a rich fractal and scaling structure of their geometric features. We will first outline the basic features of the ordinary model. Over the years a variety of percolation models has been introduced some of which with completely different scaling and universal properties from the original model with either continuous or discontinuous transitions depending on the control parameter, dimensionality and the type of the underlying rules and networks. We will try to take a glimpse at a number of selective variations including Achlioptas process, half-restricted process and spanning cluster-avoiding process as examples of the so-called explosive percolation. We will also introduce non-self-averaging percolation and discuss correlated percolation and bootstrap percolation with special emphasis on their recent progress. Directed percolation process will be also discussed as a prototype of systems displaying a nonequilibrium phase transition into an absorbing state. In the past decade, after the invention of stochastic Löwner evolution (SLE) by Oded Schramm, two-dimensional (2D) percolation has become a central problem in probability theory leading to the two recent Fields medals. After a short review on SLE, we will provide an overview on existence of the scaling limit and conformal invariance of the critical percolation. We will also establish a connection with the magnetic models based on the percolation properties of the Fortuin–Kasteleyn and geometric spin clusters. As an application we will discuss how percolation

Chloroplast Redox Poise

DEFF Research Database (Denmark)

Steccanella, Verdiana

the redox status of the plastoquinone pool and chlorophyll biosynthesis. Furthermore, in the plant cell, the equilibrium between redox reactions and ROS signals is also maintained by various balancing mechanisms among which the thioredoxin reductase-thioredoxin system (TR-Trx) stands out as a mediator......The redox state of the chloroplast is maintained by a delicate balance between energy production and consumption and is affected by the need to avoid increased production of reactive oxygen species (ROS). Redox power and ROS generated in the chloroplast are essential for maintaining physiological...... metabolic pathways and for optimizing chloroplast functions. The redox poise of photosynthetic electron transport components like plastoquinone is crucial to initiate signaling cascades and might also be involved in key biosynthetic pathways such as chlorophyll biosynthesis. We, therefore, explored...

Field production and functional evaluation of chloroplast-derived interferon-alpha2b.

Science.gov (United States)

Arlen, Philip A; Falconer, Regina; Cherukumilli, Sri; Cole, Amy; Cole, Alexander M; Oishi, Karen K; Daniell, Henry

2007-07-01

Type I interferons (IFNs) inhibit viral replication and cell growth and enhance the immune response, and therefore have many clinical applications. IFN-alpha2b ranks third in world market use for a biopharmaceutical, behind only insulin and erythropoietin. The average annual cost of IFN-alpha2b for the treatment of hepatitis C infection is $26,000, and is therefore unavailable to the majority of patients in developing countries. Therefore, we expressed IFN-alpha2b in tobacco chloroplasts, and transgenic lines were grown in the field after obtaining United States Department of Agriculture Animal and Plant Health Inspection Service (USDA-APHIS) approval. Stable, site-specific integration of transgenes into chloroplast genomes and homoplasmy through several generations were confirmed. IFN-alpha2b levels reached up to 20% of total soluble protein, or 3 mg per gram of leaf (fresh weight). Transgenic IFN-alpha2b had similar in vitro biological activity to commercially produced PEG-Introntrade mark when tested for its ability to protect cells against cytopathic viral replication in the vesicular stomatitis virus cytopathic effect (VSV CPE) assay and to inhibit early-stage human immunodeficiency virus (HIV) infection. The antitumour and immunomodulating properties of IFN-alpha2b were also seen in vivo. Chloroplast-derived IFN-alpha2b increased the expression of major histocompatibility complex class I (MHC I) on splenocytes and the total number of natural killer (NK) cells. Finally, IFN-alpha2b purified from chloroplast transgenic lines (cpIFN-alpha2b) protected mice from a highly metastatic tumour line. This demonstration of high levels of expression of IFN-alpha2b, transgene containment and biological activity akin to that of commercial preparations of IFN-alpha2b facilitated the first field production of a plant-derived human blood protein, a critical step towards human clinical trials and commercialization.

Field production and functional evaluation of chloroplast-derived interferon-α2b

Science.gov (United States)

Arlen, Philip A.; Falconer, Regina; Cherukumilli, Sri; Cole, Amy; Cole, Alexander M.; Oishi, Karen K.; Daniell, Henry

2008-01-01

Summary Type I interferons (IFNs) inhibit viral replication and cell growth and enhance the immune response, and therefore have many clinical applications. IFN-α2b ranks third in world market use for a biopharmaceutical, behind only insulin and erythropoietin. The average annual cost of IFN-α2b for the treatment of hepatitis C infection is $26 000, and is therefore unavailable to the majority of patients in developing countries. Therefore, we expressed IFN-α2b in tobacco chloroplasts, and transgenic lines were grown in the field after obtaining United States Department of Agriculture Animal and Plant Health Inspection Service (USDA-APHIS) approval. Stable, site-specific integration of transgenes into chloroplast genomes and homoplasmy through several generations were confirmed. IFN-α2b levels reached up to 20% of total soluble protein, or 3 mg per gram of leaf (fresh weight). Transgenic IFN-α2b had similar in vitro biological activity to commercially produced PEG-Intron™ when tested for its ability to protect cells against cytopathic viral replication in the vesicular stomatitis virus cytopathic effect (VSV CPE) assay and to inhibit early-stage human immunodeficiency virus (HIV) infection. The antitumour and immunomodulating properties of IFN-α2b were also seen in vivo . Chloroplast-derived IFN-α2b increased the expression of major histocompatibility complex class I (MHC I) on splenocytes and the total number of natural killer (NK) cells. Finally, IFN-α2b purified from chloroplast transgenic lines (cpIFN-α2b) protected mice from a highly metastatic tumour line. This demonstration of high levels of expression of IFN-α2b, transgene containment and biological activity akin to that of commercial preparations of IFN-α2b facilitated the first field production of a plant-derived human blood protein, a critical step towards human clinical trials and commercialization. PMID:17490449

Signature of Thermal Rigidity Percolation

International Nuclear Information System (INIS)

Huerta, Adrián

2013-01-01

To explore the role that temperature and percolation of rigidity play in determining the macroscopic properties, we propose a model that adds translational degrees of freedom to the spins of the well known Ising hamiltonian. In particular, the Ising model illustrate the longstanding idea that the growth of correlations on approach to a critical point could be describable in terms of the percolation of some sort of p hysical cluster . For certain parameters of this model we observe two well defined peaks of C V , that suggest the existence of two kinds of p hysical percolation , namely connectivity and rigidity percolation. Thermal fluctuations give rise to two different kinds of elementary excitations, i.e. droplets and configuron, as suggested by Angell in the framework of a bond lattice model approach. The later is reflected in the fluctuations of redundant constraints that gives stability to the structure and correlate with the order parameter

Long-range correlated percolation

International Nuclear Information System (INIS)

Weinrib, A.

1984-01-01

This paper is a study of the percolation problem with long-range correlations in the site or bond occupations. An extension of the Harris criterion for the relevance of the correlations is derived for the case that the correlations decay as x/sup -a/ for large distances x. For a d the correlations are relevant if dν-2<0. Applying this criterion to the behavior that results when the correlations are relevant, we argue that the new behavior will have ν/sub long/ = 2/a. It is shown that the correlated bond percolation problem is equivalent to a q-state Potts model with quenched disorder in the limit q→1. With the use of this result, a renormalization-group study of the problem is presented, expanding in epsilon = 6-d and in delta = 4-a. In addition to the normal percolation fixed point, we find a new long-range fixed point. The crossover to this new fixed point follows the extended Harris criterion, and the fixed point has exponents ν/sub long/ = 2/a (as predicted) and eta/sub long/ = (1/11)(delta-epsilon). Finally, several results on the percolation properties of the Ising model at its critical point are shown to be in agreement with the predictions of this paper

Percolation with multiple giant clusters

International Nuclear Information System (INIS)

Ben-Naim, E; Krapivsky, P L

2005-01-01

We study mean-field percolation with freezing. Specifically, we consider cluster formation via two competing processes: irreversible aggregation and freezing. We find that when the freezing rate exceeds a certain threshold, the percolation transition is suppressed. Below this threshold, the system undergoes a series of percolation transitions with multiple giant clusters ('gels') formed. Giant clusters are not self-averaging as their total number and their sizes fluctuate from realization to realization. The size distribution F k , of frozen clusters of size k, has a universal tail, F k ∼ k -3 . We propose freezing as a practical mechanism for controlling the gel size. (letter to the editor)

Multifragmentation and percolation

International Nuclear Information System (INIS)

Campi, X.; Desbois, J.

1985-01-01

Percolation theory is applied to the problem of nucleus break-up. A model of nuclear percolation is proposed in which the rules for linkage of nucleons to form a cluster are defined in real and momentum spaces. This model exhibits a rather well defined threshold at rho ≅ 0.6. Analytical expressions for cluster size distributions at fixed concentration rho are given. Decay of excited clusters (by evaporation and fission) to give stable nuclear fragments is incorporated. The distribution law for rho in inclusive reactions is studied and the calculated mass yields are compared to experimental results

The role of chloroplasts in plant pathology.

Science.gov (United States)

Sowden, Robert G; Watson, Samuel J; Jarvis, Paul

2018-04-13

Plants have evolved complex tolerance systems to survive abiotic and biotic stresses. Central to these programmes is a sophisticated conversation of signals between the chloroplast and the nucleus. In this review, we examine the antagonism between abiotic stress tolerance (AST) and immunity: we propose that to generate immunogenic signals, plants must disable AST systems, in particular those that manage reactive oxygen species (ROS), while the pathogen seeks to reactivate or enhance those systems to achieve virulence. By boosting host systems of AST, pathogens trick the plant into suppressing chloroplast immunogenic signals and steer the host into making an inappropriate immune response. Pathogens disrupt chloroplast function, both transcriptionally-by secreting effectors that alter host gene expression by interacting with defence-related kinase cascades, with transcription factors, or with promoters themselves-and post-transcriptionally, by delivering effectors that enter the chloroplast or alter the localization of host proteins to change chloroplast activities. These mechanisms reconfigure the chloroplast proteome and chloroplast-originating immunogenic signals in order to promote infection. © 2017 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

Percolation and epidemics in random clustered networks

Science.gov (United States)

Miller, Joel C.

2009-08-01

The social networks that infectious diseases spread along are typically clustered. Because of the close relation between percolation and epidemic spread, the behavior of percolation in such networks gives insight into infectious disease dynamics. A number of authors have studied percolation or epidemics in clustered networks, but the networks often contain preferential contacts in high degree nodes. We introduce a class of random clustered networks and a class of random unclustered networks with the same preferential mixing. Percolation in the clustered networks reduces the component sizes and increases the epidemic threshold compared to the unclustered networks.

Reconstitution of CF1-depleted thylakoid membranes with complete and fragmented chloroplast ATPase. The role of the delta subunit for proton conduction through CF0

NARCIS (Netherlands)

Engelbrecht, Siegfried; Lill, H; Junge, Wolfgang

1986-01-01

Chloroplast ATPase (CF1) was isolated from spinach, pea and maize thylakoids by EDTA extraction followed by anion-exchange chromatography. CF1 was purified and resolved by HPLC into integral CF1, and CF1 lacking the delta & epsilon subunits: CF1(-delta) and CF1(-epsilon). Washing Mono-Q-bound CF1

Direct chloroplast sequencing: comparison of sequencing platforms and analysis tools for whole chloroplast barcoding.

Directory of Open Access Journals (Sweden)

Marta Brozynska

Full Text Available Direct sequencing of total plant DNA using next generation sequencing technologies generates a whole chloroplast genome sequence that has the potential to provide a barcode for use in plant and food identification. Advances in DNA sequencing platforms may make this an attractive approach for routine plant identification. The HiSeq (Illumina and Ion Torrent (Life Technology sequencing platforms were used to sequence total DNA from rice to identify polymorphisms in the whole chloroplast genome sequence of a wild rice plant relative to cultivated rice (cv. Nipponbare. Consensus chloroplast sequences were produced by mapping sequence reads to the reference rice chloroplast genome or by de novo assembly and mapping of the resulting contigs to the reference sequence. A total of 122 polymorphisms (SNPs and indels between the wild and cultivated rice chloroplasts were predicted by these different sequencing and analysis methods. Of these, a total of 102 polymorphisms including 90 SNPs were predicted by both platforms. Indels were more variable with different sequencing methods, with almost all discrepancies found in homopolymers. The Ion Torrent platform gave no apparent false SNP but was less reliable for indels. The methods should be suitable for routine barcoding using appropriate combinations of sequencing platform and data analysis.

Anomalous critical and supercritical phenomena in explosive percolation

Science.gov (United States)

D'Souza, Raissa M.; Nagler, Jan

2015-07-01

The emergence of large-scale connectivity on an underlying network or lattice, the so-called percolation transition, has a profound impact on the system’s macroscopic behaviours. There is thus great interest in controlling the location of the percolation transition to either enhance or delay its onset and, more generally, in understanding the consequences of such control interventions. Here we review explosive percolation, the sudden emergence of large-scale connectivity that results from repeated, small interventions designed to delay the percolation transition. These transitions exhibit drastic, unanticipated and exciting consequences that make explosive percolation an emerging paradigm for modelling real-world systems ranging from social networks to nanotubes.

Transient foreign gene expression in chloroplasts of cultured tobacco cells after biolistic delivery of chloroplast vectors.

OpenAIRE

Daniell, H; Vivekananda, J; Nielsen, B L; Ye, G N; Tewari, K K; Sanford, J C

1990-01-01

Expression of chloramphenicol acetyltransferase (cat) by suitable vectors in chloroplasts of cultured tobacco cells, delivered by high-velocity microprojectiles, is reported here. Several chloroplast expression vectors containing bacterial cat genes, placed under the control of either psbA promoter region from pea (pHD series) or rbcL promoter region from maize (pAC series) have been used in this study. In addition, chloroplast expression vectors containing replicon fragments from pea, tobacc...

Integral equation hierarchy for continuum percolation

International Nuclear Information System (INIS)

Given, J.A.

1988-01-01

In this thesis a projection operator technique is presented that yields hierarchies of integral equations satisfied exactly by the n-point connectedness functions in a continuum version of the site-bond percolation problem. The n-point connectedness functions carry the same structural information for a percolation problem as then-point correlation functions do for a thermal problem. This method extends the Potts model mapping of Fortuin and Kastelyn to the continuum by exploiting an s-state generalization of the Widom-Rowlinson model, a continuum model for phase separation. The projection operator technique is used to produce an integral equation hierarchy for percolation similar to the Born-Green heirarchy. The Kirkwood superposition approximation (SA) is extended to percolation in order to close this hierarchy and yield a nonlinear integral equation for the two-point connectedness function. The fact that this function, in the SA, is the analytic continuation to negative density of the two-point correlation function in a corresponding thermal problem is discussed. The BGY equation for percolation is solved numerically, both by an expansion in powers of the density, and by an iterative technique due to Kirkwood. It is argued both analytically and numerically, that the BYG equation for percolation, unlike its thermal counterpart, shows non-classical critical behavior, with η = 1 and γ = 0.05 ± .1. Finally a sequence of refinements to the superposition approximations based in the theory of fluids by Rice and Lekner is discussed

Expression and characterization of antimicrobial peptides Retrocyclin-101 and Protegrin-1 in chloroplasts to control viral and bacterial infections.

Science.gov (United States)

Lee, Seung-Bum; Li, Baichuan; Jin, Shuangxia; Daniell, Henry

2011-01-01

Retrocyclin-101 (RC101) and Protegrin-1 (PG1) are two important antimicrobial peptides that can be used as therapeutic agents against bacterial and/or viral infections, especially those caused by the HIV-1 or sexually transmitted bacteria. Because of their antimicrobial activity and complex secondary structures, they have not yet been produced in microbial systems and their chemical synthesis is prohibitively expensive. Therefore, we created chloroplast transformation vectors with the RC101 or PG1 coding sequence, fused with GFP to confer stability, furin or Factor Xa cleavage site to liberate the mature peptide from their fusion proteins and a His-tag to aid in their purification. Stable integration of RC101 into the tobacco chloroplast genome and homoplasmy were confirmed by Southern blots. RC101 and PG1 accumulated up to 32%-38% and 17%∼26% of the total soluble protein. Both RC101 and PG1 were cleaved from GFP by corresponding proteases in vitro, and Factor Xa-like protease activity was observed within chloroplasts. Confocal microscopy studies showed location of GFP fluorescence within chloroplasts. Organic extraction resulted in 10.6-fold higher yield of RC101 than purification by affinity chromatography using His-tag. In planta bioassays with Erwinia carotovora confirmed the antibacterial activity of RC101 and PG1 expressed in chloroplasts. RC101 transplastomic plants were resistant to tobacco mosaic virus infections, confirming antiviral activity. Because RC101 and PG1 have not yet been produced in other cell culture or microbial systems, chloroplasts can be used as bioreactors for producing these proteins. Adequate yield of purified antimicrobial peptides from transplastomic plants should facilitate further preclinical studies. © 2010 The Authors. Plant Biotechnology Journal © 2010 Society for Experimental Biology and Blackwell Publishing Ltd.

Growth dominates choice in network percolation

Science.gov (United States)

Vijayaraghavan, Vikram S.; Noël, Pierre-André; Waagen, Alex; D'Souza, Raissa M.

2013-09-01

The onset of large-scale connectivity in a network (i.e., percolation) often has a major impact on the function of the system. Traditionally, graph percolation is analyzed by adding edges to a fixed set of initially isolated nodes. Several years ago, it was shown that adding nodes as well as edges to the graph can yield an infinite order transition, which is much smoother than the traditional second-order transition. More recently, it was shown that adding edges via a competitive process to a fixed set of initially isolated nodes can lead to a delayed, extremely abrupt percolation transition with a significant jump in large but finite systems. Here we analyze a process that combines both node arrival and edge competition. If started from a small collection of seed nodes, we show that the impact of node arrival dominates: although we can significantly delay percolation, the transition is of infinite order. Thus, node arrival can mitigate the trade-off between delay and abruptness that is characteristic of explosive percolation transitions. This realization may inspire new design rules where network growth can temper the effects of delay, creating opportunities for network intervention and control.

Bootstrap percolation: a renormalisation group approach

International Nuclear Information System (INIS)

Branco, N.S.; Santos, Raimundo R. dos; Queiroz, S.L.A. de.

1984-02-01

In bootstrap percolation, sites are occupied at random with probability p, but each site is considered active only if at least m of its neighbours are also active. Within an approximate position-space renormalization group framework on a square lattice we obtain the behaviour of the critical concentration p (sub)c and of the critical exponents ν and β for m = 0 (ordinary percolation), 1,2 and 3. We find that the bootstrap percolation problem can be cast into different universality classes, characterized by the values of m. (author) [pt

A special percolation problem in ceramic composites

International Nuclear Information System (INIS)

Ang Chen; Xi Dai; Yu Zhi; Yahua Bao

1993-11-01

The interface effect is taken into consideration, and a special percolation model is proposed for a two-phases metal/ceramic composite in the present paper. The computer simulation shows that the percolation threshold of this interface-controlled percolation behaviour is 4.5% in the three dimensional f.c.c. lattices, which is in good agreement with the experimental data. (author). 9 refs, 3 figs

Formation of putative chloroplast cytochromes in isolated developing pea chloroplasts

International Nuclear Information System (INIS)

Thaver, S.S.; Bhava, D.; Castelfranco, P.A.

1986-01-01

In addition to chlorophyll-protein complexes, other proteins were labeled when isolated developing pea chloroplasts were incubated with [ 14 C]-5-aminolevulinic acid [ 14 C]-ALA. The major labeled band (M/sub r/ = 43 kDa by LDS-PAGE) was labeled even in the presence of chloramphenicol. Heme-dependent peroxidase activity (as detected by the tetramethyl benzidine-H 2 O 2 stain) was not visibly associated with this band. The radioactive band was stable to heat, 5% HCl in acetone, and was absent if the incubation with [ 14 C]-5-aminolevulinic acid was carried out in the presence of N-methyl protoporphyrin IX dimethyl ester (a specific inhibitor of ferrochelatase). Organic solvent extraction procedures for the enrichment of cytochrome f from chloroplast membranes also extracted this unknown labeled product. It was concluded that this labeled product was probably a c-type cytochrome. The effect of exogenous iron, iron chelators, gabaculine (an inhibitor of ALA synthesis) and other incubation conditions upon the in vitro formation of putative chloroplast cytochromes will be discussed

Plasmonic percolation: Plasmon-manifested dielectric-to-metal transition

KAUST Repository

Chen, Huanjun

2012-08-28

Percolation generally refers to the phenomenon of abrupt variations in electrical, magnetic, or optical properties caused by gradual volume fraction changes of one component across a threshold in bicomponent systems. Percolation behaviors have usually been observed in macroscopic systems, with most studies devoted to electrical percolation. We report on our observation of plasmonic percolation in Au nanorod core-Pd shell nanostructures. When the Pd volume fraction in the shell consisting of palladium and water approaches the plasmonic percolation threshold, ∼70%, the plasmon of the nanostructure transits from red to blue shifts with respect to that of the unshelled Au nanorod. This plasmonic percolation behavior is also confirmed by the scattering measurements on the individual core-shell nanostructures. Quasistatic theory and numerical simulations show that the plasmonic percolation originates from a positive-to-negative transition in the real part of the dielectric function of the shell as the Pd volume fraction is increased. The observed plasmonic percolation is found to be independent of the metal type in the shell. Moreover, compared to the unshelled Au nanorods with similar plasmon wavelengths, the Au nanorod core-Pd shell nanostructures exhibit larger refractive index sensitivities, which is ascribed to the expulsion of the electric field intensity from the Au nanorod core by the adsorbed Pd nanoparticles. © 2012 American Chemical Society.

Plasmonic percolation: Plasmon-manifested dielectric-to-metal transition

KAUST Repository

Chen, Huanjun; Wang, Feng; Li, Kun; Woo, Katchoi; Wang, Jianfang; Li, Quan; Sun, Ling Dong; Zhang, Xixiang; Lin, Haiqing; YAN, Chunhua

2012-01-01

Percolation generally refers to the phenomenon of abrupt variations in electrical, magnetic, or optical properties caused by gradual volume fraction changes of one component across a threshold in bicomponent systems. Percolation behaviors have usually been observed in macroscopic systems, with most studies devoted to electrical percolation. We report on our observation of plasmonic percolation in Au nanorod core-Pd shell nanostructures. When the Pd volume fraction in the shell consisting of palladium and water approaches the plasmonic percolation threshold, ∼70%, the plasmon of the nanostructure transits from red to blue shifts with respect to that of the unshelled Au nanorod. This plasmonic percolation behavior is also confirmed by the scattering measurements on the individual core-shell nanostructures. Quasistatic theory and numerical simulations show that the plasmonic percolation originates from a positive-to-negative transition in the real part of the dielectric function of the shell as the Pd volume fraction is increased. The observed plasmonic percolation is found to be independent of the metal type in the shell. Moreover, compared to the unshelled Au nanorods with similar plasmon wavelengths, the Au nanorod core-Pd shell nanostructures exhibit larger refractive index sensitivities, which is ascribed to the expulsion of the electric field intensity from the Au nanorod core by the adsorbed Pd nanoparticles. © 2012 American Chemical Society.

Phylogenomic Analysis and Dynamic Evolution of Chloroplast Genomes in Salicaceae

Directory of Open Access Journals (Sweden)

Yuan Huang

2017-06-01

Full Text Available Chloroplast genomes of plants are highly conserved in both gene order and gene content. Analysis of the whole chloroplast genome is known to provide much more informative DNA sites and thus generates high resolution for plant phylogenies. Here, we report the complete chloroplast genomes of three Salix species in family Salicaceae. Phylogeny of Salicaceae inferred from complete chloroplast genomes is generally consistent with previous studies but resolved with higher statistical support. Incongruences of phylogeny, however, are observed in genus Populus, which most likely results from homoplasy. By comparing three Salix chloroplast genomes with the published chloroplast genomes of other Salicaceae species, we demonstrate that the synteny and length of chloroplast genomes in Salicaceae are highly conserved but experienced dynamic evolution among species. We identify seven positively selected chloroplast genes in Salicaceae, which might be related to the adaptive evolution of Salicaceae species. Comparative chloroplast genome analysis within the family also indicates that some chloroplast genes are lost or became pseudogenes, infer that the chloroplast genes horizontally transferred to the nucleus genome. Based on the complete nucleus genome sequences from two Salicaceae species, we remarkably identify that the entire chloroplast genome is indeed transferred and integrated to the nucleus genome in the individual of the reference genome of P. trichocarpa at least once. This observation, along with presence of the large nuclear plastid DNA (NUPTs and NUPTs-containing multiple chloroplast genes in their original order in the chloroplast genome, favors the DNA-mediated hypothesis of organelle to nucleus DNA transfer. Overall, the phylogenomic analysis using chloroplast complete genomes clearly elucidates the phylogeny of Salicaceae. The identification of positively selected chloroplast genes and dynamic chloroplast-to-nucleus gene transfers in

Percolation of overlapping squares or cubes on a lattice

International Nuclear Information System (INIS)

Koza, Zbigniew; Kondrat, Grzegorz; Suszczyński, Karol

2014-01-01

Porous media are often modeled as systems of overlapping obstacles, which leads to the problem of two percolation thresholds in such systems, one for the porous matrix and the other for the void space. Here we investigate these percolation thresholds in the model of overlapping squares or cubes of linear size k > 1 randomly distributed on a regular lattice. We find that the percolation threshold of obstacles is a nonmonotonic function of k, whereas the percolation threshold of the void space is well approximated by a function linear in 1/k. We propose a generalization of the excluded volume approximation to discrete systems and use it to investigate the transition between continuous and discrete percolation, finding a remarkable agreement between the theory and numerical results. We argue that the continuous percolation threshold of aligned squares on a plane is the same for the solid and void phases and estimate the continuous percolation threshold of the void space around aligned cubes in a 3D space as 0.036(1). We also discuss the connection of the model to the standard site percolation with complex neighborhood. (paper)

Geometric structure of percolation clusters.

Science.gov (United States)

Xu, Xiao; Wang, Junfeng; Zhou, Zongzheng; Garoni, Timothy M; Deng, Youjin

2014-01-01

We investigate the geometric properties of percolation clusters by studying square-lattice bond percolation on the torus. We show that the density of bridges and nonbridges both tend to 1/4 for large system sizes. Using Monte Carlo simulations, we study the probability that a given edge is not a bridge but has both its loop arcs in the same loop and find that it is governed by the two-arm exponent. We then classify bridges into two types: branches and junctions. A bridge is a branch iff at least one of the two clusters produced by its deletion is a tree. Starting from a percolation configuration and deleting the branches results in a leaf-free configuration, whereas, deleting all bridges produces a bridge-free configuration. Although branches account for ≈43% of all occupied bonds, we find that the fractal dimensions of the cluster size and hull length of leaf-free configurations are consistent with those for standard percolation configurations. By contrast, we find that the fractal dimensions of the cluster size and hull length of bridge-free configurations are given by the backbone and external perimeter dimensions, respectively. We estimate the backbone fractal dimension to be 1.643 36(10).

Finite-size scaling of clique percolation on two-dimensional Moore lattices

Science.gov (United States)

Dong, Jia-Qi; Shen, Zhou; Zhang, Yongwen; Huang, Zi-Gang; Huang, Liang; Chen, Xiaosong

2018-05-01

Clique percolation has attracted much attention due to its significance in understanding topological overlap among communities and dynamical instability of structured systems. Rich critical behavior has been observed in clique percolation on Erdős-Rényi (ER) random graphs, but few works have discussed clique percolation on finite dimensional systems. In this paper, we have defined a series of characteristic events, i.e., the historically largest size jumps of the clusters, in the percolating process of adding bonds and developed a new finite-size scaling scheme based on the interval of the characteristic events. Through the finite-size scaling analysis, we have found, interestingly, that, in contrast to the clique percolation on an ER graph where the critical exponents are parameter dependent, the two-dimensional (2D) clique percolation simply shares the same critical exponents with traditional site or bond percolation, independent of the clique percolation parameters. This has been corroborated by bridging two special types of clique percolation to site percolation on 2D lattices. Mechanisms for the difference of the critical behaviors between clique percolation on ER graphs and on 2D lattices are also discussed.

Chloroplast Chaperonin: An Intricate Protein Folding Machine for Photosynthesis

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Qian Zhao

2018-01-01

Full Text Available Group I chaperonins are large cylindrical-shaped nano-machines that function as a central hub in the protein quality control system in the bacterial cytosol, mitochondria and chloroplasts. In chloroplasts, proteins newly synthesized by chloroplast ribosomes, unfolded by diverse stresses, or translocated from the cytosol run the risk of aberrant folding and aggregation. The chloroplast chaperonin system assists these proteins in folding into their native states. A widely known protein folded by chloroplast chaperonin is the large subunit of ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco, an enzyme responsible for the fixation of inorganic CO2 into organic carbohydrates during photosynthesis. Chloroplast chaperonin was initially identified as a Rubisco-binding protein. All photosynthetic eucaryotes genomes encode multiple chaperonin genes which can be divided into α and β subtypes. Unlike the homo-oligomeric chaperonins from bacteria and mitochondria, chloroplast chaperonins are more complex and exists as intricate hetero-oligomers containing both subtypes. The Group I chaperonin requires proper interaction with a detachable lid-like co-chaperonin in the presence of ATP and Mg2+ for substrate encapsulation and conformational transition. Besides the typical Cpn10-like co-chaperonin, a unique co-chaperonin consisting of two tandem Cpn10-like domains joined head-to-tail exists in chloroplasts. Since chloroplasts were proposed as sensors to various environmental stresses, this diversified chloroplast chaperonin system has the potential to adapt to complex conditions by accommodating specific substrates or through regulation at both the transcriptional and post-translational levels. In this review, we discuss recent progress on the unique structure and function of the chloroplast chaperonin system based on model organisms Chlamydomonas reinhardtii and Arabidopsis thaliana. Knowledge of the chloroplast chaperonin system may ultimately lead

The complete chloroplast genome sequence of strawberry (Fragaria  × ananassa Duch.) and comparison with related species of Rosaceae.

Science.gov (United States)

Cheng, Hui; Li, Jinfeng; Zhang, Hong; Cai, Binhua; Gao, Zhihong; Qiao, Yushan; Mi, Lin

2017-01-01

Compared with other members of the family Rosaceae, the chloroplast genomes of Fragaria species exhibit low variation, and this situation has limited phylogenetic analyses; thus, complete chloroplast genome sequencing of Fragaria species is needed. In this study, we sequenced the complete chloroplast genome of F . ×  ananassa 'Benihoppe' using the Illumina HiSeq 2500-PE150 platform and then performed a combination of de novo assembly and reference-guided mapping of contigs to generate complete chloroplast genome sequences. The chloroplast genome exhibits a typical quadripartite structure with a pair of inverted repeats (IRs, 25,936 bp) separated by large (LSC, 85,531 bp) and small (SSC, 18,146 bp) single-copy (SC) regions. The length of the F . ×  ananassa 'Benihoppe' chloroplast genome is 155,549 bp, representing the smallest Fragaria chloroplast genome observed to date. The genome encodes 112 unique genes, comprising 78 protein-coding genes, 30 tRNA genes and four rRNA genes. Comparative analysis of the overall nucleotide sequence identity among ten complete chloroplast genomes confirmed that for both coding and non-coding regions in Rosaceae, SC regions exhibit higher sequence variation than IRs. The Ka/Ks ratio of most genes was less than 1, suggesting that most genes are under purifying selection. Moreover, the mVISTA results also showed a high degree of conservation in genome structure, gene order and gene content in Fragaria , particularly among three octoploid strawberries which were F . ×  ananassa 'Benihoppe', F . chiloensis (GP33) and F . virginiana (O477). However, when the sequences of the coding and non-coding regions of F . ×  ananassa 'Benihoppe' were compared in detail with those of F . chiloensis (GP33) and F . virginiana (O477), a number of SNPs and InDels were revealed by MEGA 7. Six non-coding regions ( trnK - matK , trnS - trnG , atpF - atpH , trnC - petN , trnT - psbD and trnP - psaJ ) with a percentage of variable sites greater than

The complete chloroplast genome sequence of strawberry (Fragaria  × ananassa Duch. and comparison with related species of Rosaceae

Directory of Open Access Journals (Sweden)

Hui Cheng

2017-10-01

Full Text Available Compared with other members of the family Rosaceae, the chloroplast genomes of Fragaria species exhibit low variation, and this situation has limited phylogenetic analyses; thus, complete chloroplast genome sequencing of Fragaria species is needed. In this study, we sequenced the complete chloroplast genome of F. × ananassa ‘Benihoppe’ using the Illumina HiSeq 2500-PE150 platform and then performed a combination of de novo assembly and reference-guided mapping of contigs to generate complete chloroplast genome sequences. The chloroplast genome exhibits a typical quadripartite structure with a pair of inverted repeats (IRs, 25,936 bp separated by large (LSC, 85,531 bp and small (SSC, 18,146 bp single-copy (SC regions. The length of the F. × ananassa ‘Benihoppe’ chloroplast genome is 155,549 bp, representing the smallest Fragaria chloroplast genome observed to date. The genome encodes 112 unique genes, comprising 78 protein-coding genes, 30 tRNA genes and four rRNA genes. Comparative analysis of the overall nucleotide sequence identity among ten complete chloroplast genomes confirmed that for both coding and non-coding regions in Rosaceae, SC regions exhibit higher sequence variation than IRs. The Ka/Ks ratio of most genes was less than 1, suggesting that most genes are under purifying selection. Moreover, the mVISTA results also showed a high degree of conservation in genome structure, gene order and gene content in Fragaria, particularly among three octoploid strawberries which were F. × ananassa ‘Benihoppe’, F. chiloensis (GP33 and F. virginiana (O477. However, when the sequences of the coding and non-coding regions of F. × ananassa ‘Benihoppe’ were compared in detail with those of F. chiloensis (GP33 and F. virginiana (O477, a number of SNPs and InDels were revealed by MEGA 7. Six non-coding regions (trnK-matK, trnS-trnG, atpF-atpH, trnC-petN, trnT-psbD and trnP-psaJ with a percentage of variable sites greater than 1

Utilization of complete chloroplast genomes for phylogenetic studies

NARCIS (Netherlands)

Ramlee, Shairul Izan Binti

2016-01-01

Chloroplast DNA sequence polymorphisms are a primary source of data in many plant phylogenetic studies. The chloroplast genome is relatively conserved in its evolution making it an ideal molecule to retain phylogenetic signals. The chloroplast genome is also largely, but not completely, free from

Statistical mechanics of high-density bond percolation

Science.gov (United States)

Timonin, P. N.

2018-05-01

High-density (HD) percolation describes the percolation of specific κ -clusters, which are the compact sets of sites each connected to κ nearest filled sites at least. It takes place in the classical patterns of independently distributed sites or bonds in which the ordinary percolation transition also exists. Hence, the study of series of κ -type HD percolations amounts to the description of classical clusters' structure for which κ -clusters constitute κ -cores nested one into another. Such data are needed for description of a number of physical, biological, and information properties of complex systems on random lattices, graphs, and networks. They range from magnetic properties of semiconductor alloys to anomalies in supercooled water and clustering in biological and social networks. Here we present the statistical mechanics approach to study HD bond percolation on an arbitrary graph. It is shown that the generating function for κ -clusters' size distribution can be obtained from the partition function of the specific q -state Potts-Ising model in the q →1 limit. Using this approach we find exact κ -clusters' size distributions for the Bethe lattice and Erdos-Renyi graph. The application of the method to Euclidean lattices is also discussed.

Percolation Magnetism in Ferroelectric Nanoparticles

Science.gov (United States)

Golovina, Iryna S.; Lemishko, Serhii V.; Morozovska, Anna N.

2017-06-01

Nanoparticles of potassium tantalate (KTaO3) and potassium niobate (KNbO3) were synthesized by oxidation of metallic tantalum in molten potassium nitrate with the addition of potassium hydroxide. Magnetization curves obtained on these ferroelectric nanoparticles exhibit a weak ferromagnetism, while these compounds are nonmagnetic in a bulk. The experimental data are used as a start point for theoretical calculations. We consider a microscopic mechanism that leads to the emerging of a ferromagnetic ordering in ferroelectric nanoparticles. Our approach is based on the percolation of magnetic polarons assuming the dominant role of the oxygen vacancies. It describes the formation of surface magnetic polarons, in which an exchange interaction between electrons trapped in oxygen vacancies is mediated by magnetic impurity Fe3+ ions. The dependences of percolation radius on concentration of the oxygen vacancies and magnetic defects are determined in the framework of percolation theory.

Percolation Magnetism in Ferroelectric Nanoparticles.

Science.gov (United States)

Golovina, Iryna S; Lemishko, Serhii V; Morozovska, Anna N

2017-12-01

Nanoparticles of potassium tantalate (KTaO 3 ) and potassium niobate (KNbO 3 ) were synthesized by oxidation of metallic tantalum in molten potassium nitrate with the addition of potassium hydroxide. Magnetization curves obtained on these ferroelectric nanoparticles exhibit a weak ferromagnetism, while these compounds are nonmagnetic in a bulk. The experimental data are used as a start point for theoretical calculations. We consider a microscopic mechanism that leads to the emerging of a ferromagnetic ordering in ferroelectric nanoparticles. Our approach is based on the percolation of magnetic polarons assuming the dominant role of the oxygen vacancies. It describes the formation of surface magnetic polarons, in which an exchange interaction between electrons trapped in oxygen vacancies is mediated by magnetic impurity Fe 3+ ions. The dependences of percolation radius on concentration of the oxygen vacancies and magnetic defects are determined in the framework of percolation theory.

Percolation of polyatomic species on site diluted lattices

International Nuclear Information System (INIS)

Cornette, V.; Ramirez-Pastor, A.J.; Nieto, F.

2006-01-01

In this Letter, the percolation of (a) linear segments of size k and (b) k-mers (particles occupying k adjacent sites) of different structures and forms deposited on a diluted square lattice have been studied. The diluted lattice is built by randomly selecting a fraction of sites which are considered forbidden for deposition. The analysis of the obtained results is made in the framework of the finite size scaling theory. The characteristic parameters of the percolation problem are dependent not only on the form and structure of the k-mers but also on the properties of the lattice where they are deposited. A phase diagram separating a percolating from a non-percolating region is determined and discussed

Complex chloroplast RNA metabolism: just debugging the genetic programme?

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Schmitz-Linneweber Christian

2008-08-01

Full Text Available Abstract Background The gene expression system of chloroplasts is far more complex than that of their cyanobacterial progenitor. This gain in complexity affects in particular RNA metabolism, specifically the transcription and maturation of RNA. Mature chloroplast RNA is generated by a plethora of nuclear-encoded proteins acquired or recruited during plant evolution, comprising additional RNA polymerases and sigma factors, and sequence-specific RNA maturation factors promoting RNA splicing, editing, end formation and translatability. Despite years of intensive research, we still lack a comprehensive explanation for this complexity. Results We inspected the available literature and genome databases for information on components of RNA metabolism in land plant chloroplasts. In particular, new inventions of chloroplast-specific mechanisms and the expansion of some gene/protein families detected in land plants lead us to suggest that the primary function of the additional nuclear-encoded components found in chloroplasts is the transgenomic suppression of point mutations, fixation of which occurred due to an enhanced genetic drift exhibited by chloroplast genomes. We further speculate that a fast evolution of transgenomic suppressors occurred after the water-to-land transition of plants. Conclusion Our inspections indicate that several chloroplast-specific mechanisms evolved in land plants to remedy point mutations that occurred after the water-to-land transition. Thus, the complexity of chloroplast gene expression evolved to guarantee the functionality of chloroplast genetic information and may not, with some exceptions, be involved in regulatory functions.

Complete chloroplast genome of Gracilaria firma (Gracilariaceae, Rhodophyta), with discussion on the use of chloroplast phylogenomics in the subclass Rhodymeniophycidae.

Science.gov (United States)

Ng, Poh-Kheng; Lin, Showe-Mei; Lim, Phaik-Eem; Liu, Li-Chia; Chen, Chien-Ming; Pai, Tun-Wen

2017-01-06

The chloroplast genome of Gracilaria firma was sequenced in view of its role as an economically important marine crop with wide industrial applications. To date, there are only 15 chloroplast genomes published for the Florideophyceae. Apart from presenting the complete chloroplast genome of G. firma, this study also assessed the utility of genome-scale data to address the phylogenetic relationships within the subclass Rhodymeniophycidae. The synteny and genome structure of the chloroplast genomes across the taxa of Eurhodophytina was also examined. The chloroplast genome of Gracilaria firma maps as a circular molecule of 187,001 bp and contains 252 genes, which are distributed on both strands and consist of 35 RNA genes (3 rRNAs, 30 tRNAs, tmRNA and a ribonuclease P RNA component) and 217 protein-coding genes, including the unidentified open reading frames. The chloroplast genome of G. firma is by far the largest reported for Gracilariaceae, featuring a unique intergenic region of about 7000 bp with discontinuous vestiges of red algal plasmid DNA sequences interspersed between the nblA and cpeB genes. This chloroplast genome shows similar gene content and order to other Florideophycean taxa. Phylogenomic analyses based on the concatenated amino acid sequences of 146 protein-coding genes confirmed the monophyly of the classes Bangiophyceae and Florideophyceae with full nodal support. Relationships within the subclass Rhodymeniophycidae in Florideophyceae received moderate to strong nodal support, and the monotypic family of Gracilariales were resolved with maximum support. Chloroplast genomes hold substantial information that can be tapped for resolving the phylogenetic relationships of difficult regions in the Rhodymeniophycidae, which are perceived to have experienced rapid radiation and thus received low nodal support, as exemplified in this study. The present study shows that chloroplast genome of G. firma could serve as a key link to the full resolution of

The Chloroplast Division Protein ARC6 Acts to Inhibit Disassembly of GDP-bound FtsZ2.

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Sung, Min Woo; Shaik, Rahamthulla; TerBush, Allan D; Osteryoung, Katherine W; Vitha, Stanislav; Holzenburg, Andreas

2018-05-16

Chloroplasts host photosynthesis and fulfill other metabolic functions that are essential to plant life. They have to divide by binary fission to maintain their numbers throughout cycles of cell division. Chloroplast division is achieved by a complex ring-shaped division machinery located on both the inner (stromal) and the outer (cytosolic) side of the chloroplast envelope. The inner division ring (termed the Z ring) is formed by the assembly of tubulin-like FtsZ1 and FtsZ2 proteins. ARC6 is a key chloroplast division protein that interacts with the Z ring. ARC6 spans the inner envelope membrane, is known to stabilize or maintain the Z ring, and anchors the Z ring to the inner membrane through interaction with FtsZ2. The underlying mechanism of Z-ring stabilization is not well understood. Here, biochemical and structural characterization of ARC6 was conducted using light scattering, sedimentation, and light and transmission electron microscopy. The recombinant protein was purified as a dimer. The results indicated that a truncated form of ARC6 (tARC6), representing the stromal portion of ARC6, affects FtsZ2 assembly without forming higher-order structures, and exerts its effect via FtsZ2 dynamics. tARC6 prevented GDP-induced FtsZ2 disassembly and caused a significant net increase in FtsZ2 assembly when GDP was present. Single particle analysis and 3D reconstruction were performed to elucidate the structural basis of ARC6 activity. Together, the data reveal that a dimeric form of tARC6 binds to FtsZ2 filaments and does not increase FtsZ polymerization rates but rather inhibits GDP-associated FtsZ2 disassembly. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

Chloroplast microsatellite markers for Pseudotaxus chienii developed from the whole chloroplast genome of Taxus chinensis var. mairei (Taxaceae).

Science.gov (United States)

Deng, Qi; Zhang, Hanrui; He, Yipeng; Wang, Ting; Su, Yingjuan

2017-03-01

Pseudotaxus chienii (Taxaceae) is an old rare species endemic to China that has adapted well to ecological heterogeneity with high genetic diversity in its nuclear genome. However, the genetic variation in its chloroplast genome is unknown. Eighteen chloroplast microsatellite markers (cpSSRs) were developed from the whole chloroplast genome of Taxus chinensis var. mairei and successfully amplified in four P. chienii populations and one T. chinensis var. mairei population. Of these loci, 10 were polymorphic in P. chienii , whereas six were polymorphic in T. chinensis var. mairei . The unbiased haploid diversity per locus ranged from 0.000 to 0.641 and 0.000 to 0.545 for P. chienii and T. chinensis var. mairei , respectively. The 18 cpSSRs will be used to further investigate the chloroplast genetic structure and adaptive evolution in P. chienii populations.

Chloroplasts in anther endothecium of Zea mays (Poaceae).

Science.gov (United States)

Murphy, Katherine M; Egger, Rachel L; Walbot, Virginia

2015-11-01

Although anthers of Zea mays, Oryza sativa, and Arabidopsis thaliana have been studied intensively using genetic and biochemical analyses in the past 20 years, few updates to anther anatomical and ultrastructural descriptions have been reported. For example, no transmission electron microscopy (TEM) images of the premeiotic maize anther have been published. Here we report the presence of chloroplasts in maize anthers. TEM imaging, electron acceptor photosynthesis assay, in planta photon detection, microarray analysis, and light and fluorescence microscopy were used to investigate the presence of chloroplasts in the maize anther. Most cells of the maize subepidermal endothecium have starch-containing chloroplasts that do not conduct measurable photosynthesis in vitro. The maize anther contains chloroplasts in most subepidermal, endothecial cells. Although maize anthers receive sufficient light to photosynthesize in vivo and the maize anther transcribes >96% of photosynthesis-associated genes found in the maize leaf, no photosynthetic light reaction activity was detected in vitro. The endothecial cell layer should no longer be defined as a complete circle viewed transversely in anther lobes, because chloroplasts are observed only in cells directly beneath the epidermis and not those adjacent to the connective tissue. We propose that chloroplasts be a defining characteristic of differentiated endothecial cells and that nonsubepidermal endothecial cells that lack chloroplasts be defined as a separate cell type, the interendothecium. © 2015 Botanical Society of America.

The relationship between synchronization and percolation for regular networks

Science.gov (United States)

Li, Zhe; Ren, Tao; Xu, Yanjie; Jin, Jianyu

2018-02-01

Synchronization and percolation are two essential phenomena in complex dynamical networks. They have been studied widely, but previously treated as unrelated. In this paper, the relationship between synchronization and percolation are revealed for regular networks. Firstly, we discovered a bridge between synchronization and percolation by using the eigenvalues of the Laplacian matrix to describe the synchronizability and using the eigenvalues of the adjacency matrix to describe the percolation threshold. Then, we proposed a method to find the relationship for regular networks based on the topology of networks. Particularly, if the degree distribution of the network is subject to delta function, we show that only the eigenvalues of the adjacency matrix need to be calculated. Finally, several examples are provided to demonstrate how to apply our proposed method to discover the relationship between synchronization and percolation for regular networks.

Percolation Model for the Existence of a Mitochondrial Eve

CERN Document Server

Neves, A G M

2005-01-01

We look at the process of inheritance of mitochondrial DNA as a percolation model on trees equivalent to the Galton-Watson process. The model is exactly solvable for its percolation threshold $p_c$ and percolation probability critical exponent. In the approximation of small percolation probability, and assuming limited progeny number, we are also able to find the maximum and minimum percolation probabilities over all probability distributions for the progeny number constrained to a given $p_c$. As a consequence, we can relate existence of a mitochondrial Eve to quantitative knowledge about demographic evolution of early mankind. In particular, we show that a mitochondrial Eve may exist even in an exponentially growing population, provided that the average number of children per individual is constrained to a small range depending on the probability $p$ that a newborn child is a female.

Percolating cluster of center vortices and confinement

International Nuclear Information System (INIS)

Gliozzi, Ferdinando; Panero, Marco; Provero, Paolo

2003-01-01

We study the role of percolating clusters of center vortices in configurations of an Ising gauge theory in 3D. It is known that low energy features of gauge theories can be described in terms of an 'effective string picture', and that confinement properties are associated with topologically non-trivial configurations. We focus our attention upon percolating clusters of center vortices, and present numerical evidence for the fact that these objects play a preminent role in confinement phenomenon, since their removal sweeps off confinement altogether. Moreover, numerical simulations show that the string fluctuations, and in particular the Mischer term, are completely encoded in the percolating cluster

Effects and mechanism of acid rain on plant chloroplast ATP synthase.

Science.gov (United States)

Sun, Jingwen; Hu, Huiqing; Li, Yueli; Wang, Lihong; Zhou, Qing; Huang, Xiaohua

2016-09-01

Acid rain can directly or indirectly affect plant physiological functions, especially photosynthesis. The enzyme ATP synthase is the key in photosynthetic energy conversion, and thus, it affects plant photosynthesis. To clarify the mechanism by which acid rain affects photosynthesis, we studied the effects of acid rain on plant growth, photosynthesis, chloroplast ATP synthase activity and gene expression, chloroplast ultrastructure, intracellular H(+) level, and water content of rice seedlings. Acid rain at pH 4.5 remained the chloroplast structure unchanged but increased the expression of six chloroplast ATP synthase subunits, promoted chloroplast ATP synthase activity, and increased photosynthesis and plant growth. Acid rain at pH 4.0 or less decreased leaf water content, destroyed chloroplast structure, inhibited the expression of six chloroplast ATP synthase subunits, decreased chloroplast ATP synthase activity, and reduced photosynthesis and plant growth. In conclusion, acid rain affected the chloroplast ultrastructure, chloroplast ATPase transcription and activity, and P n by changing the acidity in the cells, and thus influencing the plant growth and development. Finally, the effects of simulated acid rain on the test indices were found to be dose-dependent.

Mechanism of protein import across the chloroplast envelope.

Science.gov (United States)

Chen, K; Chen, X; Schnell, D J

2000-01-01

The development and maintenance of chloroplasts relies on the contribution of protein subunits from both plastid and nuclear genomes. Most chloroplast proteins are encoded by nuclear genes and are post-translationally imported into the organelle across the double membrane of the chloroplast envelope. Protein import into the chloroplast consists of two essential elements: the specific recognition of the targeting signals (transit sequences) of cytoplasmic preproteins by receptors at the outer envelope membrane and the subsequent translocation of preproteins simultaneously across the double membrane of the envelope. These processes are mediated via the co-ordinate action of protein translocon complexes in the outer (Toc apparatus) and inner (Tic apparatus) envelope membranes.

Percolation via Combined Electrostatic and Chemical Doping in Complex Oxide Films

Science.gov (United States)

Orth, Peter P.; Fernandes, Rafael M.; Walter, Jeff; Leighton, C.; Shklovskii, B. I.

2017-03-01

Stimulated by experimental advances in electrolyte gating methods, we investigate theoretically percolation in thin films of inhomogeneous complex oxides, such as La1 -xSrxCoO3 (LSCO), induced by a combination of bulk chemical and surface electrostatic doping. Using numerical and analytical methods, we identify two mechanisms that describe how bulk dopants reduce the amount of electrostatic surface charge required to reach percolation: (i) bulk-assisted surface percolation and (ii) surface-assisted bulk percolation. We show that the critical surface charge strongly depends on the film thickness when the film is close to the chemical percolation threshold. In particular, thin films can be driven across the percolation transition by modest surface charge densities. If percolation is associated with the onset of ferromagnetism, as in LSCO, we further demonstrate that the presence of critical magnetic clusters extending from the film surface into the bulk results in considerable enhancement of the saturation magnetization, with pronounced experimental consequences. These results should significantly guide experimental work seeking to verify gate-induced percolation transitions in such materials.

Oryza sativa Chloroplast Signal Recognition Particle 43 (OscpSRP43 Is Required for Chloroplast Development and Photosynthesis.

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Xiang-guang Lv

Full Text Available A rice chlorophyll-deficient mutant w67 was isolated from an ethyl methane sulfonate (EMS-induced IR64 (Oryza sativa L. ssp. indica mutant bank. The mutant exhibited a distinct yellow-green leaf phenotype in the whole plant growth duration with significantly reduced levels of chlorophyll and carotenoid, impaired chloroplast development and lowered capacity of photosynthesis compared with the wild-type IR64. Expression of a number of genes associated with chlorophyll metabolism, chloroplast biogenesis and photosynthesis was significantly altered in the mutant. Genetic analysis indicated that the yellow-green phenotype was controlled by a single recessive nuclear gene located on the short arm of chromosome 3. Using map-based strategy, the mutation was isolated and predicted to encode a chloroplast signal recognition particle 43 KD protein (cpSRP43 with 388 amino acid residuals. A single base substitution from A to T at position 160 resulted in a premature stop codon. OscpSRP43 was constitutively expressed in various organs with the highest level in the leaf. Functional complementation could rescue the mutant phenotype and subcellular localization showed that the cpSRP43:GFP fusion protein was targeted to the chloroplast. The data suggested that Oryza sativa cpSRP43 (OscpSRP43 was required for the normal development of chloroplasts and photosynthesis in rice.

Estimation of water percolation by different methods using TDR

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Alisson Jadavi Pereira da Silva

2014-02-01

Full Text Available Detailed knowledge on water percolation into the soil in irrigated areas is fundamental for solving problems of drainage, pollution and the recharge of underground aquifers. The aim of this study was to evaluate the percolation estimated by time-domain-reflectometry (TDR in a drainage lysimeter. We used Darcy's law with K(θ functions determined by field and laboratory methods and by the change in water storage in the soil profile at 16 points of moisture measurement at different time intervals. A sandy clay soil was saturated and covered with plastic sheet to prevent evaporation and an internal drainage trial in a drainage lysimeter was installed. The relationship between the observed and estimated percolation values was evaluated by linear regression analysis. The results suggest that percolation in the field or laboratory can be estimated based on continuous monitoring with TDR, and at short time intervals, of the variations in soil water storage. The precision and accuracy of this approach are similar to those of the lysimeter and it has advantages over the other evaluated methods, of which the most relevant are the possibility of estimating percolation in short time intervals and exemption from the predetermination of soil hydraulic properties such as water retention and hydraulic conductivity. The estimates obtained by the Darcy-Buckingham equation for percolation levels using function K(θ predicted by the method of Hillel et al. (1972 provided compatible water percolation estimates with those obtained in the lysimeter at time intervals greater than 1 h. The methods of Libardi et al. (1980, Sisson et al. (1980 and van Genuchten (1980 underestimated water percolation.

Fatty acid synthesis by spinach chloroplasts, 2

International Nuclear Information System (INIS)

Yamada, Mitsuhiro; Nakamura, Yasunori

1975-01-01

By incorporation of 3 H 2 O into the fatty acid chain in the presence of unlabelled precursor, we showed that fatty acids are synthesized from PGA, PEP and pyruvate by intact spinach chloroplasts in the light. 13 C-tracer experiments confirmed that 1-C of pyruvate is decarboxylated and 2-C is incorporated into fatty acids by the chloroplasts. The patterns of fatty acids synthesized from PGA and pyruvate were the same as that from acetate. The highest rate of fatty acid synthesis was reached at the physiological concentration of PGA (3 mM) and pyruvate (1 mM). These results indicate the operation of the following path in the chloroplasts in light: PGA→PEP→pyruvate→acetylCoA→fatty acids. Since citrate and OAA were much less active and malate and glyoxylate were inert as precursors for fatty acid synthesis, PEP or pyruvate carboxylation, citrate lyase reaction and malate synthetase reaction are not involved in the formation of acetylCoA and fatty acids. Since pyruvate was much more effective as a substrate for fatty acid synthesis than lactate, acetaldehyde or acetate, direct decarboxylation path is considered to be the primary path from pyruvate to acetylCoA. The insignificant effect of chloroplast-washing on fatty acid synthesis from PGA and pyruvate indicates that the glycolytic path from PGA to pyruvate is associated with the chloroplasts. Since pyruvate was more effectively incorporated into fatty acids than acetylCoA, it is unlikely that pyruvate decarboxylation to acetylCoA is due to mitochondria contaminating the chloroplast preparation. On the basis of measurements of 3 H 2 O incorporation in the light and dark, the activity of fatty acid synthesis in spincah leaves appears to be shared by the activities in chloroplasts (87%) and other organelles (13%). (author)

Redirecting the Cyanobacterial Bicarbonate Transporters BicA and SbtA to the Chloroplast Envelope: Soluble and Membrane Cargos Need Different Chloroplast Targeting Signals in Plants.

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Vivien eRolland

2016-02-01

Full Text Available Most major crops used for human consumption are C3 plants, which yields are limited by photosynthetic inefficiency. To circumvent this, it has been proposed to implement the cyanobacterial CO2-concentrating mechanism (CCM, principally consisting of bicarbonate transporters and carboxysomes, into plant chloroplasts. As it is currently not possible to recover homoplasmic transplastomic monocots, foreign genes must be introduced in these plants via nuclear transformation. Consequently, it is paramount to ensure that resulting proteins reach the appropriate sub-cellular compartment, which for cyanobacterial transporters BicA and SbtA, is the chloroplast inner-envelope membrane (IEM. At present, targeting signals to redirect large transmembrane proteins from non-chloroplastic organisms to plant chloroplast envelopes are unknown. The goal of this study was to identify such signals, using agrobacteria-mediated transient expression and confocal microscopy to determine the sub-cellular localization of ~37 GFP-tagged chimeras. Initially, fragments of chloroplast proteins known to target soluble cargos to the stroma were tested for their ability to redirect BicA, but they proved ineffective. Next, different N-terminal regions from Arabidopsis IEM transporters were tested. We demonstrated that the N-terminus of AtHP59, AtPLGG1 or AtNTT1 (92-115 amino acids, containing a cleavable chloroplast transit peptide (cTP and a membrane protein leader (MPL, was sufficient to redirect BicA or SbtA to the chloroplast envelope. This constitutes the first evidence that nuclear-encoded transmembrane proteins from non-chloroplastic organisms can be targeted to the envelope of plant chloroplasts; a finding which represents an important advance in chloroplast engineering by opening up the door to further manipulation of the chloroplastic envelope.

Percolation of interdependent network of networks

International Nuclear Information System (INIS)

Havlin, Shlomo; Stanley, H. Eugene; Bashan, Amir; Gao, Jianxi; Kenett, Dror Y.

2015-01-01

Complex networks appear in almost every aspect of science and technology. Previous work in network theory has focused primarily on analyzing single networks that do not interact with other networks, despite the fact that many real-world networks interact with and depend on each other. Very recently an analytical framework for studying the percolation properties of interacting networks has been introduced. Here we review the analytical framework and the results for percolation laws for a Network Of Networks (NONs) formed by n interdependent random networks. The percolation properties of a network of networks differ greatly from those of single isolated networks. In particular, because the constituent networks of a NON are connected by node dependencies, a NON is subject to cascading failure. When there is strong interdependent coupling between networks, the percolation transition is discontinuous (first-order) phase transition, unlike the well-known continuous second-order transition in single isolated networks. Moreover, although networks with broader degree distributions, e.g., scale-free networks, are more robust when analyzed as single networks, they become more vulnerable in a NON. We also review the effect of space embedding on network vulnerability. It is shown that for spatially embedded networks any finite fraction of dependency nodes will lead to abrupt transition

Manipulation of Glutathione and Amino Acid Biosynthesis in the Chloroplast1

Science.gov (United States)

Noctor, Graham; Arisi, Ana-Carolina M.; Jouanin, Lise; Foyer, Christine H.

1998-01-01

Poplars (Populus tremula × Populus alba) were transformed to overexpress Escherichia coli γ-glutamylcysteine synthetase (γ-ECS) or glutathione synthetase in the chloroplast. Five independent lines of each transformant strongly expressed the introduced gene and possessed markedly enhanced activity of the gene product. Glutathione (GSH) contents were unaffected by high chloroplastic glutathione synthetase activity. Enhanced chloroplastic γ-ECS activity markedly increased γ-glutamylcysteine and GSH levels. These effects are similar to those previously observed in poplars overexpressing these enzymes in the cytosol. Similar to cytosolic γ-ECS overexpression, chloroplastic overexpression did not deplete foliar cysteine or methionine pools and did not lead to morphological changes. Light was required for maximal accumulation of GSH in poplars overexpressing γ-ECS in the chloroplast. High chloroplastic, but not cytosolic, γ-ECS activities were accompanied by increases in amino acids synthesized in the chloroplast. We conclude that (a) GSH synthesis can occur in the chloroplast and the cytosol and may be up-regulated in both compartments by increased γ-ECS activity, (b) interactions between GSH synthesis and the pathways supplying the necessary substrates are similar in both compartments, and (c) chloroplastic up-regulation of GSH synthesis is associated with an activating effect on the synthesis of specific amino acids formed in the chloroplast. PMID:9765532

Aerodynamics and Percolation: Unfolding Laminar Separation Bubble on Airfoils

Science.gov (United States)

Traphan, Dominik; Wester, Tom T. B.; Gülker, Gerd; Peinke, Joachim; Lind, Pedro G.

2018-04-01

As a fundamental phenomenon of fluid mechanics, recent studies suggested laminar-turbulent transition belonging to the universality class of directed percolation. Here, the onset of a laminar separation bubble on an airfoil is analyzed in terms of the directed percolation model using particle image velocimetry data. Our findings indicate a clear significance of percolation models in a general flow situation beyond fundamental ones. We show that our results are robust against fluctuations of the parameter, namely, the threshold of turbulence intensity, that maps velocimetry data into binary cells (turbulent or laminar). In particular, this percolation approach enables the precise determination of the transition point of the laminar separation bubble, an important problem in aerodynamics.

C4 photosynthetic machinery: insights from maize chloroplast proteomics

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Qi eZhao

2013-04-01

Full Text Available C4 plants exhibit much higher CO2 assimilation rates than C3 plants. The specialized differentiation of mesophyll cell (M and bundle sheath cell (BS type chloroplasts is unique to C4 plants and improves photosynthesis efficiency. Maize (Zea mays is an important crop and model with C4 photosynthetic machinery. Current high-throughput quantitative proteomics approaches (e.g., 2DE, iTRAQ, and shotgun proteomics have been employed to investigate maize chloroplast structure and function. These proteomic studies have provided valuable information on C4 chloroplast protein components, photosynthesis, and other metabolic mechanisms underlying chloroplast biogenesis, stromal and membrane differentiation, as well as response to salinity, high/low temperature, and light stress. This review presents an overview of proteomics advances in maize chloroplast biology.

Introduction to percolation theory

CERN Document Server

Stauffer, Dietrich

1991-01-01

Percolation theory deals with clustering, criticallity, diffusion, fractals, phase transitions and disordered systems. This book covers the basic theory for the graduate, and also professionals dealing with it for the first time

Development of Chloroplast Genomic Resources in Chinese Yam (Dioscorea polystachya

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Junling Cao

2018-01-01

Full Text Available Chinese yam has been used both as a food and in traditional herbal medicine. Developing more effective genetic markers in this species is necessary to assess its genetic diversity and perform cultivar identification. In this study, new chloroplast genomic resources were developed using whole chloroplast genomes from six genotypes originating from different geographical locations. The Dioscorea polystachya chloroplast genome is a circular molecule consisting of two single-copy regions separated by a pair of inverted repeats. Comparative analyses of six D. polystachya chloroplast genomes revealed 141 single nucleotide polymorphisms (SNPs. Seventy simple sequence repeats (SSRs were found in the six genotypes, including 24 polymorphic SSRs. Forty-three common indels and five small inversions were detected. Phylogenetic analysis based on the complete chloroplast genome provided the best resolution among the genotypes. Our evaluation of chloroplast genome resources among these genotypes led us to consider the complete chloroplast genome sequence of D. polystachya as a source of reliable and valuable molecular markers for revealing biogeographical structure and the extent of genetic variation in wild populations and for identifying different cultivars.

An Arabidopsis chloroplast-targeted Hsp101 homologue, APG6, has an essential role in chloroplast development as well as heat-stress response.

Science.gov (United States)

Myouga, Fumiyoshi; Motohashi, Reiko; Kuromori, Takashi; Nagata, Noriko; Shinozaki, Kazuo

2006-10-01

Analysis of albino or pale-green (apg) mutants is important for identifying nuclear genes responsible for chloroplast development and pigment synthesis. We have identified 38 apg mutants by screening 11 000 Arabidopsis Ds-tagged lines. One mutant, apg6, contains a Ds insertion in a gene encoding APG6 (ClpB3), a homologue of the heat-shock protein Hsp101 (ClpB1). We isolated somatic revertants and identified two Ds-tagged and one T-DNA-tagged mutant alleles of apg6. All three alleles gave the same pale-green phenotype. These results suggest that APG6 is important for chloroplast development. The APG6 protein contains a transit peptide and is localized in chloroplasts. The plastids of apg6 pale-green cells were smaller than those of the wild type, and contained undeveloped thylakoid membranes. APG6 mRNA accumulated in response to heat shock in various organs, but not in response to other abiotic stresses. Under normal conditions, APG6 is constitutively expressed in the root tips, the organ boundary region, the reproductive tissues of mature plants where plastids exist as proplastids, and slightly in the stems and leaves. In addition, constitutive overexpression of APG6 in transgenic plants inhibited chloroplast development and resulted in a mild pale-green phenotype. The amounts of chloroplast proteins related to photosynthesis were markedly decreased in apg6 mutants. These results suggest that APG6 functions as a molecular chaperone involved in plastid differentiation mediating internal thylakoid membrane formation and conferring thermotolerance to chloroplasts during heat stress. The APG6 protein is not only involved in heat-stress response in chloroplasts, but is also essential for chloroplast development.

The evolution of blue-greens and the origins of chloroplasts

Science.gov (United States)

Schwartz, R. M.; Dayhoff, M. O.

1981-01-01

All of the available molecular data support the theory that the chloroplasts of eukaryote cells were originally free-living blue-greens. Of great interest is what the relationships are between contemporary types of blue-greens and eukaryote chloroplasts and whether the chloroplasts of the various eukaryotes are the result of one or more than one symbiosis. By combining information from phylogenetic trees based on cytochrome c6 and 2Fe-2S ferredoxin sequences, it is shown that the chloroplasts of a number of eukaryote algae as well as the protist Euglena are polyphyletic; the chloroplasts of green algae and the higher plants may be the result of a single symbiosis.

Nitrogen control of chloroplast development: Progress report

International Nuclear Information System (INIS)

Schmidt, G.W.

1987-11-01

A manifestation of nitrogen deficiency in vascular plants and algae is chlorosis, indicating that chloroplast biogenesis can be strongly restricted by direct or indirect effects of nitrogen assimilation products. To define the molecular basis of nitrogen responses we are using Chlamydomonas reinhardtii. Depending on the levels of ammonium, steady-state deficiency conditions are established such that the cellular levels of chlorophylls and xanthophylls are depressed. Chloroplasts in nitrogen-deficient cells contain appreciable levels of carbon assimilation enzyme and thylakoids with high electron transport activities. However, the light harvesting complexes are nearly absent and Photosystem I exhibits unusual characteristics. Studies of rates of protein synthesis by in vivo pulse-chase labeling and levels of RNAs encoded by the chloroplast and nuclear genomes have been initiated: the accumulation of transcripts for the nuclear light-harvesting apoproteins is dramatically altered qualitatively and quantitatively; there is no major effect on chloroplast RNAs but, in general, these are inefficiently utilized for protein synthesis until nitrogen is provided to the cultures. Supplying nitrogen results in an almost immediate release of chloroplast mRNAs from a translational arrest but the stimulation of the accumulation of nuclear transcripts for light-harvesting apoproteins does not occur until after a 1-2 hour lag

Nitrogen control of chloroplast development: Progress report

Energy Technology Data Exchange (ETDEWEB)

Schmidt, G.W.

1987-11-01

A manifestation of nitrogen deficiency in vascular plants and algae is chlorosis, indicating that chloroplast biogenesis can be strongly restricted by direct or indirect effects of nitrogen assimilation products. To define the molecular basis of nitrogen responses we are using Chlamydomonas reinhardtii. Depending on the levels of ammonium, steady-state deficiency conditions are established such that the cellular levels of chlorophylls and xanthophylls are depressed. Chloroplasts in nitrogen-deficient cells contain appreciable levels of carbon assimilation enzyme and thylakoids with high electron transport activities. However, the light harvesting complexes are nearly absent and Photosystem I exhibits unusual characteristics. Studies of rates of protein synthesis by in vivo pulse-chase labeling and levels of RNAs encoded by the chloroplast and nuclear genomes have been initiated: the accumulation of transcripts for the nuclear light-harvesting apoproteins is dramatically altered qualitatively and quantitatively; there is no major effect on chloroplast RNAs but, in general, these are inefficiently utilized for protein synthesis until nitrogen is provided to the cultures. Supplying nitrogen results in an almost immediate release of chloroplast mRNAs from a translational arrest but the stimulation of the accumulation of nuclear transcripts for light-harvesting apoproteins does not occur until after a 1-2 hour lag.

Innovation diffusion in networks : the microeconomics of percolation

NARCIS (Netherlands)

Zeppini, P.; Frenken, K.; Izquierdo, L.R.

2013-01-01

We implement a diffusion model for an innovative product in a market with a structure of social relationships. Diffusion is described with a percolation approach in the price space. Percolation shows a phase transition from a diffusion to a no-diffusion regime. This has strong implications for

Innovation diffusion in networks: the microeconomics of percolation

NARCIS (Netherlands)

Zeppini, P.; Frenken, K.; Izquierdo, L.R.

2013-01-01

We implement a diffusion model for an innovative product in a market with a structure of social relationships. Diffusion is described with a percolation approach in the price space. Percolation shows a phase transition from a diffusion to a no-diffusion regime. This has strong implications for

Definition of percolation thresholds on self-affine surfaces

NARCIS (Netherlands)

Marrink, S.J.; Paterson, Lincoln; Knackstedt, Mark A.

2000-01-01

We study the percolation transition on a two-dimensional substrate with long-range self-affine correlations. We find that the position of the percolation threshold on a correlated lattice is no longer unique and depends on the spanning rule employed. Numerical results are provided for spanning

Fluid leakage near the percolation threshold

Science.gov (United States)

Dapp, Wolf B.; Müser, Martin H.

2016-02-01

Percolation is a concept widely used in many fields of research and refers to the propagation of substances through porous media (e.g., coffee filtering), or the behaviour of complex networks (e.g., spreading of diseases). Percolation theory asserts that most percolative processes are universal, that is, the emergent powerlaws only depend on the general, statistical features of the macroscopic system, but not on specific details of the random realisation. In contrast, our computer simulations of the leakage through a seal—applying common assumptions of elasticity, contact mechanics, and fluid dynamics—show that the critical behaviour (how the flow ceases near the sealing point) solely depends on the microscopic details of the last constriction. It appears fundamentally impossible to accurately predict from statistical properties of the surfaces alone how strongly we have to tighten a water tap to make it stop dripping and also how it starts dripping once we loosen it again.

Experimental percolation studies of random networks

Science.gov (United States)

Feinerman, A.; Weddell, J.

2017-06-01

This report establishes an experimental method of studying electrically percolating networks at a higher resolution than previously implemented. This method measures the current across a conductive sheet as a function of time as elliptical pores are cut into the sheet. This is done utilizing a Universal Laser System X2-600 100 W CO2 laser system with a 76 × 46 cm2 field and 394 dpc (dots/cm) resolution. This laser can cut a random system of elliptical pores into a conductive sheet with a potential voltage applied across it and measures the current versus time. This allows for experimental verification of a percolation threshold as a function of the ellipse's aspect ratio (minor/major diameter). We show that as an ellipse's aspect ratio approaches zero, the percolation threshold approaches one. The benefit of this method is that it can experimentally measure the effect of removing small pores, as well as pores with complex geometries, such as an asterisk from a conductive sheet.

On the structure of the spinach chloroplast

NARCIS (Netherlands)

Thomas, J.B.; Bustraan, M.; Paris, C.H.

1952-01-01

The structure of spinach chloroplasts was investigated with the aid of the electron microscope. It has been established that: 1. 1. the outer membrane of the chloroplasts is composed of both proteins and lipoids. 2. 2. the stroma is also built up by these components. 3. 3. within the

Progress in high-dimensional percolation and random graphs

CERN Document Server

Heydenreich, Markus

2017-01-01

This text presents an engaging exposition of the active field of high-dimensional percolation that will likely provide an impetus for future work. With over 90 exercises designed to enhance the reader’s understanding of the material, as well as many open problems, the book is aimed at graduate students and researchers who wish to enter the world of this rich topic.  The text may also be useful in advanced courses and seminars, as well as for reference and individual study. Part I, consisting of 3 chapters, presents a general introduction to percolation, stating the main results, defining the central objects, and proving its main properties. No prior knowledge of percolation is assumed. Part II, consisting of Chapters 4–9, discusses mean-field critical behavior by describing the two main techniques used, namely, differential inequalities and the lace expansion. In Parts I and II, all results are proved, making this the first self-contained text discussing high-dimensiona l percolation.  Part III, consist...

One-dimensional long-range percolation: A numerical study

Science.gov (United States)

Gori, G.; Michelangeli, M.; Defenu, N.; Trombettoni, A.

2017-07-01

In this paper we study bond percolation on a one-dimensional chain with power-law bond probability C /rd +σ , where r is the distance length between distinct sites and d =1 . We introduce and test an order-N Monte Carlo algorithm and we determine as a function of σ the critical value Cc at which percolation occurs. The critical exponents in the range 0 values for Cc are compared with a known exact bound, while the critical exponent ν is compared with results from mean-field theory, from an expansion around the point σ =1 and from the ɛ -expansion used with the introduction of a suitably defined effective dimension deff relating the long-range model with a short-range one in dimension deff. We finally present a formulation of our algorithm for bond percolation on general graphs, with order N efficiency on a large class of graphs including short-range percolation and translationally invariant long-range models in any spatial dimension d with σ >0 .

Protein methylation reactions in intact pea chloroplasts

International Nuclear Information System (INIS)

Niemi, K.J.

1989-01-01

Post-translational protein methylation was investigated in Pisum sativum chloroplasts. Intact pea chloroplasts were incubated with ( 3 H-methyl)-S-adenosylmethionine under various conditions. The chloroplasts were then separated into stromal and thylakoid fractions and analyzed for radioactivity transferred to protein. Light enhanced the magnitude of labeling in both fractions. One thylakoid polypeptide with an apparent molecular mass of 43 kDa was labeled only in the light. Several other thylakoid and stromal proteins were labeled in both light and dark-labeling conditions. Both base-labile methylation, carboxy-methylesters and base-stable groups, N-methylations were found. Further characterization of the methyl-transfer reactions will be presented

Quantum walks of two interacting particles on percolation graphs

Science.gov (United States)

Siloi, Ilaria; Benedetti, Claudia; Piccinini, Enrico; Paris, Matteo G. A.; Bordone, Paolo

2017-10-01

We address the dynamics of two indistinguishable interacting particles moving on a dynamical percolation graph, i.e., a graph where the edges are independent random telegraph processes whose values jump between 0 and 1, thus mimicking percolation. The interplay between the particle interaction strength, initial state and the percolation rate determine different dynamical regimes for the walkers. We show that, whenever the walkers are initially localised within the interaction range, fast noise enhances the particle spread compared to the noiseless case.

Analysis of radionuclide transport through fracture networks by percolation theory

International Nuclear Information System (INIS)

Ahn, Joonhong; Furuhama, Yutaka; Li, Yadong; Suzuki, Atsuyuki

1991-01-01

Presented are results of numerical simulations for radionuclide diffusion through fracture networks in geologic layers. Actual fracture networks are expressed as two-dimensional honeycomb percolation lattices. Random-walk simulations of diffusion on percolation lattices are made by the exact-enumeration method, and compared with those from Fickian diffusion with constant and decreasing diffusion coefficients. Mean-square displacement of a random-walker on percolation lattices increases more slowly with time than that for Fickian diffusion with the constant diffusion coefficient. Though the same relation of mean-square displacement vs. time as for the percolation lattices can be obtained for a continuum with decreasing diffusion coefficients, spatial distribution of probability densities of finding the random-walker on the percolation lattice differs from that on a continuum with the decreasing diffusion coefficient. The percolation model results in slow spreading near the origin and fast spreading in the outer region, whereas the decreasing-diffusion coefficient model shows the reverse because of smaller diffusion coefficient in the outer region. We could derive a general formula that can include both Fickian and anomalous diffusion in terms of fractal and fracton dimensionalities and the anomalous diffusion exponent. (author)

A protocol for expression of foreign genes in chloroplasts.

Science.gov (United States)

Verma, Dheeraj; Samson, Nalapalli P; Koya, Vijay; Daniell, Henry

2008-01-01

Several major costs associated with the production of biopharmaceuticals or vaccines in fermentation-based systems could be minimized by using plant chloroplasts as bioreactors, which facilitates rapid scale-up. Oral delivery of chloroplast-derived therapeutic proteins through plant cells eliminates expensive purification steps, low temperature storage, transportation and sterile injections for their delivery. Chloroplast transformation technology (CTT) has also been successfully used to engineer valuable agronomic traits and for the production of industrial enzymes and biomaterials. Here, we provide a detailed protocol for the construction of chloroplast expression and integration vectors, selection and regeneration of transformants, evaluation of transgene integration and inheritance, confirmation of transgene expression and extraction, and quantitation and purification of foreign proteins. Integration of appropriate transgenes into chloroplast genomes and the resulting high levels of functional protein expression can be achieved in approximately 6 months in lettuce and tobacco. CTT is eco-friendly because transgenes are maternally inherited in most crop plants.

Bounds for percolation thresholds on directed and undirected graphs

Science.gov (United States)

Hamilton, Kathleen; Pryadko, Leonid

2015-03-01

Percolation theory is an efficient approach to problems with strong disorder, e.g., in quantum or classical transport, composite materials, and diluted magnets. Recently, the growing role of big data in scientific and industrial applications has led to a renewed interest in graph theory as a tool for describing complex connections in various kinds of networks: social, biological, technological, etc. In particular, percolation on graphs has been used to describe internet stability, spread of contagious diseases and computer viruses; related models describe market crashes and viral spread in social networks. We consider site-dependent percolation on directed and undirected graphs, and present several exact bounds for location of the percolation transition in terms of the eigenvalues of matrices associated with graphs, including the adjacency matrix and the Hashimoto matrix used to enumerate non-backtracking walks. These bounds correspond t0 a mean field approximation and become asymptotically exact for graphs with no short cycles. We illustrate this convergence numerically by simulating percolation on several families of graphs with different cycle lengths. This research was supported in part by the NSF Grant PHY-1416578 and by the ARO Grant W911NF-11-1-0027.

Dielectric and diamagnetic susceptibilities near percolative superconductor-insulator transitions.

Science.gov (United States)

Loh, Yen Lee; Karki, Pragalv

2017-10-25

Coarse-grained superconductor-insulator composites exhibit a superconductor-insulator transition governed by classical percolation, which should be describable by networks of inductors and capacitors. We study several classes of random inductor-capacitor networks on square lattices. We present a unifying framework for defining electric and magnetic response functions, and we extend the Frank-Lobb bond-propagation algorithm to compute these quantities by network reduction. We confirm that the superfluid stiffness scales approximately as [Formula: see text] as the superconducting bond fraction p approaches the percolation threshold p c . We find that the diamagnetic susceptibility scales as [Formula: see text] below percolation, and as [Formula: see text] above percolation. For models lacking self-capacitances, the electric susceptibility scales as [Formula: see text]. Including a self-capacitance on each node changes the critical behavior to approximately [Formula: see text].

The complete chloroplast genome of the Dendrobium strongylanthum (Orchidaceae: Epidendroideae).

Science.gov (United States)

Li, Jing; Chen, Chen; Wang, Zhe-Zhi

2016-07-01

Complete chloroplast genome sequence is very useful for studying the phylogenetic and evolution of species. In this study, the complete chloroplast genome of Dendrobium strongylanthum was constructed from whole-genome Illumina sequencing data. The chloroplast genome is 153 058 bp in length with 37.6% GC content and consists of two inverted repeats (IRs) of 26 316 bp. The IR regions are separated by large single-copy region (LSC, 85 836 bp) and small single-copy (SSC, 14 590 bp) region. A total of 130 chloroplast genes were successfully annotated, including 84 protein coding genes, 38 tRNA genes, and eight rRNA genes. Phylogenetic analyses showed that the chloroplast genome of Dendrobium strongylanthum is related to that of the Dendrobium officinal.

De Novo Assembly of Complete Chloroplast Genomes from Non-model Species Based on a K-mer Frequency-Based Selection of Chloroplast Reads from total DNA Sequences.

NARCIS (Netherlands)

Izan, Shairul; Esselink, G.; Visser, R.G.F.; Smulders, M.J.M.; Borm, T.J.A.

2017-01-01

Whole Genome Shotgun (WGS) sequences of plant species often contain an abundance of reads that are derived from the chloroplast genome. Up to now these reads have generally been identified and assembled into chloroplast genomes based on homology to chloroplasts from related species. This

Oxidative damage to chloroplasts from Chlorella vulgaris exposed to ultraviolet-B radiation

International Nuclear Information System (INIS)

Malanga, G.; Calmanovici, G.; Puntarulo, S.

1997-01-01

Upon UV-B irradiation, Chlorella vulgaris cells and isolated chloroplasts increased in size and starch accumulation. Photosynthetic capacity and chlorophyll content of chloroplasts isolated from irradiated algae decreased by 72 and 66%, as compared to chloroplasts isolated from control cells. Dihydrorhodamine 123 conversion to rhodamine 123 was used as a sensitive method for detection of peroxide (presumably hydrogen peroxide) formation in isolated chloroplasts. The accumulation of rhodamine 123 is higher in irradiated than in nonirradiated chloroplasts and the increased accumulation of rhodamine 123 depended on the UV-B dose. Quantitation of alkyl radical-EPR signals in chloroplasts indicated that UV-B exposure significantly increased radical content in the membranes. The content of an oxidized DNA base (8-hydroxy-2′-deoxyguanosine) in chloroplasts was increased by 72 and 175% after irradiation of the algal culture with 17.3 and 42.6 kJ m −2 , respectively. The chloroplastic activity of superoxide dismutase decreased by 50% as compared with control values after irradiation with 42.6 kJ m −2 and no changes in ascorbate peroxidase activity and ascorbic acid content were detected at the irradiation doses tested. The β-carotene content in chloroplasts was not affected by the irradiation, but the α-tocopherol content increased approximately 4-fold after UV-B irradiation. The results suggest that oxidative damage related to UV-B exposure is responsible for alterations in chloroplasts function and integrity, and that an antioxidant response is triggered in chloroplasts through an increase in α-tocopherol content. (author)

Orientation of the pigment molecules in the chloroplast

NARCIS (Netherlands)

Goedheer, J.C.

1955-01-01

Dichroism, absorption anisotropy, and anomal dispersion of birefringence were measured in the big lamellate chloroplasts of Mougeotia. The results of these measurements indicate a certain orientation of the chlorophyll molecules, and to a smaller extent, of the carotenoids in the chloroplast. In

Pb-induced avoidance-like chloroplast movements in fronds of Lemna trisulca L.

Directory of Open Access Journals (Sweden)

Sławomir Samardakiewicz

Full Text Available Lead ions are particularly dangerous to the photosynthetic apparatus, but little is known about the effects of trace metals, including Pb, on regulation of chloroplast redistribution. In this study a new effect of lead on chloroplast distribution patterns and movements was demonstrated in mesophyll cells of a small-sized aquatic angiosperm Lemna trisulca L. (star duckweed. An analysis of confocal microscopy images of L. trisulca fronds treated with lead (15 μM Pb2+, 24 h in darkness or in weak white light revealed an enhanced accumulation of chloroplasts in the profile position along the anticlinal cell walls, in comparison to untreated plants. The rearrangement of chloroplasts in their response to lead ions in darkness was similar to the avoidance response of chloroplasts in plants treated with strong white light. Transmission electron microscopy X-ray microanalysis showed that intracellular chloroplast arrangement was independent of the location of Pb deposits, suggesting that lead causes redistribution of chloroplasts, which looks like a light-induced avoidance response, but is not a real avoidance response to the metal. Furthermore, a similar redistribution of chloroplasts in L. trisulca cells in darkness was observed also under the influence of exogenously applied hydrogen peroxide (H2O2. In addition, we detected an enhanced accumulation of endogenous H2O2 after treatment of plants with lead. Interestingly, H2O2-specific scavenger catalase partly abolished the Pb-induced chloroplast response. These results suggest that H2O2 can be involved in the avoidance-like movement of chloroplasts induced by lead. Analysis of photometric measurements revealed also strong inhibition (but not complete of blue-light-induced chloroplast movements by lead. This inhibition may result from disturbances in the actin cytoskeleton, as we observed fragmentation and disappearance of actin filaments around chloroplasts. Results of this study show that the

PDV2 has a dosage effect on chloroplast division in Arabidopsis.

Science.gov (United States)

Chang, Ning; Sun, Qingqing; Li, Yiqiong; Mu, Yajuan; Hu, Jinglei; Feng, Yue; Liu, Xiaomin; Gao, Hongbo

2017-03-01

PDV2 has a dosage effect on chloroplast division in Arabidopsis thaliana , but this effect may vary in different plants. Chloroplasts have to be divided as plants grow to maintain an optimized number in the cell. Chloroplasts are divided by protein complexes across the double membranes from the stroma side to the cytosolic side. PDV2 is a chloroplast division protein on the chloroplast outer membrane. It recruits the dynamin-related GTPase ARC5 to the division site. The C-terminus of PDV2 and the C-terminus of ARC6 interact in the intermembrane space, which is important for the localization of PDV2. Previously, it was shown that overexpression of PDV2 can increase the division of chloroplasts in Arabidopsis and moss, so the authors concluded that PDV2 determines the rate of chloroplast division in land plants. PDV2 was also shown to inhibit the GTPase activity of ARC5 by in vitro experiment. These results look to be contradictory. Here, we identified a null allele of PDV2 in Arabidopsis and studied plants with different levels of PDV2. Our results suggested that the chloroplast division phenotype in Arabidopsis is sensitive to the level of PDV2, while this is not the case for ARC6. The level of PDV2 protein is reduced sharply in fast-growing leaves, while the level of ARC6 is not. The levels of PDV2 and ARC6 in several other plant species at different developmental stages were also investigated. The results indicated that their expression pattern varies in different species. Thus, PDV2 is an important positive factor of chloroplast division with an apparent dosage effect in Arabidopsis, but this effect for different chloroplast division proteins in different plants may vary.

Polymer Percolation Threshold in Multi-Component HPMC Matrices Tablets

Directory of Open Access Journals (Sweden)

Maryam Maghsoodi

2011-06-01

Full Text Available Introduction: The percolation theory studies the critical points or percolation thresholds of the system, where onecomponent of the system undergoes a geometrical phase transition, starting to connect the whole system. The application of this theory to study the release rate of hydrophilic matrices allows toexplain the changes in release kinetics of swellable matrix type system and results in a clear improvement of the design of controlled release dosage forms. Methods: In this study, the percolation theory has been applied to multi-component hydroxypropylmethylcellulose (HPMC hydrophilic matrices. Matrix tablets have been prepared using phenobarbital as drug,magnesium stearate as a lubricant employing different amount of lactose and HPMC K4M as a fillerandmatrix forming material, respectively. Ethylcelullose (EC as a polymeric excipient was also examined. Dissolution studies were carried out using the paddle method. In order to estimate the percolation threshold, the behaviour of the kinetic parameters with respect to the volumetric fraction of HPMC at time zero, was studied. Results: In both HPMC/lactose and HPMC/EC/lactose matrices, from the point of view of the percolation theory, the optimum concentration for HPMC, to obtain a hydrophilic matrix system for the controlled release of phenobarbital is higher than 18.1% (v/v HPMC. Above 18.1% (v/v HPMC, an infinite cluster of HPMC would be formed maintaining integrity of the system and controlling the drug release from the matrices. According to results, EC had no significant influence on the HPMC percolation threshold. Conclusion: This may be related to broad functionality of the swelling hydrophilic matrices.

Percolation Systems away from the Critical Point

OpenAIRE

Dhar, Deepak

2001-01-01

This article reviews some effects of disorder in percolation systems even away from the critical density p_c. For densities below p_c, the statistics of large clusters defines the animals problem. Its relation to the directed animals problem and the Lee-Yang edge singularity problem is described. Rare compact clusters give rise to Griffiths singuraties in the free energy of diluted ferromagnets, and lead to a very slow relaxation of magnetization. In biassed diffusion on percolation clusters,...

Anaerobic Treatment Of Percolate From Faecal Sludge Drying Beds ...

African Journals Online (AJOL)

Composite percolate samples, from sludge drying beds of a pilot co-composting plant in Kumasi, Ghana, were characterised and subjected to laboratory scale anaerobic treatment. Two categories of percolate samples were investigated; samples seeded with anaerobic sludge and samples without seeding. The average ...

Chloroplast Translation: Structural and Functional Organization, Operational Control, and Regulation[OPEN

Science.gov (United States)

2018-01-01

Chloroplast translation is essential for cellular viability and plant development. Its positioning at the intersection of organellar RNA and protein metabolism makes it a unique point for the regulation of gene expression in response to internal and external cues. Recently obtained high-resolution structures of plastid ribosomes, the development of approaches allowing genome-wide analyses of chloroplast translation (i.e., ribosome profiling), and the discovery of RNA binding proteins involved in the control of translational activity have greatly increased our understanding of the chloroplast translation process and its regulation. In this review, we provide an overview of the current knowledge of the chloroplast translation machinery, its structure, organization, and function. In addition, we summarize the techniques that are currently available to study chloroplast translation and describe how translational activity is controlled and which cis-elements and trans-factors are involved. Finally, we discuss how translational control contributes to the regulation of chloroplast gene expression in response to developmental, environmental, and physiological cues. We also illustrate the commonalities and the differences between the chloroplast and bacterial translation machineries and the mechanisms of protein biosynthesis in these two prokaryotic systems. PMID:29610211

Factors affecting water balance and percolate production for a landfill in operation.

Science.gov (United States)

Poulsen, Tjalfe G; Møoldrup, Per

2005-02-01

Percolate production and precipitation data for a full-scale landfill in operation measured over a 13-year period were used to evaluate the impact and importance of the hydrological conditions of landfill sections on the percolate production rates. Both active (open) and closed landfill sections were included in the evaluation. A simple top cover model requiring a minimum of input data was used to simulate the percolate production as a function of precipitation and landfill section hydrology. The results showed that changes over time in the hydrology of individual landfill sections (such as section closure or plantation of trees on top of closed sections) can change total landfill percolate production by more than 100%; thus, percolate production at an active landfill can be very different from percolate production at the same landfill after closure. Furthermore, plantation of willow on top of closed sections can increase the evapotranspiration rate thereby reducing percolate production rates by up to 47% compared to a grass cover. This process, however, depends upon the availability of water in the top layer, and so the evaporation rate will be less than optimal during the summer where soil-water contents in the top cover are low.

Percolation of secret correlations in a network

OpenAIRE

Leverrier, Anthony; García-Patrón, Raúl

2011-01-01

In this work, we explore the analogy between entanglement and secret classical correlations in the context of large networks, more precisely the question of percolation of secret correlations in a network. It is known that entanglement percolation in quantum networks can display a highly nontrivial behavior depending on the topology of the network and on the presence of entanglement between the nodes. Here we show that this behavior, thought to be of a genuine quantum nature, also occurs in a...

Percolation of secret correlations in a network

Energy Technology Data Exchange (ETDEWEB)

Leverrier, Anthony; Garcia-Patron, Raul [ICFO-Institut de Ciencies Fotoniques, 08860 Castelldefels (Barcelona) (Spain); Research Laboratory of Electronics, MIT, Cambridge, MA 02139 (United States) and Max-Planck Institut fur Quantenoptik, Hans-Kopfermann Str. 1, D-85748 Garching (Germany)

2011-09-15

In this work, we explore the analogy between entanglement and secret classical correlations in the context of large networks--more precisely, the question of percolation of secret correlations in a network. It is known that entanglement percolation in quantum networks can display a highly nontrivial behavior depending on the topology of the network and on the presence of entanglement between the nodes. Here we show that this behavior, thought to be of a genuine quantum nature, also occurs in a classical context.

Percolation of secret correlations in a network

International Nuclear Information System (INIS)

Leverrier, Anthony; Garcia-Patron, Raul

2011-01-01

In this work, we explore the analogy between entanglement and secret classical correlations in the context of large networks--more precisely, the question of percolation of secret correlations in a network. It is known that entanglement percolation in quantum networks can display a highly nontrivial behavior depending on the topology of the network and on the presence of entanglement between the nodes. Here we show that this behavior, thought to be of a genuine quantum nature, also occurs in a classical context.

Percolation testing at the F- and H-Area Seepage Basins

International Nuclear Information System (INIS)

McHood, M.D.

1993-01-01

The design of the F- and H-Area Seepage Basin contaminated groundwater remediation system requires information from multiple well pump tests (Reference 1). Soil percolation rates are needed in order to support the multiple well pump test planning. The objective of this task was to determine characteristic percolation rates for soils in four select areas where infiltration galleries are proposed. These infiltration galleries will be temporary installations built on the ground surface and used to disposes of water from the multiple well pump tests. A procedure defining the specific work process for collecting percolation rate data is contained in Appendix 3. Results from these percolation tests will be used in the design of infiltration galleries for the disposal of well water extracted during the multiple well pump tests

Mergers and acquisitions: malaria and the great chloroplast heist.

Science.gov (United States)

McFadden, G I

2000-01-01

The origin of the relict chloroplast recently identified in malarial parasites has been mysterious. Several new papers suggest that the parasites obtained their chloroplasts in an ancient endosymbiotic event that also created some major algal groups.

Controlling percolation with limited resources

Science.gov (United States)

Schröder, Malte; Araújo, Nuno A. M.; Sornette, Didier; Nagler, Jan

2017-12-01

Connectivity, or the lack thereof, is crucial for the function of many man-made systems, from financial and economic networks over epidemic spreading in social networks to technical infrastructure. Often, connections are deliberately established or removed to induce, maintain, or destroy global connectivity. Thus, there has been a great interest in understanding how to control percolation, the transition to large-scale connectivity. Previous work, however, studied control strategies assuming unlimited resources. Here, we depart from this unrealistic assumption and consider the effect of limited resources on the effectiveness of control. We show that, even for scarce resources, percolation can be controlled with an efficient intervention strategy. We derive such an efficient strategy and study its implications, revealing a discontinuous transition as an unintended side effect of optimal control.

A generalized model for site percolation with two independent concentrations

International Nuclear Information System (INIS)

Lin Jiancheng.

1987-05-01

In this paper the usual site percolation problem with single concentration is generalized to the one that contains two independent concentrations. Using the real space renormalization technique we derive an exact transformation for the one dimensional lattice and a cluster transformation for triangle lattice in two dimensions. The critical exponents and the percolation threshold concentrations obtained are the same as those of the usual single concentration percolation problem. Critical line and flow diagram in the two concentration parameters space are also given. (author). 10 refs, 6 figs

Percolation of binary disk systems: Modeling and theory

International Nuclear Information System (INIS)

Meeks, Kelsey; Pantoya, Michelle L.

2017-01-01

The dispersion and connectivity of particles with a high degree of polydispersity is relevant to problems involving composite material properties and reaction decomposition prediction and has been the subject of much study in the literature. This paper utilizes Monte Carlo models to predict percolation thresholds for a two-dimensional systems containing disks of two different radii. Monte Carlo simulations and spanning probability are used to extend prior models into regions of higher polydispersity than those previously considered. A correlation to predict the percolation threshold for binary disk systems is proposed based on the extended dataset presented in this work and compared to previously published correlations. Finally, a set of boundary conditions necessary for a good fit is presented, and a condition for maximizing percolation threshold for binary disk systems is suggested.

The chloroplast genome of a symbiodinium sp. clade C3 isolate

KAUST Repository

Barbrook, Adrian C.

2014-01-01

Dinoflagellate algae of the genus Symbiodinium form important symbioses within corals and other benthic marine animals. Dinoflagellates possess an extremely reduced plastid genome relative to those examined in plants and other algae. In dinoflagellates the plastid genes are located on small plasmids, commonly referred to as \\'minicircles\\'. However, the chloroplast genomes of dinoflagellates have only been extensively characterised from a handful of species. There is also evidence of considerable variation in the chloroplast genome organisation across those species that have been examined. We therefore characterised the chloroplast genome from an environmental coral isolate, in this case containing a symbiont belonging to the Symbiodinium sp. clade C3. The gene content of the genome is well conserved with respect to previously characterised genomes. However, unlike previously characterised dinoflagellate chloroplast genomes we did not identify any \\'empty\\' minicircles. The sequences of this chloroplast genome show a high rate of evolution relative to other algal species. Particularly notable was a surprisingly high level of sequence divergence within the core polypeptides of photosystem I, the reasons for which are currently unknown. This chloroplast genome also possesses distinctive codon usage and GC content. These features suggest that chloroplast genomes in Symbiodinium are highly plastic. © 2013 Adrian C. Barbrook.

The chloroplast genome of a symbiodinium sp. clade C3 isolate

KAUST Repository

Barbrook, Adrian C.; Voolstra, Christian R.; Howe, Christopher J.

2014-01-01

Dinoflagellate algae of the genus Symbiodinium form important symbioses within corals and other benthic marine animals. Dinoflagellates possess an extremely reduced plastid genome relative to those examined in plants and other algae. In dinoflagellates the plastid genes are located on small plasmids, commonly referred to as 'minicircles'. However, the chloroplast genomes of dinoflagellates have only been extensively characterised from a handful of species. There is also evidence of considerable variation in the chloroplast genome organisation across those species that have been examined. We therefore characterised the chloroplast genome from an environmental coral isolate, in this case containing a symbiont belonging to the Symbiodinium sp. clade C3. The gene content of the genome is well conserved with respect to previously characterised genomes. However, unlike previously characterised dinoflagellate chloroplast genomes we did not identify any 'empty' minicircles. The sequences of this chloroplast genome show a high rate of evolution relative to other algal species. Particularly notable was a surprisingly high level of sequence divergence within the core polypeptides of photosystem I, the reasons for which are currently unknown. This chloroplast genome also possesses distinctive codon usage and GC content. These features suggest that chloroplast genomes in Symbiodinium are highly plastic. © 2013 Adrian C. Barbrook.

Chloroplast overexpression of rice caffeic acid O-methyltransferase increases melatonin production in chloroplasts via the 5-methoxytryptamine pathway in transgenic rice plants.

Science.gov (United States)

Choi, Geun-Hee; Lee, Hyoung Yool; Back, Kyoungwhan

2017-08-01

Recent analyses of the enzymatic features of various melatonin biosynthetic genes from bacteria, animals, and plants have led to the hypothesis that melatonin could be synthesized via the 5-methoxytryptamine (5-MT) pathway. 5-MT is known to be synthesized in vitro from serotonin by the enzymatic action of O-methyltransferases, including N-acetylserotonin methyltransferase (ASMT) and caffeic acid O-methyltransferase (COMT), leading to melatonin synthesis by the subsequent enzymatic reaction with serotonin N-acetyltransferase (SNAT). Here, we show that 5-MT was produced and served as a precursor for melatonin synthesis in plants. When rice seedlings were challenged with senescence treatment, 5-MT levels and melatonin production were increased in transgenic rice seedlings overexpressing the rice COMT in chloroplasts, while no such increases were observed in wild-type or transgenic seedlings overexpressing the rice COMT in the cytosol, suggesting a 5-MT transport limitation from the cytosol to chloroplasts. In contrast, cadmium treatment led to results different from those in senescence. The enhanced melatonin production was not observed in the chloroplast COMT lines relative over the cytosol COMT lines although 5-MT levels were equally induced in all genotypes upon cadmium treatment. The transgenic seedlings with enhanced melatonin in their chloroplasts exhibited improved seedling growth vs the wild type under continuous light conditions. This is the first report describing enhanced melatonin production in chloroplasts via the 5-MT pathway with the ectopic overexpression of COMT in chloroplasts in plants. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Cadmium Disrupts Subcellular Organelles, Including Chloroplasts, Resulting in Melatonin Induction in Plants

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Hyoung-Yool Lee

2017-10-01

Full Text Available Cadmium is a well-known elicitor of melatonin synthesis in plants, including rice. However, the mechanisms by which cadmium induces melatonin induction remain elusive. To investigate whether cadmium influences physical integrities in subcellular organelles, we treated tobacco leaves with either CdCl2 or AlCl3 and monitored the structures of subcellular organelles—such as chloroplasts, mitochondria, and the endoplasmic reticulum (ER—using confocal microscopic analysis. Unlike AlCl3 treatment, CdCl2 (0.5 mM treatment significantly disrupted chloroplasts, mitochondria, and ER. In theory, the disruption of chloroplasts enabled chloroplast-expressed serotonin N-acetyltransferase (SNAT to encounter serotonin in the cytoplasm, leading to the synthesis of N-acetylserotonin followed by melatonin synthesis. In fact, the disruption of chloroplasts by cadmium, not by aluminum, gave rise to a huge induction of melatonin in rice leaves, which suggests that cadmium-treated chloroplast disruption plays an important role in inducing melatonin in plants by removing physical barriers, such as chloroplast double membranes, allowing SNAT to gain access to the serotonin substrate enriched in the cytoplasm.

De Novo Assembly of Complete Chloroplast Genomes from Non-model Species Based on a K-mer Frequency-Based Selection of Chloroplast Reads from Total DNA Sequences

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Shairul Izan

2017-08-01

Full Text Available Whole Genome Shotgun (WGS sequences of plant species often contain an abundance of reads that are derived from the chloroplast genome. Up to now these reads have generally been identified and assembled into chloroplast genomes based on homology to chloroplasts from related species. This re-sequencing approach may select against structural differences between the genomes especially in non-model species for which no close relatives have been sequenced before. The alternative approach is to de novo assemble the chloroplast genome from total genomic DNA sequences. In this study, we used k-mer frequency tables to identify and extract the chloroplast reads from the WGS reads and assemble these using a highly integrated and automated custom pipeline. Our strategy includes steps aimed at optimizing assemblies and filling gaps which are left due to coverage variation in the WGS dataset. We have successfully de novo assembled three complete chloroplast genomes from plant species with a range of nuclear genome sizes to demonstrate the universality of our approach: Solanum lycopersicum (0.9 Gb, Aegilops tauschii (4 Gb and Paphiopedilum henryanum (25 Gb. We also highlight the need to optimize the choice of k and the amount of data used. This new and cost-effective method for de novo short read assembly will facilitate the study of complete chloroplast genomes with more accurate analyses and inferences, especially in non-model plant genomes.

Complete sequencing of five araliaceae chloroplast genomes and the phylogenetic implications.

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Rong Li

Full Text Available BACKGROUND: The ginseng family (Araliaceae includes a number of economically important plant species. Previously phylogenetic studies circumscribed three major clades within the core ginseng plant family, yet the internal relationships of each major group have been poorly resolved perhaps due to rapid radiation of these lineages. Recent studies have shown that phyogenomics based on chloroplast genomes provides a viable way to resolve complex relationships. METHODOLOGY/PRINCIPAL FINDINGS: We report the complete nucleotide sequences of five Araliaceae chloroplast genomes using next-generation sequencing technology. The five chloroplast genomes are 156,333-156,459 bp in length including a pair of inverted repeats (25,551-26,108 bp separated by the large single-copy (86,028-86,566 bp and small single-copy (18,021-19,117 bp regions. Each chloroplast genome contains the same 114 unique genes consisting of 30 transfer RNA genes, four ribosomal RNA genes, and 80 protein coding genes. Gene size, content, and order, AT content, and IR/SC boundary structure are similar among all Araliaceae chloroplast genomes. A total of 140 repeats were identified in the five chloroplast genomes with palindromic repeat as the most common type. Phylogenomic analyses using parsimony, likelihood, and Bayesian inference based on the complete chloroplast genomes strongly supported the monophyly of the Asian Palmate group and the Aralia-Panax group. Furthermore, the relationships among the sampled taxa within the Asian Palmate group were well resolved. Twenty-six DNA markers with the percentage of variable sites higher than 5% were identified, which may be useful for phylogenetic studies of Araliaceae. CONCLUSION: The chloroplast genomes of Araliaceae are highly conserved in all aspects of genome features. The large-scale phylogenomic data based on the complete chloroplast DNA sequences is shown to be effective for the phylogenetic reconstruction of Araliaceae.

Practical Guidelines for Water Percolation Capacity Determination of the Ground

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Mihael Brenčič

2011-06-01

Full Text Available Determination of water infiltration capacity of ground soils and rocks represents important part of design and construction procedures of the facilities for the infiltration of clean precipitation water. With their help percolation capacity of ground as well as response of the infiltration facilities to the inflowing precipitation water is estimated.Comparing to other in situ hydrogeological tests they can be understood as simple. However, in every day’s practiceseveral problems during their on site application and desk interpretation can arise. Paper represents review of existingpractical engineering procedures during the performance of percolation tests. Procedures are described for the borehole and shaft percolation tests execution and calculation theory for stationary and non‑stationary percolation tests are given. Theory is illustrated with practical exercises. Interpretations of typical departures from theoretical presumptions according to Hvorslev test of non-stationary test are illustrated.

Application of percolation leaching in Fuzhou uranium mine

International Nuclear Information System (INIS)

Jiang Lang; Wang Haita; He Jiangming

2006-01-01

In order to solve these problems such as high cost by conventional agitation leaching, low permeability and low leaching rate by heap leach, a percolation leaching method was developed. Two-year's production results show that leaching rate of uranium is up to 90% by this method. Compared with conventional agitation leaching, the power, sulfuric acid and lime consumption by the percolation leaching decreased by 60%, 27% and 77% respectively. (authors)

The complete chloroplast genome sequence of Helwingia himalaica (Helwingiaceae, Aquifoliales) and a chloroplast phylogenomic analysis of the Campanulidae

OpenAIRE

Yao, Xin; Liu, Ying-Ying; Tan, Yun-Hong; Song, Yu; Corlett, Richard T.

2016-01-01

Complete chloroplast genome sequences have been very useful for understanding phylogenetic relationships in angiosperms at the family level and above, but there are currently large gaps in coverage. We report the chloroplast genome for Helwingia himalaica, the first in the distinctive family Helwingiaceae and only the second genus to be sequenced in the order Aquifoliales. We then combine this with 36 published sequences in the large (c. 35,000 species) subclass Campanulidae in order to inves...

A comparison of rice chloroplast genomes

DEFF Research Database (Denmark)

Tang, Jiabin; Xia, Hong'ai; Cao, Mengliang

2004-01-01

Using high quality sequence reads extracted from our whole genome shotgun repository, we assembled two chloroplast genome sequences from two rice (Oryza sativa) varieties, one from 93-11 (a typical indica variety) and the other from PA64S (an indica-like variety with maternal origin of japonica......), which are both parental varieties of the super-hybrid rice, LYP9. Based on the patterns of high sequence coverage, we partitioned chloroplast sequence variations into two classes, intravarietal and intersubspecific polymorphisms. Intravarietal polymorphisms refer to variations within 93-11 or PA64S...

The TOC complex: preprotein gateway to the chloroplast.

Science.gov (United States)

Andrès, Charles; Agne, Birgit; Kessler, Felix

2010-06-01

Photosynthetic eukaryotes strongly depend on chloroplast metabolic pathways. Most if not all involve nuclear encoded proteins. These are synthesized as cytosolic preproteins with N-terminal, cleavable targeting sequences (transit peptide). Preproteins are imported by a major pathway composed of two proteins complexes: TOC and TIC (Translocon of the Outer and Inner membranes of the Chloroplasts, respectively). These selectively recognize the preproteins and facilitate their transport across the chloroplast envelope. The TOC core complex consists of three types of components, each belonging to a small family: Toc34, Toc75 and Toc159. Toc34 and Toc159 isoforms represent a subfamily of the GTPase superfamily. The members of the Toc34 and Toc159 subfamily act as GTP-dependent receptors at the chloroplast surface and distinct members of each occur in defined, substrate-specific TOC complexes. Toc75, a member of the Omp85 family, is conserved from prokaryotes and functions as the unique protein-conducting channel at the outer membrane. In this review we will describe the current state of knowledge regarding the composition and function of the TOC complex.

The complete chloroplast genome sequence of Aster spathulifolius (Asteraceae); genomic features and relationship with Asteraceae.

Science.gov (United States)

Choi, Kyoung Su; Park, SeonJoo

2015-11-10

Aster spathulifolius, a member of the Asteraceae family, is distributed along the coast of Japan and Korea. This plant is used for medicinal and ornamental purposes. The complete chloroplast (cp) genome of A. sphathulifolius consists of 149,473 bp that include a pair of inverted repeats of 24,751 bp separated by a large single copy region of 81,998 bp and a small single copy region of 17,973 bp. The chloroplast genome contains 78 coding genes, four rRNA genes and 29 tRNA genes. When compared to other cpDNA sequences of Asteraceae, A. spathulifolius showed the closest relationship with Jacobaea vulgaris, and its atpB gene was found to be a pseudogene, unlike J. vulgaris. Furthermore, evaluation of the gene compositions of J. vulgaris, Helianthus annuus, Guizotia abyssinica and A. spathulifolius revealed that 13.6-kb showed inversion from ndhF to rps15, unlike Lactuca of Asteraceae. Comparison of the synonymous (Ks) and nonsynonymous (Ka) substitution rates with J. vulgaris revealed that synonymous genes related to a small subunit of the ribosome showed the highest value (0.1558), while nonsynonymous rates of genes related to ATP synthase genes were highest (0.0118). These findings revealed that substitution has occurred at similar rates in most genes, and the substitution rates suggested that most genes is a purified selection. Copyright © 2015 Elsevier B.V. All rights reserved.

Percolation Threshold Parameters of Fluids

Czech Academy of Sciences Publication Activity Database

Škvor, J.; Nezbeda, Ivo

2009-01-01

Roč. 79, č. 4 (2009), 041141-041147 ISSN 1539-3755 Institutional research plan: CEZ:AV0Z40720504 Keywords : percolation threshold * universality * infinite cluster Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.400, year: 2009

Social percolation and the influence of mass media

Science.gov (United States)

Proykova, Ana; Stauffer, Dietrich

2002-09-01

In the marketing model of Solomon and Weisbuch, people buy a product only if their neighbours tell them of its quality, and if this quality is higher than their own quality expectations. Now we introduce additional information from the mass media, which is analogous to the ghost field in percolation theory. The mass media shift the percolative phase transition observed in the model, and decrease the time after which the stationary state is reached.

Logarithmic corrections to scaling in critical percolation and random resistor networks.

Science.gov (United States)

Stenull, Olaf; Janssen, Hans-Karl

2003-09-01

We study the critical behavior of various geometrical and transport properties of percolation in six dimensions. By employing field theory and renormalization group methods we analyze fluctuation induced logarithmic corrections to scaling up to and including the next-to-leading order correction. Our study comprehends the percolation correlation function, i.e., the probability that two given points are connected, and some of the fractal masses describing percolation clusters. To be specific, we calculate the mass of the backbone, the red bonds, and the shortest path. Moreover, we study key transport properties of percolation as represented by the random resistor network. We investigate the average two-point resistance as well as the entire family of multifractal moments of the current distribution.

Sonication-based isolation and enrichment of Chlorella protothecoides chloroplasts for illumina genome sequencing

Energy Technology Data Exchange (ETDEWEB)

Angelova, Angelina [University of Arizona; Park, Sang-Hycuk [University of Arizona; Kyndt, John [Bellevue University; Fitzsimmons, Kevin [University of Arizona; Brown, Judith K [University of Arizona

2013-09-01

With the increasing world demand for biofuel, a number of oleaginous algal species are being considered as renewable sources of oil. Chlorella protothecoides Krüger synthesizes triacylglycerols (TAGs) as storage compounds that can be converted into renewable fuel utilizing an anabolic pathway that is poorly understood. The paucity of algal chloroplast genome sequences has been an important constraint to chloroplast transformation and for studying gene expression in TAGs pathways. In this study, the intact chloroplasts were released from algal cells using sonication followed by sucrose gradient centrifugation, resulting in a 2.36-fold enrichment of chloroplasts from C. protothecoides, based on qPCR analysis. The C. protothecoides chloroplast genome (cpDNA) was determined using the Illumina HiSeq 2000 sequencing platform and found to be 84,576 Kb in size (8.57 Kb) in size, with a GC content of 30.8 %. This is the first report of an optimized protocol that uses a sonication step, followed by sucrose gradient centrifugation, to release and enrich intact chloroplasts from a microalga (C. prototheocoides) of sufficient quality to permit chloroplast genome sequencing with high coverage, while minimizing nuclear genome contamination. The approach is expected to guide chloroplast isolation from other oleaginous algal species for a variety of uses that benefit from enrichment of chloroplasts, ranging from biochemical analysis to genomics studies.

Characterization of the snowy cotyledon 1 mutant of Arabidopsis thaliana: the impact of chloroplast elongation factor G on chloroplast development and plant vitality.

Science.gov (United States)

Albrecht, Verónica; Ingenfeld, Anke; Apel, Klaus

2006-03-01

During seedling development chloroplast formation marks the transition from heterotrophic to autotrophic growth. The development and activity of chloroplasts may differ in cotyledons that initially serve as a storage organ and true leaves whose primary function is photosynthesis. A genetic screen was used for the identification of genes that affect selectively chloroplast function in cotyledons of Arabidopsis thaliana. Several mutants exhibiting pale cotyledons and green true leaves were isolated and dubbed snowy cotyledon (sco). One of the mutants, sco1, was characterized in more detail. The mutated gene was identified using map-based cloning. The mutant contains a point mutation in a gene encoding the chloroplast elongation factor G, leading to an amino acid exchange within the predicted 70S ribosome-binding domain. The mutation results in a delay in the onset of germination. At this early developmental stage embryos still contain undifferentiated proplastids, whose proper function seems necessary for seed germination. In light-grown sco1 seedlings the greening of cotyledons is severely impaired, whereas the following true leaves develop normally as in wild-type plants. Despite this apparent similarity of chloroplast development in true leaves of mutant and wild-type plants various aspects of mature plant development are also affected by the sco1 mutation such as the onset of flowering, the growth rate, and seed production. The onset of senescence in the mutant and the wild-type plants occurs, however, at the same time, suggesting that in the mutant this particular developmental step does not seem to suffer from reduced protein translation efficiency in chloroplasts.

Inhibition of chloroplast protein synthesis following light chilling of tomato

International Nuclear Information System (INIS)

Kent, J.; Ort, D.

1989-01-01

In the present study we looked at the effects of a high light chill on the pulsed incorporation of 35 S methionine into total, stromal, and thylakoid proteins of lightly abraded leaflets of 18-21 day old tomato (Lycopersicon esculentum Mill ca. Floramerica) seedlings. Based on gel fluorographic patterns of marker proteins that are indicative of the net rates of chloroplast and cytoplasmic protein synthesis, there appears to be a nearly complete cessation of chloroplastic protein synthesis. No labeling is observed for either the stromal large subunit of Rubisco or the thylakoid-bound alpha and beta subunits of the coupling factor. One notable exception, however, appears to be the 32 kd, D1 protein. Its net synthetic rate remains high despite the inhibition of other chloroplastically synthesized proteins. The small subunit of Rubicso, LHCP-II, as well as several other proteins of known cytoplasmic origin, were still synthesized, albeit, at lower than control rates. Light chilling of chill-insensitive spinach produced a similar, but less dramatic differential behavior between chloroplastic and cytoplasmic protein synthesis. It appears, in chilling-sensitive plants, that chloroplast protein synthesis exhibits a greater sensitivity to low temperature inhibition than does cytoplasmic protein synthesis and that recovery of chloroplast protein synthesis may play an important role in recovery of photosynthetic activity following chilling

Percolation transitions in two dimensions

NARCIS (Netherlands)

Feng, X.; Deng, Y.; Blöte, H.W.J.

2008-01-01

We investigate bond- and site-percolation models on several two-dimensional lattices numerically, by means of transfer-matrix calculations and Monte Carlo simulations. The lattices include the square, triangular, honeycomb kagome, and diced lattices with nearest-neighbor bonds, and the square

Chloroplasts activity and PAP-signaling regulate programmed cell death in Arabidopsis

KAUST Repository

Bruggeman, Quentin

2016-01-09

Programmed cell death (PCD) is a crucial process both for plant development and responses to biotic and abiotic stress. There is accumulating evidence that chloroplasts may play a central role during plant PCD as for mitochondria in animal cells, but it is still unclear whether they participate in PCD onset, execution, or both. To tackle this question, we have analyzed the contribution of chloroplast function to the cell death phenotype of the myoinositol phosphate synthase1 (mips1) mutant that forms spontaneous lesions in a light-dependent manner. We show that photosynthetically active chloroplasts are required for PCD to occur in mips1, but this process is independent of the redox state of the chloroplast. Systematic genetic analyses with retrograde signaling mutants reveal that 3’-phosphoadenosine 5’-phosphate, a chloroplast retrograde signal that modulates nuclear gene expression in response to stress, can inhibit cell death and compromises plant innate immunity via inhibition of the RNA-processing 5’-3’ exoribonucleases. Our results provide evidence for the role of chloroplast-derived signal and RNA metabolism in the control of cell death and biotic stress response. © 2016 American Society of Plant Biologists. All Rights Reserved.

Frataxin Is Localized to Both the Chloroplast and Mitochondrion and Is Involved in Chloroplast Fe-S Protein Function in Arabidopsis.

Directory of Open Access Journals (Sweden)

Valeria R Turowski

Full Text Available Frataxin plays a key role in eukaryotic cellular iron metabolism, particularly in mitochondrial heme and iron-sulfur (Fe-S cluster biosynthesis. However, its precise role has yet to be elucidated. In this work, we studied the subcellular localization of Arabidopsis frataxin, AtFH, using confocal microscopy, and found a novel dual localization for this protein. We demonstrate that plant frataxin is targeted to both the mitochondria and the chloroplast, where it may play a role in Fe-S cluster metabolism as suggested by functional studies on nitrite reductase (NIR and ferredoxin (Fd, two Fe-S containing chloroplast proteins, in AtFH deficient plants. Our results indicate that frataxin deficiency alters the normal functioning of chloroplasts by affecting the levels of Fe, chlorophyll, and the photosynthetic electron transport chain in this organelle.

Analysis of protein interactions at native chloroplast membranes by ellipsometry.

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Verena Kriechbaumer

Full Text Available Membrane bound receptors play vital roles in cell signaling, and are the target for many drugs, yet their interactions with ligands are difficult to study by conventional techniques due to the technical difficulty of monitoring these interactions in lipid environments. In particular, the ability to analyse the behaviour of membrane proteins in their native membrane environment is limited. Here, we have developed a quantitative approach to detect specific interactions between low-abundance chaperone receptors within native chloroplast membranes and their soluble chaperone partners. Langmuir-Schaefer film deposition was used to deposit native chloroplasts onto gold-coated glass slides, and interactions between the molecular chaperones Hsp70 and Hsp90 and their receptors in the chloroplast membranes were detected and quantified by total internal reflection ellipsometry (TIRE. We show that native chloroplast membranes deposited on gold-coated glass slides using Langmuir-Schaefer films retain functional receptors capable of binding chaperones with high specificity and affinity. Taking into account the low chaperone receptor abundance in native membranes, these binding properties are consistent with data generated using soluble forms of the chloroplast chaperone receptors, OEP61 and Toc64. Therefore, we conclude that chloroplasts have the capacity to selectively bind chaperones, consistent with the notion that chaperones play an important role in protein targeting to chloroplasts. Importantly, this method of monitoring by TIRE does not require any protein labelling. This novel combination of techniques should be applicable to a wide variety of membranes and membrane protein receptors, thus presenting the opportunity to quantify protein interactions involved in fundamental cellular processes, and to screen for drugs that target membrane proteins.

The demise of chloroplast DNA in Arabidopsis.

Science.gov (United States)

Rowan, Beth A; Oldenburg, Delene J; Bendich, Arnold J

2004-09-01

Although it might be expected that chloroplast DNA (cpDNA) would be stably maintained in mature leaves, we report the surprising observation that cpDNA levels decline during plastid development in Arabidopsis thaliana (Col.) until most of the leaves contain little or no DNA long before the onset of senescence. We measured the cpDNA content in developing cotyledons, rosette leaves, and cauline leaves. The amount of cpDNA per chloroplast decreases as the chloroplasts develop, reaching undetectable levels in mature leaves. In young cauline leaves, most individual molecules of cpDNA are found in complex, branched forms. In expanded cauline leaves, cpDNA is present in smaller branched forms only at the base of the leaf and is virtually absent in the distal part of the leaf. We conclude that photosynthetic activity may persist long after the demise of the cpDNA. Copyright 2004 Springer-Verlag

Phosphorus compounds, proteins, nuclease and acid phosphatase activities in isolated spinach chloroplasts

Directory of Open Access Journals (Sweden)

E. Mikulska

2015-01-01

Full Text Available This paper deals with attempts to elaborate a simple method of spinach chloroplast isolation ensuring a high proportion of intact chloroplasts. We obtained 3 preparations of isolated chloroplasts. Several preliminary analyses of the obtained chloroplast fraction were also performed. Phosphorus compounds, total protein and the enzyme activities of RNase, DNase and GPase were determined. We found: 0,36-0,59% of RNA, 0,19-0,24% of DNA, 2,1-2,9% of phospholipids and 26-28% of protein. RNase activity was very high.

Long range correlations, event simulation and parton percolation

International Nuclear Information System (INIS)

Pajares, C.

2011-01-01

We study the RHIC data on long range rapidity correlations, comparing their main trends with different string model simulations. Particular attention is paid to color percolation model and its similarities with color glass condensate. As both approaches corresponds, at high density, to a similar physical picture, both of them give rise to a similar behavior on the energy and the centrality of the main observables. Color percolation explains the transition from low density to high density.

Percolation-enhanced nonlinear scattering from semicontinuous metal films

Science.gov (United States)

Breit, M.; von Plessen, G.; Feldmann, J.; Podolskiy, V. A.; Sarychev, A. K.; Shalaev, V. M.; Gresillon, S.; Rivoal, J. C.; Gadenne, P.

2001-03-01

Strongly enhanced second-harmonic generation (SHG), which is characterized by nearly isotropic distribution, is observed for gold-glass films near the percolation threshold. The diffuse-like SHG scattering, which can be thought of as nonlinear critical opalescence, is in sharp contrast with highly collimated linear reflection and transmission from these nanostructured semicontinuous metal films. Our observations, which can be explained by giant fluctuations of local nonlinear sources for SHG, verify recent predictions of percolation-enhanced nonlinear scattering.

Effective modelling of percolation at the landscape scale using data-based approaches

Science.gov (United States)

Selle, Benny; Lischeid, Gunnar; Huwe, Bernd

2008-06-01

Process-based models have been extensively applied to assess the impact of landuse change on water quantity and quality at landscape scales. However, the routine application of those models suffers from large computational efforts, lack of transparency and the requirement of many input parameters. Data-based models such as Feed-Forward Multilayer Perceptrons (MLP) and Classification and Regression Trees (CART) may be used as effective models, i.e. simple approximations of complex process-based models. These data-based approaches can subsequently be applied for scenario analysis and as a transparent management tool provided climatic boundary conditions and the basic model assumptions of the process-based models do not change dramatically. In this study, we apply MLP, CART and Multiple Linear Regression (LR) to model the spatially distributed and spatially aggregated percolation in soils using weather, groundwater and soil data. The percolation data is obtained via numerical experiments with Hydrus1D. Thus, the complex process-based model is approximated using simpler data-based approaches. The MLP model explains most of the percolation variance in time and space without using any soil information. This reflects the effective dimensionality of the process-based model and suggests that percolation in the study area may be modelled much simpler than using Hydrus1D. The CART model shows that soil properties play a negligible role for percolation under wet climatic conditions. However, they become more important if the conditions turn drier. The LR method does not yield satisfactory predictions for the spatially distributed percolation however the spatially aggregated percolation is well approximated. This may indicate that the soils behave simpler (i.e. more linear) when percolation dynamics are upscaled.

Dynamics of bootstrap percolation

Indian Academy of Sciences (India)

precise criterion for the occurrence of a mixed transition is not very clear, and has been the subject ... ology, electronic communication, and social networks. It has also acquired a ... percolation theory is to start with a lattice with a fraction p of its sites occupied randomly, and ..... samples of a 104-node network. Probability is ...

Connectivity percolation in suspensions of attractive square-well spherocylinders.

Science.gov (United States)

Dixit, Mohit; Meyer, Hugues; Schilling, Tanja

2016-01-01

We have studied the connectivity percolation transition in suspensions of attractive square-well spherocylinders by means of Monte Carlo simulation and connectedness percolation theory. In the 1980s the percolation threshold of slender fibers has been predicted to scale as the fibers' inverse aspect ratio [Phys. Rev. B 30, 3933 (1984)PRBMDO1098-012110.1103/PhysRevB.30.3933]. The main finding of our study is that the attractive spherocylinder system reaches this inverse scaling regime at much lower aspect ratios than found in suspensions of hard spherocylinders. We explain this difference by showing that third virial corrections of the pair connectedness functions, which are responsible for the deviation from the scaling regime, are less important for attractive potentials than for hard particles.

Comparative studies on codon usage pattern of chloroplasts and ...

Indian Academy of Sciences (India)

Unknown

different genomic organization and mutation pressures in nuclear and chloroplast genes. The results of Nc-plots and neutrality plots ... As an important organelle of plants, the chloroplast has its own genomic environment and ... leading to the suggestion that the translation mechanism and patterns of codon usage in ...

Dated tribe-wide whole chloroplast genome phylogeny indicates recurrent hybridizations within Triticeae.

Science.gov (United States)

Bernhardt, Nadine; Brassac, Jonathan; Kilian, Benjamin; Blattner, Frank R

2017-06-16

Triticeae, the tribe of wheat grasses, harbours the cereals barley, rye and wheat and their wild relatives. Although economically important, relationships within the tribe are still not understood. We analysed the phylogeny of chloroplast lineages among nearly all monogenomic Triticeae taxa and polyploid wheat species aiming at a deeper understanding of the tribe's evolution. We used on- and off-target reads of a target-enrichment experiment followed by Illumina sequencing. The read data was used to assemble the plastid locus ndhF for 194 individuals and the whole chloroplast genome for 183 individuals, representing 53 Triticeae species and 15 genera. We conducted Bayesian and multispecies coalescent analyses to infer relationships and estimate divergence times of the taxa. We present the most comprehensive dated Triticeae chloroplast phylogeny and review previous hypotheses in the framework of our results. Monophyly of Triticeae chloroplasts could not be confirmed, as either Bromus or Psathyrostachys captured a chloroplast from a lineage closely related to a Bromus-Triticeae ancestor. The most recent common ancestor of Triticeae occurred approximately between ten and 19 million years ago. The comparison of the chloroplast phylogeny with available nuclear data in several cases revealed incongruences indicating past hybridizations. Recent events of chloroplast capture were detected as individuals grouped apart from con-specific accessions in otherwise monopyhletic groups.

Exploring photosynthesis evolution by comparative analysis of metabolic networks between chloroplasts and photosynthetic bacteria

Directory of Open Access Journals (Sweden)

Hou Jing

2006-04-01

Full Text Available Abstract Background Chloroplasts descended from cyanobacteria and have a drastically reduced genome following an endosymbiotic event. Many genes of the ancestral cyanobacterial genome have been transferred to the plant nuclear genome by horizontal gene transfer. However, a selective set of metabolism pathways is maintained in chloroplasts using both chloroplast genome encoded and nuclear genome encoded enzymes. As an organelle specialized for carrying out photosynthesis, does the chloroplast metabolic network have properties adapted for higher efficiency of photosynthesis? We compared metabolic network properties of chloroplasts and prokaryotic photosynthetic organisms, mostly cyanobacteria, based on metabolic maps derived from genome data to identify features of chloroplast network properties that are different from cyanobacteria and to analyze possible functional significance of those features. Results The properties of the entire metabolic network and the sub-network that consists of reactions directly connected to the Calvin Cycle have been analyzed using hypergraph representation. Results showed that the whole metabolic networks in chloroplast and cyanobacteria both possess small-world network properties. Although the number of compounds and reactions in chloroplasts is less than that in cyanobacteria, the chloroplast's metabolic network has longer average path length, a larger diameter, and is Calvin Cycle -centered, indicating an overall less-dense network structure with specific and local high density areas in chloroplasts. Moreover, chloroplast metabolic network exhibits a better modular organization than cyanobacterial ones. Enzymes involved in the same metabolic processes tend to cluster into the same module in chloroplasts. Conclusion In summary, the differences in metabolic network properties may reflect the evolutionary changes during endosymbiosis that led to the improvement of the photosynthesis efficiency in higher plants. Our

Phenomenology of quarkyonic percolation at FAIR

International Nuclear Information System (INIS)

Torrieri, Giorgio; Lottini, Stefano

2013-01-01

We will give an introduction to the concept of quarkyonic matter, presenting an overview of what is meant by this term in the literature. We will then argue that the quarkyonic phase, as defined in the original paper, is a percolation-type phase transition whose phase transition line is strongly curved in ρ B − N c space, where N C is the number of colors and ρ B the baryon density. With a toy model estimate, we show that it might be possible to obtain a percolating but confined phase at N c = 3, N f = 2 at densities larger than one baryon per one baryon size. We conclude by discussing how this phase can be observed at FAIR.

Chloroplast behaviour and interactions with other organelles in Arabidopsis thaliana pavement cells.

Science.gov (United States)

Barton, Kiah A; Wozny, Michael R; Mathur, Neeta; Jaipargas, Erica-Ashley; Mathur, Jaideep

2018-01-29

Chloroplasts are a characteristic feature of green plants. Mesophyll cells possess the majority of chloroplasts and it is widely believed that, with the exception of guard cells, the epidermal layer in most higher plants does not contain chloroplasts. However, recent observations on Arabidopsis thaliana have shown a population of chloroplasts in pavement cells that are smaller than mesophyll chloroplasts and have a high stroma to grana ratio. Here, using stable transgenic lines expressing fluorescent proteins targeted to the plastid stroma, plasma membrane, endoplasmic reticulum, tonoplast, nucleus, mitochondria, peroxisomes, F-actin and microtubules, we characterize the spatiotemporal relationships between the pavement cell chloroplasts (PCCs) and their subcellular environment. Observations on the PCCs suggest a source-sink relationship between the epidermal and the mesophyll layers, and experiments with the Arabidopsis mutants glabra2 ( gl2 ) and immutans ( im ), which show altered epidermal plastid development, underscored their developmental plasticity. Our findings lay down the foundation for further investigations aimed at understanding the precise role and contributions of PCCs in plant interactions with the environment. © 2018. Published by The Company of Biologists Ltd.

Extending the biosynthetic repertoires of cyanobacteria and chloroplasts

DEFF Research Database (Denmark)

Nielsen, Agnieszka Janina Zygadlo; Mellor, Silas Busck; Vavitsas, Konstantinos

2016-01-01

The chloroplasts found in plants and algae, and photosynthetic microorganisms such as cyanobacteria, are emerging hosts for sustainable production of valuable biochemicals, using only inorganic nutrients, water, CO2 and light as inputs. In the past decade, many bioengineering efforts have focused...... on metabolic engineering and synthetic biology in the chloroplast or in cyanobacteria for the production of fuels, chemicals, as well as complex, high-value bioactive molecules. Biosynthesis of all these compounds can be performed in photosynthetic organelles/organisms by heterologous expression...... of chloroplasts and cyanobacteria as biosynthetic compartments and hosts, and we estimate the production levels to be expected from photosynthetic hosts in light of the fraction of electrons and carbon that can potentially be diverted from photosynthesis. The supply of reducing power, in the form of electrons...

Inactivation of VHSV by Percolation and Salt Under Experimental Conditions

DEFF Research Database (Denmark)

Skall, Helle Frank; Olesen, Niels Jørgen; Jørgensen, Claus

2012-01-01

At the moment the only legal method in Denmark to sanitize wastewater from fish cutting plants is by percolation. To evaluate the inactivation effect of percolation on VHSV an experimental examination was initiated. A column packed with gravel as top- and bottom layer (total of 22 cm) and a mid l...

Percolation and nucleation approaches to nuclear fragmentation: criticality in very small systems

Energy Technology Data Exchange (ETDEWEB)

Santiago, A.J. [Universidade do Estado, Rio de Janeiro, RJ (Brazil). Inst. de Fisica; Chung, K.C.

1994-12-01

Different criteria for criticality in very small systems are discussed in the context of percolation and nucleation approaches to nuclear fragmentation. It is shown that the probability threshold in percolation and interaction radius threshold in nucleation are very strongly dependent upon the adopted criterion. By using Monte Carlo method, similarities and dissimilarities between nucleation and percolation pictures are also pointed out. (author). 17 refs, 5 figs, 2 tabs.

Percolation and nucleation approaches to nuclear fragmentation: criticality in very small systems

International Nuclear Information System (INIS)

Santiago, A.J.; Chung, K.C.

1994-12-01

Different criteria for criticality in very small systems are discussed in the context of percolation and nucleation approaches to nuclear fragmentation. It is shown that the probability threshold in percolation and interaction radius threshold in nucleation are very strongly dependent upon the adopted criterion. By using Monte Carlo method, similarities and dissimilarities between nucleation and percolation pictures are also pointed out. (author). 17 refs, 5 figs, 2 tabs

Percolation, statistical topography, and transport in random media

International Nuclear Information System (INIS)

Isichenko, M.B.

1992-01-01

A review of classical percolation theory is presented, with an emphasis on novel applications to statistical topography, turbulent diffusion, and heterogeneous media. Statistical topography involves the geometrical properties of the isosets (contour lines or surfaces) of a random potential ψ(x). For rapidly decaying correlations of ψ, the isopotentials fall into the same universality class as the perimeters of percolation clusters. The topography of long-range correlated potentials involves many length scales and is associated either with the correlated percolation problem or with Mandelbrot's fractional Brownian reliefs. In all cases, the concept of fractal dimension is particularly fruitful in characterizing the geometry of random fields. The physical applications of statistical topography include diffusion in random velocity fields, heat and particle transport in turbulent plasmas, quantum Hall effect, magnetoresistance in inhomogeneous conductors with the classical Hall effect, and many others where random isopotentials are relevant. A geometrical approach to studying transport in random media, which captures essential qualitative features of the described phenomena, is advocated

Controlling electrical percolation in multicomponent carbon nanotube dispersions.

Science.gov (United States)

Kyrylyuk, Andriy V; Hermant, Marie Claire; Schilling, Tanja; Klumperman, Bert; Koning, Cor E; van der Schoot, Paul

2011-04-10

Carbon nanotube reinforced polymeric composites can have favourable electrical properties, which make them useful for applications such as flat-panel displays and photovoltaic devices. However, using aqueous dispersions to fabricate composites with specific physical properties requires that the processing of the nanotube dispersion be understood and controlled while in the liquid phase. Here, using a combination of experiment and theory, we study the electrical percolation of carbon nanotubes introduced into a polymer matrix, and show that the percolation threshold can be substantially lowered by adding small quantities of a conductive polymer latex. Mixing colloidal particles of different sizes and shapes (in this case, spherical latex particles and rod-like nanotubes) introduces competing length scales that can strongly influence the formation of the system-spanning networks that are needed to produce electrically conductive composites. Interplay between the different species in the dispersions leads to synergetic or antagonistic percolation, depending on the ease of charge transport between the various conductive components.

Protein methylation in pea chloroplasts

International Nuclear Information System (INIS)

Niemi, K.J.; Adler, J.; Selman, B.R.

1990-01-01

The methylation of chloroplast proteins has been investigated by incubating intact pea (Pisum sativum) chloroplasts with [ 3 H-methyl]-S-adenosylmethionine. Incubation in the light increases the amount of methylation in both the thylakoid and stromal fractions. Numerous thylakoid proteins serve as substrates for the methyltransfer reactions. Three of these thylakoid proteins are methylated to a significantly greater extent in the light than in the dark. The primary stromal polypeptide methylated is the large subunit of ribulose bisphosphate carboxylase/oxygenase. One other stromal polypeptide is also methylated much more in the light than in the dark. Two distinct types of protein methylation occur. One methylinkage is stable to basic conditions whereas a second type is base labile. The base-stable linkage is indicative of N-methylation of amino acid residues while base-lability is suggestive of carboxymethylation of amino acid residues. Labeling in the light increases the percentage of methylation that is base labile in the thylakoid fraction while no difference is observed in the amount of base-labile methylations in light-labeled and dark-labeled stromal proteins. Also suggestive of carboxymethylation is the detection of volatile [ 3 H]methyl radioactivity which increases during the labeling period and is greater in chloroplasts labeled in the light as opposed to being labeled in the dark; this implies in vivo turnover of the [ 3 H]methyl group

Percolation effects in supercapacitors with thin, transparent carbon nanotube electrodes.

Science.gov (United States)

King, Paul J; Higgins, Thomas M; De, Sukanta; Nicoloso, Norbert; Coleman, Jonathan N

2012-02-28

We have explored the effects of percolation on the properties of supercapacitors with thin nanotube networks as electrodes. We find the equivalent series resistance, R(ESR), and volumetric capacitance, C(V), to be thickness independent for relatively thick electrodes. However, once the electrode thickness falls below a threshold thickness (∼100 nm for R(ESR) and ∼20 nm for C(V)), the properties of the electrode become thickness dependent. We show the thickness dependence of both R(ESR) and C(V) to be consistent with percolation theory. While this is expected for R(ESR), that the capacitance follows a percolation scaling law is not. This occurs because, for sparse networks, the capacitance is proportional to the fraction of nanotubes connected to the main network. This fraction, in turn, follows a percolation scaling law. This allows us to understand and quantify the limitations on the achievable capacitance for transparent supercapacitors. We find that supercapacitors with thickness independent R(ESR) and C(V) occupy a well-defined region of the Ragone plot. However, supercapacitors whose electrodes are limited by percolation occupy a long tail to lower values of energy and power density. For example, replacing electrodes with transparency of T = 80% with thinner networks displaying T = 97% will result in a 20-fold reduction of both power and energy density.

Purifying Nanomaterials

Science.gov (United States)

Hung, Ching-Cheh (Inventor); Hurst, Janet (Inventor)

2014-01-01

A method of purifying a nanomaterial and the resultant purified nanomaterial in which a salt, such as ferric chloride, at or near its liquid phase temperature, is used to penetrate and wet the internal surfaces of a nanomaterial to dissolve impurities that may be present, for example, from processes used in the manufacture of the nanomaterial.

Analysis of chlorophyll fluorescence reveals stage specific patterns of chloroplast-containing cells during Arabidopsis embryogenesis

Directory of Open Access Journals (Sweden)

RICARDO I TEJOS

2010-01-01

Full Text Available The basic body plan of a plant is established early in embryogenesis when cells differentiate, giving rise to the apical and basal regions of the embryo. Using chlorophyll fluorescence as a marker for chloroplasts, we have detected specific patterns of chloroplast-containing cells at specific stages of embryogenesis. Non-randomly distributed chloroplast-containing cells are seen as early as the globular stage of embryogenesis in Arabidopsis. In the heart stage of embryogenesis, chloroplast containing cells are detected in epidermal cells as well as a central region of the heart stage embryo, forming a triangular septum of chloroplast-containing cells that divides the embryo into three equal sectors. Torpedo stage embryos have chloroplast-containing epidermal cells and a central band of chloroplast-containing cells in the cortex layer, just below the shoot apical meristem. In the walking-stick stage of embryogenesis, chloroplasts are present in the epidermal, cortex and endodermal cells. The chloroplasts appear reduced or absent from the provascular and columella cells of walking-stick stage embryos. These results suggest that there is a tight regulation of plastid differentiation during embryogenesis that generates specific patterns of chloroplast-containing cells in specific cell layers at specific stages of embryogenesis.

Soil Respiration Controls Ionic Nutrient Concentration In Percolating Water In Rice Fields

Science.gov (United States)

Kimura, M.

2004-12-01

Soil water in the plow layer in rice fields contains various kinds of cations and anions, and they are lost from the plow layer by water percolation. Some portions of CO2 produced by respirations of rice roots and soil microorganisms are also leached by water percolation to the subsoil layer as HCO3-. As the electrical neutrality of inorganic substances in percolating water is maintained when they are assumed to be in the form of simple cations and anions, soil respiration accelerates the leaching of ionic nutrients from the plow layer by water percolation. The proportion of inorganic carbon (Σ CO2) originated from photosynthates in the total Σ CO2 in soil solution in the plow layer was from 28 to 36 % in the rice straw amended soil and from 16 to 31 % in the soil without rice straw amendment in a soil pot experiment with rice plant after the maximum tillering stage. Most of Σ CO2 in percolating water from the plow layer accumulates in the subsoil layer. Periodical measurement of Σ CO2 in percolating water at 13 and 40 cm soil depths indicated that 10 % of total soil organic C in the plow layer was leached down from the plow layer (13 cm), and that about 90 % of it was retained in the subsoil layer to the depth of 40 cm. Water soluble organic materials are also leached from the plow layer by water percolation, and the leaching is accelerated by soil reduction. Soil reduction decreased the content of organic materials that were bound with ferric iron in soil (extractable by 0.1M Na4P2O7 + NaBH4) and increased the content of organic materials that were extractable by the neutral chelating solution (0.1M Na4P2O7). In addition, water percolation transformed the latter organic materials to those that were extractable by water and a neutral salt. Considerable portions of organic materials in percolating water are adsorbed in the subsoil layer, and then partially decomposed and polymerized to specific soil organic materials in the subsoil. Organic materials that were

The diurnal logic of the expression of the chloroplast genome in Chlamydomonas reinhardtii.

Directory of Open Access Journals (Sweden)

Adam D Idoine

Full Text Available Chloroplasts are derived from cyanobacteria and have retained a bacterial-type genome and gene expression machinery. The chloroplast genome encodes many of the core components of the photosynthetic apparatus in the thylakoid membranes. To avoid photooxidative damage and production of harmful reactive oxygen species (ROS by incompletely assembled thylakoid protein complexes, chloroplast gene expression must be tightly regulated and co-ordinated with gene expression in the nucleus. Little is known about the control of chloroplast gene expression at the genome-wide level in response to internal rhythms and external cues. To obtain a comprehensive picture of organelle transcript levels in the unicellular model alga Chlamydomonas reinhardtii in diurnal conditions, a qRT-PCR platform was developed and used to quantify 68 chloroplast, 21 mitochondrial as well as 71 nuclear transcripts in cells grown in highly controlled 12 h light/12 h dark cycles. Interestingly, in anticipation of dusk, chloroplast transcripts from genes involved in transcription reached peak levels first, followed by transcripts from genes involved in translation, and finally photosynthesis gene transcripts. This pattern matches perfectly the theoretical demands of a cell "waking up" from the night. A similar trend was observed in the nuclear transcripts. These results suggest a striking internal logic in the expression of the chloroplast genome and a previously unappreciated complexity in the regulation of chloroplast genes.

Structure-Function Analysis of Chloroplast Proteins via Random Mutagenesis Using Error-Prone PCR.

Science.gov (United States)

Dumas, Louis; Zito, Francesca; Auroy, Pascaline; Johnson, Xenie; Peltier, Gilles; Alric, Jean

2018-06-01

Site-directed mutagenesis of chloroplast genes was developed three decades ago and has greatly advanced the field of photosynthesis research. Here, we describe a new approach for generating random chloroplast gene mutants that combines error-prone polymerase chain reaction of a gene of interest with chloroplast complementation of the knockout Chlamydomonas reinhardtii mutant. As a proof of concept, we targeted a 300-bp sequence of the petD gene that encodes subunit IV of the thylakoid membrane-bound cytochrome b 6 f complex. By sequencing chloroplast transformants, we revealed 149 mutations in the 300-bp target petD sequence that resulted in 92 amino acid substitutions in the 100-residue target subunit IV sequence. Our results show that this method is suited to the study of highly hydrophobic, multisubunit, and chloroplast-encoded proteins containing cofactors such as hemes, iron-sulfur clusters, and chlorophyll pigments. Moreover, we show that mutant screening and sequencing can be used to study photosynthetic mechanisms or to probe the mutational robustness of chloroplast-encoded proteins, and we propose that this method is a valuable tool for the directed evolution of enzymes in the chloroplast. © 2018 American Society of Plant Biologists. All rights reserved.

Percolation processes

International Nuclear Information System (INIS)

Kunz, H.

1980-01-01

Percolation is a unifying which appeared to be rather useful in trying to understand some properties of disordered physical systems, or some phase transitions in polymers, like gelation or vulcanisation. Although implicitely used in the pioneering work of Flory in 1941 on the sol-gel transition of polymers, it was first introduced in a well-defined way by the mathematicians Hammersley and Broadbent in 1957, who obtained the first rigorous result. Since then, the subject has seen a variety of new applications and its recent study has largely benefited from the vigorous development of critical phenomena after the introduction of the RG ideas and techniques. (author)

Chloroplast Iron Transport Proteins - Function and Impact on Plant Physiology.

Science.gov (United States)

López-Millán, Ana F; Duy, Daniela; Philippar, Katrin

2016-01-01

Chloroplasts originated about three billion years ago by endosymbiosis of an ancestor of today's cyanobacteria with a mitochondria-containing host cell. During evolution chloroplasts of higher plants established as the site for photosynthesis and thus became the basis for all life dependent on oxygen and carbohydrate supply. To fulfill this task, plastid organelles are loaded with the transition metals iron, copper, and manganese, which due to their redox properties are essential for photosynthetic electron transport. In consequence, chloroplasts for example represent the iron-richest system in plant cells. However, improvement of oxygenic photosynthesis in turn required adaptation of metal transport and homeostasis since metal-catalyzed generation of reactive oxygen species (ROS) causes oxidative damage. This is most acute in chloroplasts, where radicals and transition metals are side by side and ROS-production is a usual feature of photosynthetic electron transport. Thus, on the one hand when bound by proteins, chloroplast-intrinsic metals are a prerequisite for photoautotrophic life, but on the other hand become toxic when present in their highly reactive, radical generating, free ionic forms. In consequence, transport, storage and cofactor-assembly of metal ions in plastids have to be tightly controlled and are crucial throughout plant growth and development. In the recent years, proteins for iron transport have been isolated from chloroplast envelope membranes. Here, we discuss their putative functions and impact on cellular metal homeostasis as well as photosynthetic performance and plant metabolism. We further consider the potential of proteomic analyses to identify new players in the field.

A Matter of Time: Faster Percolator Analysis via Efficient SVM Learning for Large-Scale Proteomics.

Science.gov (United States)

Halloran, John T; Rocke, David M

2018-05-04

Percolator is an important tool for greatly improving the results of a database search and subsequent downstream analysis. Using support vector machines (SVMs), Percolator recalibrates peptide-spectrum matches based on the learned decision boundary between targets and decoys. To improve analysis time for large-scale data sets, we update Percolator's SVM learning engine through software and algorithmic optimizations rather than heuristic approaches that necessitate the careful study of their impact on learned parameters across different search settings and data sets. We show that by optimizing Percolator's original learning algorithm, l 2 -SVM-MFN, large-scale SVM learning requires nearly only a third of the original runtime. Furthermore, we show that by employing the widely used Trust Region Newton (TRON) algorithm instead of l 2 -SVM-MFN, large-scale Percolator SVM learning is reduced to nearly only a fifth of the original runtime. Importantly, these speedups only affect the speed at which Percolator converges to a global solution and do not alter recalibration performance. The upgraded versions of both l 2 -SVM-MFN and TRON are optimized within the Percolator codebase for multithreaded and single-thread use and are available under Apache license at bitbucket.org/jthalloran/percolator_upgrade .

Pseudo-random-number generators and the square site percolation threshold.

Science.gov (United States)

Lee, Michael J

2008-09-01

Selected pseudo-random-number generators are applied to a Monte Carlo study of the two-dimensional square-lattice site percolation model. A generator suitable for high precision calculations is identified from an application specific test of randomness. After extended computation and analysis, an ostensibly reliable value of p_{c}=0.59274598(4) is obtained for the percolation threshold.

Continuum percolation of polydisperse rods in quadrupole fields: Theory and simulations

Science.gov (United States)

Finner, Shari P.; Kotsev, Mihail I.; Miller, Mark A.; van der Schoot, Paul

2018-01-01

We investigate percolation in mixtures of nanorods in the presence of external fields that align or disalign the particles with the field axis. Such conditions are found in the formulation and processing of nanocomposites, where the field may be electric, magnetic, or due to elongational flow. Our focus is on the effect of length polydispersity, which—in the absence of a field—is known to produce a percolation threshold that scales with the inverse weight average of the particle length. Using a model of non-interacting spherocylinders in conjunction with connectedness percolation theory, we show that a quadrupolar field always increases the percolation threshold and that the universal scaling with the inverse weight average no longer holds if the field couples to the particle length. Instead, the percolation threshold becomes a function of higher moments of the length distribution, where the order of the relevant moments crucially depends on the strength and type of field applied. The theoretical predictions compare well with the results of our Monte Carlo simulations, which eliminate finite size effects by exploiting the fact that the universal scaling of the wrapping probability function holds even in anisotropic systems. Theory and simulation demonstrate that the percolation threshold of a polydisperse mixture can be lower than that of the individual components, confirming recent work based on a mapping onto a Bethe lattice as well as earlier computer simulations involving dipole fields. Our work shows how the formulation of nanocomposites may be used to compensate for the adverse effects of aligning fields that are inevitable under practical manufacturing conditions.

Chloroplasts as source and target of cellular redox regulation: a discussion on chloroplast redox signals in the context of plant physiology.

Science.gov (United States)

Baier, Margarete; Dietz, Karl-Josef

2005-06-01

During the evolution of plants, chloroplasts have lost the exclusive genetic control over redox regulation and antioxidant gene expression. Together with many other genes, all genes encoding antioxidant enzymes and enzymes involved in the biosynthesis of low molecular weight antioxidants were transferred to the nucleus. On the other hand, photosynthesis bears a high risk for photo-oxidative damage. Concomitantly, an intricate network for mutual regulation by anthero- and retrograde signals has emerged to co-ordinate the activities of the different genetic and metabolic compartments. A major focus of recent research in chloroplast regulation addressed the mechanisms of redox sensing and signal transmission, the identification of regulatory targets, and the understanding of adaptation mechanisms. In addition to redox signals communicated through signalling cascades also used in pathogen and wounding responses, specific chloroplast signals control nuclear gene expression. Signalling pathways are triggered by the redox state of the plastoquinone pool, the thioredoxin system, and the acceptor availability at photosystem I, in addition to control by oxolipins, tetrapyrroles, carbohydrates, and abscisic acid. The signalling function is discussed in the context of regulatory circuitries that control the expression of antioxidant enzymes and redox modulators, demonstrating the principal role of chloroplasts as the source and target of redox regulation.

Critical current simulation in granular superconductors above the percolation threshold

Science.gov (United States)

Riedinger, Roland

1992-02-01

In the phase-coherent regime without applied external magnetic field, the critical superconducting current is limited by intragranular junctions which behave like Josephson junctions. We study the percolation aspects specific to lattices of such junctions and/or the mixing of superconductor with normal grains by averaging over configurations. We illustrate on 2 and 3 dimensional examples. The power laws valid near the percolation threshold are valid well above it, in two and three dimensions. We discuss the other models limiting the superconducting current, the vortex creep and superconducting order parameter fluctuations. Dans la limite de champ magnétique nul et de cohérence de phase du paramètre d'ordre supraconducteur, le courant supraconducteur maximal dans un réseau est limité par les jonctions intergranulaires qui se comportent comme des jonctions Josephson. Nous analysons les problèmes de percolation spécifiques aux réseaux de jonctions et du mélange de grains normaux et supraconducteurs. Nous donnons des exemples bidimensionnels et tridimensionnels ; après moyenne sur les configurations et analyse en taille finie, nous montrons que les lois de puissance valables au voisinage du seuil de percolation s'étendent sur un grand domaine au-delà du seuil de percolation, à deux et trois dimensions. Nous discutons les autres modèles limitant le courant supraconducteur, ancrage de vortex et fluctuations du paramètre d'ordre.

Arabidopsis VARIEGATED 3 encodes a chloroplast-targeted, zinc-finger protein required for chloroplast and palisade cell development

DEFF Research Database (Denmark)

Næsted, Henrik; Holm, Agnethe; Jenkins, Tom

2004-01-01

The stable, recessive Arabidopsis variegated 3 (var3) mutant exhibits a variegated phenotype due to somatic areas lacking or containing developmentally retarded chloroplasts and greatly reduced numbers of palisade cells. The VAR3 gene, isolated by transposon tagging, encodes the 85.9 kDa VAR3...... that pigment profiles are qualitatively similar in wild type and var3, although var3 accumulates lower levels of chlorophylls and carotenoids. These results indicate that VAR3 is a part of a protein complex required for normal chloroplast and palisade cell development....

Ion and metabolite transport in the chloroplast of algae: lessons from land plants.

Science.gov (United States)

Marchand, Justine; Heydarizadeh, Parisa; Schoefs, Benoît; Spetea, Cornelia

2018-06-01

Chloroplasts are endosymbiotic organelles and play crucial roles in energy supply and metabolism of eukaryotic photosynthetic organisms (algae and land plants). They harbor channels and transporters in the envelope and thylakoid membranes, mediating the exchange of ions and metabolites with the cytosol and the chloroplast stroma and between the different chloroplast subcompartments. In secondarily evolved algae, three or four envelope membranes surround the chloroplast, making more complex the exchange of ions and metabolites. Despite the importance of transport proteins for the optimal functioning of the chloroplast in algae, and that many land plant homologues have been predicted, experimental evidence and molecular characterization are missing in most cases. Here, we provide an overview of the current knowledge about ion and metabolite transport in the chloroplast from algae. The main aspects reviewed are localization and activity of the transport proteins from algae and/or of homologues from other organisms including land plants. Most chloroplast transporters were identified in the green alga Chlamydomonas reinhardtii, reside in the envelope and participate in carbon acquisition and metabolism. Only a few identified algal transporters are located in the thylakoid membrane and play role in ion transport. The presence of genes for putative transporters in green algae, red algae, diatoms, glaucophytes and cryptophytes is discussed, and roles in the chloroplast are suggested. A deep knowledge in this field is required because algae represent a potential source of biomass and valuable metabolites for industry, medicine and agriculture.

Monte Carlo simulations of electrical percolation in multicomponent thin films with nanofillers

Science.gov (United States)

Ni, Xiaojuan; Hui, Chao; Su, Ninghai; Jiang, Wei; Liu, Feng

2018-02-01

We developed a 2D disk-stick percolation model to investigate the electrical percolation behavior of an insulating thin film reinforced with 1D and 2D conductive nanofillers via Monte Carlo simulation. Numerical predictions of the percolation threshold in single component thin films showed good agreement with the previous published work, validating our model for investigating the characteristics of the percolation phenomena. Parametric studies of size effect, i.e., length of 1D nanofiller and diameter of 2D nanofiller, were carried out to predict the electrical percolation threshold for hybrid systems. The relationships between the nanofillers in two hybrid systems was established, which showed differences from previous linear assumption. The effective electrical conductance was evaluated through Kirchhoff’s current law by transforming it into a resistor network. The equivalent resistance was obtained from the distribution of nodal voltages by solving a system of linear equations with a Gaussian elimination method. We examined the effects of stick length, relative concentration, and contact patterns of 1D/2D inclusions on electrical performance. One novel aspect of our study is its ability to investigate the effective conductance of nanocomposites as a function of relative concentrations, which shows there is a synergistic effect when nanofillers with different dimensionalities combine properly. Our work provides an important theoretical basis for designing the conductive networks and predicting the percolation properties of multicomponent nanocomposites.

Does a voltage-sensitive outer envelope transport mechanism contributes to the chloroplast iron uptake?

Science.gov (United States)

Solti, Ádám; Kovács, Krisztina; Müller, Brigitta; Vázquez, Saúl; Hamar, Éva; Pham, Hong Diep; Tóth, Brigitta; Abadía, Javier; Fodor, Ferenc

2016-12-01

Based on the effects of inorganic salts on chloroplast Fe uptake, the presence of a voltage-dependent step is proposed to play a role in Fe uptake through the outer envelope. Although iron (Fe) plays a crucial role in chloroplast physiology, only few pieces of information are available on the mechanisms of chloroplast Fe acquisition. Here, the effect of inorganic salts on the Fe uptake of intact chloroplasts was tested, assessing Fe and transition metal uptake using bathophenantroline-based spectrophotometric detection and plasma emission-coupled mass spectrometry, respectively. The microenvironment of Fe was studied by Mössbauer spectroscopy. Transition metal cations (Cd 2+ , Zn 2+ , and Mn 2+ ) enhanced, whereas oxoanions (NO 3 - , SO 4 2- , and BO 3 3- ) reduced the chloroplast Fe uptake. The effect was insensitive to diuron (DCMU), an inhibitor of chloroplast inner envelope-associated Fe uptake. The inorganic salts affected neither Fe forms in the uptake assay buffer nor those incorporated into the chloroplasts. The significantly lower Zn and Mn uptake compared to that of Fe indicates that different mechanisms/transporters are involved in their acquisition. The enhancing effect of transition metals on chloroplast Fe uptake is likely related to outer envelope-associated processes, since divalent metal cations are known to inhibit Fe 2+ transport across the inner envelope. Thus, a voltage-dependent step is proposed to play a role in Fe uptake through the chloroplast outer envelope on the basis of the contrasting effects of transition metal cations and oxoaninons.

Statistical analysis and Monte Carlo simulation of growing self-avoiding walks on percolation

Energy Technology Data Exchange (ETDEWEB)

Zhang Yuxia [Department of Physics, Wuhan University, Wuhan 430072 (China); Sang Jianping [Department of Physics, Wuhan University, Wuhan 430072 (China); Department of Physics, Jianghan University, Wuhan 430056 (China); Zou Xianwu [Department of Physics, Wuhan University, Wuhan 430072 (China)]. E-mail: xwzou@whu.edu.cn; Jin Zhunzhi [Department of Physics, Wuhan University, Wuhan 430072 (China)

2005-09-26

The two-dimensional growing self-avoiding walk on percolation was investigated by statistical analysis and Monte Carlo simulation. We obtained the expression of the mean square displacement and effective exponent as functions of time and percolation probability by statistical analysis and made a comparison with simulations. We got a reduced time to scale the motion of walkers in growing self-avoiding walks on regular and percolation lattices.

Chloroplast two-component systems: evolution of the link between photosynthesis and gene expression.

Science.gov (United States)

Puthiyaveetil, Sujith; Allen, John F

2009-06-22

Two-component signal transduction, consisting of sensor kinases and response regulators, is the predominant signalling mechanism in bacteria. This signalling system originated in prokaryotes and has spread throughout the eukaryotic domain of life through endosymbiotic, lateral gene transfer from the bacterial ancestors and early evolutionary precursors of eukaryotic, cytoplasmic, bioenergetic organelles-chloroplasts and mitochondria. Until recently, it was thought that two-component systems inherited from an ancestral cyanobacterial symbiont are no longer present in chloroplasts. Recent research now shows that two-component systems have survived in chloroplasts as products of both chloroplast and nuclear genes. Comparative genomic analysis of photosynthetic eukaryotes shows a lineage-specific distribution of chloroplast two-component systems. The components and the systems they comprise have homologues in extant cyanobacterial lineages, indicating their ancient cyanobacterial origin. Sequence and functional characteristics of chloroplast two-component systems point to their fundamental role in linking photosynthesis with gene expression. We propose that two-component systems provide a coupling between photosynthesis and gene expression that serves to retain genes in chloroplasts, thus providing the basis of cytoplasmic, non-Mendelian inheritance of plastid-associated characters. We discuss the role of this coupling in the chronobiology of cells and in the dialogue between nuclear and cytoplasmic genetic systems.

Standard and inverse bond percolation of straight rigid rods on square lattices

Science.gov (United States)

Ramirez, L. S.; Centres, P. M.; Ramirez-Pastor, A. J.

2018-04-01

Numerical simulations and finite-size scaling analysis have been carried out to study standard and inverse bond percolation of straight rigid rods on square lattices. In the case of standard percolation, the lattice is initially empty. Then, linear bond k -mers (sets of k linear nearest-neighbor bonds) are randomly and sequentially deposited on the lattice. Jamming coverage pj ,k and percolation threshold pc ,k are determined for a wide range of k (1 ≤k ≤120 ). pj ,k and pc ,k exhibit a decreasing behavior with increasing k , pj ,k →∞=0.7476 (1 ) and pc ,k →∞=0.0033 (9 ) being the limit values for large k -mer sizes. pj ,k is always greater than pc ,k, and consequently, the percolation phase transition occurs for all values of k . In the case of inverse percolation, the process starts with an initial configuration where all lattice bonds are occupied and, given that periodic boundary conditions are used, the opposite sides of the lattice are connected by nearest-neighbor occupied bonds. Then, the system is diluted by randomly removing linear bond k -mers from the lattice. The central idea here is based on finding the maximum concentration of occupied bonds (minimum concentration of empty bonds) for which connectivity disappears. This particular value of concentration is called the inverse percolation threshold pc,k i, and determines a geometrical phase transition in the system. On the other hand, the inverse jamming coverage pj,k i is the coverage of the limit state, in which no more objects can be removed from the lattice due to the absence of linear clusters of nearest-neighbor bonds of appropriate size. It is easy to understand that pj,k i=1 -pj ,k . The obtained results for pc,k i show that the inverse percolation threshold is a decreasing function of k in the range 1 ≤k ≤18 . For k >18 , all jammed configurations are percolating states, and consequently, there is no nonpercolating phase. In other words, the lattice remains connected even when

Fractional scaling of quantum walks on percolation lattices

International Nuclear Information System (INIS)

Kendon, Viv; Knott, Paul; Leung, Godfrey; Bailey, Joe

2011-01-01

Quantum walks can be used to model processes such as transport in spin chains and bio-molecules. The enhanced spreading and mixing properties of quantum walks compared with their classical counterparts have been well-studied on regular structures and also shown to be sensitive to defects and imperfections. Using numerical simulation, we study the spreading properties of quantum walks on percolation lattices for both bond and site percolation. The randomly missing edges or sites provide a controlled amount of disorder in the regular Cartesian lattice. In one dimension (the line) we introduce a simple model of quantum tunneling to allow the walk to proceed past the missing edges or sites. This allows the quantum walk to spread faster than a classical random walk for short times, but at longer times the disorder localises the quantum walk. In two dimensions, we observe fractional scaling of the spreading with the number of steps of the walk. For percolation above the 85% level, we obtain faster spreading than classical random walks on the full lattice.

Dichroism in spinach chloroplasts

NARCIS (Netherlands)

Thomas, J.B.; Lierop, J.H. van; Ham, M. ten

1967-01-01

In spinach chloroplasts oriented at steel-water interfaces parallel to the light beam a distinct dichroism is measured at about 680 nm. This dichroism is minimal upon addition of sucrose up to a final concentration of 0.18 M to the medium, the dichroic ratio amounting to 1.02. It is concluded that

The effect of UV-B radiation on chloroplast translation in Pisum sativum

International Nuclear Information System (INIS)

Raab, M.M.; Jagendorf, A.T.

1990-01-01

UV-B radiation has previously been reported to reduce growth, flowering, and net photosynthesis. The present study examines the effect of UV-B radiation on isolated chloroplast of 7-10 day old pea seedlings. Amount of ( 3 H)-Leu incorporated into isolated chloroplasts was measured in the presence or absence of UV-B exposure. Preliminary experiments show a 30% inhibition of protein synthesis in isolated chloroplasts after only 20 mins of UV-B exposure (6.9 J/m 2 /30 min). Percent inhibition of chloroplast translation is directly correlated with UV-B exposure over a 60 min time span. Preliminary studies also show no change in both cold and radiolabeled protein profiles as expressed on 1-D PAGE and autofluorography. Comparative studies on the sensitivity of e - flow vs protein synthesis following UV-B exposure are underway. Further work on the role of oxygen free radicals and the specific site of action of UV-B damage to the translation machinery of chloroplasts will be discussed

Loopless nontrapping invasion-percolation model for fracking.

Science.gov (United States)

Norris, J Quinn; Turcotte, Donald L; Rundle, John B

2014-02-01

Recent developments in hydraulic fracturing (fracking) have enabled the recovery of large quantities of natural gas and oil from old, low-permeability shales. These developments include a change from low-volume, high-viscosity fluid injection to high-volume, low-viscosity injection. The injected fluid introduces distributed damage that provides fracture permeability for the extraction of the gas and oil. In order to model this process, we utilize a loopless nontrapping invasion percolation previously introduced to model optimal polymers in a strongly disordered medium and for determining minimum energy spanning trees on a lattice. We performed numerical simulations on a two-dimensional square lattice and find significant differences from other percolation models. Additionally, we find that the growing fracture network satisfies both Horton-Strahler and Tokunaga network statistics. As with other invasion percolation models, our model displays burst dynamics, in which the cluster extends rapidly into a connected region. We introduce an alternative definition of bursts to be a consecutive series of opened bonds whose strengths are all below a specified value. Using this definition of bursts, we find good agreement with a power-law frequency-area distribution. These results are generally consistent with the observed distribution of microseismicity observed during a high-volume frack.

Regulation of chloroplast number and DNA synthesis in higher plants. Final report

Energy Technology Data Exchange (ETDEWEB)

Mullet, J.E.

1995-11-10

The long term objective of this research is to understand the process of chloroplast development and its coordination with leaf development in higher plants. This is important because the photosynthetic capacity of plants is directly related to leaf and chloroplast development. This research focuses on obtaining a detailed description of leaf development and the early steps in chloroplast development including activation of plastid DNA synthesis, changes in plastid DNA copy number, activation of chloroplast transcription and increases in plastid number per cell. The grant will also begin analysis of specific biochemical mechanisms by isolation of the plastid DNA polymerase, and identification of genetic mutants which are altered in their accumulation of plastid DNA and plastid number per cell.

Percolation and lasing in real 3D crystals with inhomogeneous distributed random pores

Energy Technology Data Exchange (ETDEWEB)

Burlak, Gennadiy, E-mail: gburlak@uaem.mx; Calderón-Segura, Yessica

2014-11-15

We systematically study the percolation phase transition in real 3D crystals where not only the state of pores but also their radius r and displacement s are random valued numbers. The mean values R=〈r〉 and S=〈s〉 emerge as additional spatial scales in such an extended network. This leads to variations of the threshold (critical) percolation probability p{sub C} and the percolation order parameter P that become to be the intricate functions of R and S. Our numerical simulations have shown that in such extended system the incipient spanning cluster can arise even for situations where for simple periodical system the percolation does not exist. We analyzed the validity of the nearest neighbor's approximation and found that such approximation is not valid for materials with large dispersivity of pores. The lasing of nanoemitters incorporated in such percolating spanning cluster is studied too. This effect can open interesting perspectives in modern nano- and micro-information technologies.

The Beasts' model of percolative transport

International Nuclear Information System (INIS)

Dubois, M.A.; Beaufume, P.; Fromont, B.

1991-12-01

A class of nonlinear dynamical systems is introduced: it is aimed to be a tool in order to study anomalous transport and percolation phenomena. We study a simple example of this system, and explore different regimes of transport exhibited

The complete chloroplast genome of banana (Musa acuminata, Zingiberales): insight into plastid monocotyledon evolution.

Science.gov (United States)

Martin, Guillaume; Baurens, Franc-Christophe; Cardi, Céline; Aury, Jean-Marc; D'Hont, Angélique

2013-01-01

Banana (genus Musa) is a crop of major economic importance worldwide. It is a monocotyledonous member of the Zingiberales, a sister group of the widely studied Poales. Most cultivated bananas are natural Musa inter-(sub-)specific triploid hybrids. A Musa acuminata reference nuclear genome sequence was recently produced based on sequencing of genomic DNA enriched in nucleus. The Musa acuminata chloroplast genome was assembled with chloroplast reads extracted from whole-genome-shotgun sequence data. The Musa chloroplast genome is a circular molecule of 169,972 bp with a quadripartite structure containing two single copy regions, a Large Single Copy region (LSC, 88,338 bp) and a Small Single Copy region (SSC, 10,768 bp) separated by Inverted Repeat regions (IRs, 35,433 bp). Two forms of the chloroplast genome relative to the orientation of SSC versus LSC were found. The Musa chloroplast genome shows an extreme IR expansion at the IR/SSC boundary relative to the most common structures found in angiosperms. This expansion consists of the integration of three additional complete genes (rps15, ndhH and ycf1) and part of the ndhA gene. No such expansion has been observed in monocots so far. Simple Sequence Repeats were identified in the Musa chloroplast genome and a new set of Musa chloroplastic markers was designed. The complete sequence of M. acuminata ssp malaccensis chloroplast we reported here is the first one for the Zingiberales order. As such it provides new insight in the evolution of the chloroplast of monocotyledons. In particular, it reinforces that IR/SSC expansion has occurred independently several times within monocotyledons. The discovery of new polymorphic markers within Musa chloroplast opens new perspectives to better understand the origin of cultivated triploid bananas.

The complete chloroplast genome of banana (Musa acuminata, Zingiberales: insight into plastid monocotyledon evolution.

Directory of Open Access Journals (Sweden)

Guillaume Martin

Full Text Available Banana (genus Musa is a crop of major economic importance worldwide. It is a monocotyledonous member of the Zingiberales, a sister group of the widely studied Poales. Most cultivated bananas are natural Musa inter-(sub-specific triploid hybrids. A Musa acuminata reference nuclear genome sequence was recently produced based on sequencing of genomic DNA enriched in nucleus.The Musa acuminata chloroplast genome was assembled with chloroplast reads extracted from whole-genome-shotgun sequence data. The Musa chloroplast genome is a circular molecule of 169,972 bp with a quadripartite structure containing two single copy regions, a Large Single Copy region (LSC, 88,338 bp and a Small Single Copy region (SSC, 10,768 bp separated by Inverted Repeat regions (IRs, 35,433 bp. Two forms of the chloroplast genome relative to the orientation of SSC versus LSC were found. The Musa chloroplast genome shows an extreme IR expansion at the IR/SSC boundary relative to the most common structures found in angiosperms. This expansion consists of the integration of three additional complete genes (rps15, ndhH and ycf1 and part of the ndhA gene. No such expansion has been observed in monocots so far. Simple Sequence Repeats were identified in the Musa chloroplast genome and a new set of Musa chloroplastic markers was designed.The complete sequence of M. acuminata ssp malaccensis chloroplast we reported here is the first one for the Zingiberales order. As such it provides new insight in the evolution of the chloroplast of monocotyledons. In particular, it reinforces that IR/SSC expansion has occurred independently several times within monocotyledons. The discovery of new polymorphic markers within Musa chloroplast opens new perspectives to better understand the origin of cultivated triploid bananas.

Influence of polyethylene glycol on percolation dynamics of reverse microemulsions

Science.gov (United States)

Geethu, P. M.; Yadav, Indresh; Aswal, V. K.; Satapathy, D. K.

2018-04-01

We explore the influence of a hydrophilic polymer, polyethylene glycol (PEG), on the structure and the percolation dynamics of reverse microemulsions (ME) stabilized by an anionic surfactant AOT (sodium bis(2-ethylhexyl) sulfosuccinate). The percolation transition of MEs is probed using dielectric relaxation spectroscopy (DRS). Notably, an increase in percolation temperature is observed by the incorporation of PEG-polymer into larger ME droplets which is explained by considering the model of polymer adsorption at surfactant-water interface. The stability of the droplet phase of microemulsion after the incorporation of PEG is confirmed by small-angle neutron scattering (SANS) experiment. Further, a net decrease in percolation transition temperature is observed with the addition of PEG polymer for smaller ME droplets and is discussed in relation with the destabilization of droplets owing to the polymer induced bridging and the associated clustering of droplets. We conjecture that the adsorption of PEG polymer chains at the surfactant-water interface as well as the PEG-induced bridging of droplets are due to the strong ion-dipole interaction between anionic head group of AOT surfactant and dipoles present in PEG polymer chains.

Invasion percolation of single component, multiphase fluids with lattice Boltzmann models

International Nuclear Information System (INIS)

Sukop, M.C.; Or, Dani

2003-01-01

Application of the lattice Boltzmann method (LBM) to invasion percolation of single component multiphase fluids in porous media offers an opportunity for more realistic modeling of the configurations and dynamics of liquid/vapor and liquid/solid interfaces. The complex geometry of connected paths in standard invasion percolation models arises solely from the spatial arrangement of simple elements on a lattice. In reality, fluid interfaces and connectivity in porous media are naturally controlled by the details of the pore geometry, its dynamic interaction with the fluid, and the ambient fluid potential. The multiphase LBM approach admits realistic pore geometry derived from imaging techniques and incorporation of realistic hydrodynamics into invasion percolation models

Percolation approach for atomic and molecular cluster formation

International Nuclear Information System (INIS)

Knospe, O.; Seifert, G.

1987-12-01

We apply a percolation approach for the theoretical analysis of mass spectra of molecular microclusters obtained by adiabatic expansion technique. The evolution of the shape of the experimental size distributions as function of stagnation pressure and stagnation temperature are theoretically reproduced by varying the percolation parameter. Remaining discrepancies between theory and experiment are discussed. In addition, the even-odd alternation as well as the 'magic' shell structure within metallic, secondary ion mass spectra are investigated by introducing statistical weights for the cluster formation probabilities. Shell correction energies of atomic clusters as function of cluster-size are deduced from the experimental data. (orig.)

Percolation and multifragmentation of nuclei

International Nuclear Information System (INIS)

Shmakov, S.Yu.; Uzhinskij, V.V.

1989-01-01

A method to build the 'cold' nuclei as percolation clusters is suggested. Within the framework of definite assumptions of the character of nucleon-nucleon couplings breaking resulting from the nuclear reactions as description of the multifragmentation process in the hadron-nucleus and nucleus-nucleus reactions at high energies is obtained. 19 refs.; 6 figs

A simple low-cost microcontroller-based photometric instrument for monitoring chloroplast movement.

Science.gov (United States)

Berg, Robert; Königer, Martina; Schjeide, Brit-Maren; Dikmak, George; Kohler, Susan; Harris, Gary C

2006-03-01

A new microcontroller-based photometric instrument for monitoring blue light dependent changes in leaf transmission (chloroplast movement) was developed based on a modification of the double-beam technique developed by Walzcak and Gabrys [(1980) Photosynthetica 14: 65-72]. A blue and red bicolor light emitting diode (LED) provided both a variable intensity blue actinic light and a low intensity red measuring beam. A phototransistor detected the intensity of the transmitted measuring light. An inexpensive microcontroller independently and precisely controlled the light emission of the bicolor LED. A typical measurement event involved turning off the blue actinic light for 100 mus to create a narrow temporal window for turning on and measuring the transmittance of the red light. The microcontroller was programmed using LogoChip Logo (http://www.wellesley.edu/Physics/Rberg/logochip/) to record fluence rate response curves. Laser scanning confocal microscopy was utilized to correlate the changes in leaf transmission with intercellular chloroplast position. In the dark, the chloroplasts in the spongy mesophyll exhibited no evident asymmetries in their distribution, however, in the palisade layer the cell surface in contact with the overlying epidermis was devoid of chloroplasts. The low light dependent decrease in leaf transmittance in dark acclimated leaves was correlated with the movement of chloroplasts within the palisade layer into the regions previously devoid of chloroplasts. Changes in leaf transmittance were evident within one minute following the onset of illumination. Minimal leaf transmittance was correlated with chloroplasts having retreated from cell surfaces perpendicular to the incident light (avoidance reaction) in both spongy and palisade layers.

Diffusion of test particles in stochastic magnetic fields in the percolative regime

International Nuclear Information System (INIS)

Neuer, Marcus; Spatschek, Karl H.

2006-01-01

For stochastic magnetic flux functions with percolative contours the test particle transport is investigated. The calculations make use of the stochastic Liouville approach. They start from the so-called A-Langevin equations, including stochastic magnetic field components and binary collisions. Using the decorrelation trajectory method, a relation between the Lagrangian velocity correlation function and the Eulerian magnetic field correlation is derived and introduced into the Green-Kubo formalism. Finite Larmor radius effects are included. Interesting results are presented in the percolation regime corresponding to high Kubo numbers. Previous results are found to be limiting cases for small Kubo numbers. For different percolative scenarios the diffusion is analyzed and strong influences of the percolative structures on the transport scaling are found. The finite Larmor radius effects are discussed in detail. Numerical simulations of the A-Langevin equation confirm the semianalytical predictions

Functional Disruption of a Chloroplast Pseudouridine Synthase Desensitizes Arabidopsis Plants to Phosphate Starvation

Directory of Open Access Journals (Sweden)

Shan Lu

2017-08-01

Full Text Available Phosphate (Pi deficiency is a common nutritional stress of plants in both agricultural and natural ecosystems. Plants respond to Pi starvation in the environment by triggering a suite of biochemical, physiological, and developmental changes that increase survival and growth. The key factors that determine plant sensitivity to Pi starvation, however, are unclear. In this research, we identified an Arabidopsis mutant, dps1, with greatly reduced sensitivity to Pi starvation. The dps1 phenotypes are caused by a mutation in the previously characterized SVR1 (SUPPRESSION OF VARIAGATION 1 gene, which encodes a chloroplast-localized pseudouridine synthase. The mutation of SVR1 results in defects in chloroplast rRNA biogenesis, which subsequently reduces chloroplast translation. Another mutant, rps5, which contains a mutation in the chloroplast ribosomal protein RPS5 and has reduced chloroplast translation, also displayed decreased sensitivity to Pi starvation. Furthermore, wild type plants treated with lincomycin, a chemical inhibitor of chloroplast translation, showed similar growth phenotypes and Pi starvation responses as dps1 and rps5. These results suggest that impaired chloroplast translation desensitizes plants to Pi starvation. Combined with previously published results showing that enhanced leaf photosynthesis augments plant responses to Pi starvation, we propose that the decrease in responses to Pi starvation in dps1, rps5, and lincomycin-treated plants is due to their reduced demand for Pi input from the environment.

Renormalization group theory for percolation in time-varying networks.

Science.gov (United States)

Karschau, Jens; Zimmerling, Marco; Friedrich, Benjamin M

2018-05-22

Motivated by multi-hop communication in unreliable wireless networks, we present a percolation theory for time-varying networks. We develop a renormalization group theory for a prototypical network on a regular grid, where individual links switch stochastically between active and inactive states. The question whether a given source node can communicate with a destination node along paths of active links is equivalent to a percolation problem. Our theory maps the temporal existence of multi-hop paths on an effective two-state Markov process. We show analytically how this Markov process converges towards a memoryless Bernoulli process as the hop distance between source and destination node increases. Our work extends classical percolation theory to the dynamic case and elucidates temporal correlations of message losses. Quantification of temporal correlations has implications for the design of wireless communication and control protocols, e.g. in cyber-physical systems such as self-organized swarms of drones or smart traffic networks.

Percolation and spin glass transition

International Nuclear Information System (INIS)

Sadiq, A.; Tahir-Kheli, R.A.; Wortis, M.; Bhatti, N.A.

1980-10-01

The behaviour of clusters of curved and normal plaquette particles in a bond random, +-J, Ising model is studied in finite square and triangular lattices. Computer results for the concentration of antiferromagnetic bonds when percolating clusters first appears are found to be close to those reported for the occurrence and disappearance of spin glass phases in these systems. (author)

Percolation on the institute-enterprise R

Directory of Open Access Journals (Sweden)

Li Chenguang

2015-01-01

Full Text Available Realistic network-like systems are usually composed of multiple networks with interacting relations such as school-enterprise research and development (R&D collaboration networks. Here, we study the percolation properties of a special class of R&D collaboration network, namely institute-enterprise R&D collaboration networks (IERDCNs. We introduce two actual IERDCNs to show their structural properties, and we present a mathematical framework based on generating functions for analyzing an interacting network with any connection probability. Then,we illustrate the percolation threshold and structural parameter arithmetic in the sub-critical and supercritical regimes.We compare the predictions of our mathematical framework and arithmetic to data for two real R&D collaboration networks and a number of simulations. We find that our predictions are in remarkable agreement with the data. We show applications of the framework to electronics R&D collaboration networks

Effect of alkyl-N-phenylcarbamates on photochemical activity of spinach chloroplasts

International Nuclear Information System (INIS)

Sersen, F.; Kralova, K.; Macho, V.

1999-01-01

This study is aimed to investigate the effect of alkyl-N-phenylcarbamates on photosynthetic electron transport in spinach chloroplasts, to determine site of action in the photosynthetic apparatus of spinach chloroplasts and to find correlations between their structure and biological activity. (authors)

Engineering the Chloroplast Genome of Oleaginous Marine Microalga Nannochloropsis oceanica

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Qinhua Gan

2018-04-01

Full Text Available Plastid engineering offers an important tool to fill the gap between the technical and the enormous potential of microalgal photosynthetic cell factory. However, to date, few reports on plastid engineering in industrial microalgae have been documented. This is largely due to the small cell sizes and complex cell-wall structures which make these species intractable to current plastid transformation methods (i.e., biolistic transformation and polyethylene glycol-mediated transformation. Here, employing the industrial oleaginous microalga Nannochloropsis oceanica as a model, an electroporation-mediated chloroplast transformation approach was established. Fluorescent microscopy and laser confocal scanning microscopy confirmed the expression of the green fluorescence protein, driven by the endogenous plastid promoter and terminator. Zeocin-resistance selection led to an acquisition of homoplasmic strains of which a stable and site-specific recombination within the chloroplast genome was revealed by sequencing and DNA gel blotting. This demonstration of electroporation-mediated chloroplast transformation opens many doors for plastid genome editing in industrial microalgae, particularly species of which the chloroplasts are recalcitrant to chemical and microparticle bombardment transformation.

Effects of lead on enzymes of porphyrine biosynthesis in chloroplasts and erythrocytes

Energy Technology Data Exchange (ETDEWEB)

Hampp, R.; Kriebitzsch, C.; Ziegler, H.

1974-01-01

Two enzymes of the chlorophyll biosynthesis pathway, delta-aminolevulinic acid dehydratase (ALAD) and prophobilinogenase (PBGA), show a pronounced sensitivity to lead ion, as was shown in isolated chloroplasts of spinach. It has been reported by several authors that the activity of ALAD involved in the hemoglobine-biosynthesis in erythrocytes is also very sensitive to lead ions. Spinach chloroplasts were isolated and sonicated and the enzyme activity tested. Calf blood was collected with heparin and kept at 0/sup 0/C until enzyme determination. Hemolyzed erythrocytes (rapid freezing and thawing twice) were used as the source of enzymes. The incubation mixture was the same as for chloroplasts; the hemoglobin content per test was about 44 mg (ALAD) and 91 mg (PBGA). ALAD in erythrocytes is somewhat more sensitive to lead ions than ALAD in chloroplasts. PBGA in erythrocytes is also inhibited by Pb/sup 2 +/ ions, again more than the chloroplast enzyme. At all concentrations of Pb/sup 2 +/ checked in our experiments the percentage of inhibition was higher with PBGA. 3 references, 1 figure.

Conformational changes in spinach (Spinacia oleracea leaves chloroplasts in vivo

Directory of Open Access Journals (Sweden)

Janina Godziemba-Czyż

2015-01-01

Full Text Available Changes in the surface area of chloroplasts from intact cells of spinach leaves (\tSpinacia oleracea induced by blue (370—500 nm and red (600- 850 nm light of various intensity (102 - 5x105 erg cm-1s-1 were investigated. The changes are deseribed in terms of mean surface area in , μm2 and frequency of oocurrence of surface size classes. Low intensity blue light caused enlargement of the chloroplast surface (as compared with that in darkness, whereas high intensity light markedly reduced it. Exposure of chloroplasts to red light produces an increase of the surface in proportion to the intensity of the light and irradiation time.

Short-term effects of salt exposure on the maize chloroplast protein pattern.

Science.gov (United States)

Zörb, Christian; Herbst, Ramona; Forreiter, Christoph; Schubert, Sven

2009-09-01

It is of fundamental importance to understand the physiological differences leading to salt resistance and to get access to the molecular mechanisms underlying this physiological response. The aim of this work was to investigate the effects of short-term salt exposure on the proteome of maize chloroplasts in the initial phase of salt stress (up to 4 h). It could be shown that sodium ions accumulate quickly and excessively in chloroplasts in the initial phase of moderate salt stress. A change in the chloroplast protein pattern was observed without a change in water potential of the leaves. 2-DE revealed that 12 salt-responsive chloroplast proteins increased while eight chloroplast proteins decreased. Some of the maize chloroplast proteins such as CF1e and a Ca(2+)-sensing receptor show a rather transient response for the first 4 h of salt exposure. The enhanced abundance of the ferredoxin NADPH reductase, the 23 kDa polypeptide of the photosystem II, and the FtsH-like protein might reflect mechanism to attenuate the detrimental effects of Na(+) on the photosynthetic machinery. The observed transient increase and subsequent decrease of selected proteins may exhibit a counterbalancing effect of target proteins in this context. Intriguingly, several subunits of the CF1-CF0 complex are unequally affected, whereas others do not respond at all.

A database of PCR primers for the chloroplast genomes of higher plants

Science.gov (United States)

Heinze, Berthold

2007-01-01

Background Chloroplast genomes evolve slowly and many primers for PCR amplification and analysis of chloroplast sequences can be used across a wide array of genera. In some cases 'universal' primers have been designed for the purpose of working across species boundaries. However, the essential information on these primer sequences is scattered throughout the literature. Results A database is presented here which assembles published primer information for chloroplast DNA. Additional primers were designed to fill gaps where little or no primer information could be found. Amplicons are either the genes themselves (typically useful in studies of sequence variation in higher-order phylogeny) or they are spacers, introns, and intergenic regions (for studies of phylogeographic patterns within and among species). The current list of 'generic' primers consists of more than 700 sequences. Wherever possible, we give the locations of the primers in the thirteen fully sequenced chloroplast genomes (Nicotiana tabacum, Atropa belladonna, Spinacia oleracea, Arabidopsis thaliana, Populus trichocarpa, Oryza sativa, Pinus thunbergii, Marchantia polymorpha, Zea mays, Oenothera elata, Acorus calamus, Eucalyptus globulus, Medicago trunculata). Conclusion The database described here is designed to serve as a resource for researchers who are venturing into the study of poorly described chloroplast genomes, whether for large- or small-scale DNA sequencing projects, to study molecular variation or to investigate chloroplast evolution. PMID:17326828

A database of PCR primers for the chloroplast genomes of higher plants

Directory of Open Access Journals (Sweden)

Heinze Berthold

2007-02-01

Full Text Available Abstract Background Chloroplast genomes evolve slowly and many primers for PCR amplification and analysis of chloroplast sequences can be used across a wide array of genera. In some cases 'universal' primers have been designed for the purpose of working across species boundaries. However, the essential information on these primer sequences is scattered throughout the literature. Results A database is presented here which assembles published primer information for chloroplast DNA. Additional primers were designed to fill gaps where little or no primer information could be found. Amplicons are either the genes themselves (typically useful in studies of sequence variation in higher-order phylogeny or they are spacers, introns, and intergenic regions (for studies of phylogeographic patterns within and among species. The current list of 'generic' primers consists of more than 700 sequences. Wherever possible, we give the locations of the primers in the thirteen fully sequenced chloroplast genomes (Nicotiana tabacum, Atropa belladonna, Spinacia oleracea, Arabidopsis thaliana, Populus trichocarpa, Oryza sativa, Pinus thunbergii, Marchantia polymorpha, Zea mays, Oenothera elata, Acorus calamus, Eucalyptus globulus, Medicago trunculata. Conclusion The database described here is designed to serve as a resource for researchers who are venturing into the study of poorly described chloroplast genomes, whether for large- or small-scale DNA sequencing projects, to study molecular variation or to investigate chloroplast evolution.

Chloroplast Dynamics and Photosynthetic Efficiency: Final Technical Report

Energy Technology Data Exchange (ETDEWEB)

Hanson, Maureen [Cornell Univ., Ithaca, NY (United States)

2016-11-03

This project investigated the mechanism by which chloroplasts position themselves to maximize solar energy utilization, to enhance gas exchange, to minimize environmental stress, and to promote efficient exchange of metabolites with other compartments within the plant cell. Chloroplasts move within leaf cells to optimize light levels, moving toward levels of light useful for photosynthesis while moving away from excess light. Plastids sometimes extend their reach by sending out projections (stromules) that can connect anchor chloroplasts in position within the cell or provide close contacts with plasma membrane, mitochondria, peroxisomes, endoplasmic reticulum, and the nucleus. The intracellular location of chloroplasts in relation to other organelles with which they share biosynthetic pathways, such as peroxisomes and mitochondria in photorespiration, affects metabolite flow. This work contributed to the knowledge of the mechanisms of organelle movement and anchoring in specific locations in plant cells and how proteins traffic within the cell. We identified two domains on 12 of the 13 Arabidopsis myosins that were similar to the vacuole-binding (V) domain characterized in yeast and to the DIL domain characterized in yeast and mouse as required for secretory vesicle or melanosome movement, respectively. Because all of the Arabidopsis regions with homology to the V domain contain the amino acid sequence PAL, we refer to this region as the Arabidopsis PAL domain. We have used the yeast Myo2p tail structural information to model the 12 myosin XI tail domains containing the homologous PAL and DIL domains. Eight YFP::DIL domain fusions labeled peroxisomes; none labeled mitochondria or chloroplasts. Six myosin XI Vacuole domains labeled mitochondria and seven labeled Golgi bodies. The Arabidopsis myosin XI-F PAL domain and the homologous myosin XI-F PAL domain from N. benthamiana labels chloroplasts and stromules in N. benthamiana leaves. Using an Arabidopsis line

On the upper critical dimension of Bernoulli percolation

International Nuclear Information System (INIS)

Chayes, J.T.; Chayes, L.

1987-01-01

Derived is a set of inequalities for the d-dimensional independent percolation problem. Assuming the existence of critical exponents, these inequalities imply: f + nu ≥ 1 + β/sub Q/, μ + nu ≥ 1 + β/sub Q/, zeta ≥ min (1, nu'/nu), where the above exponents are f: the flow constant exponent, nu (nu'): the correlation length exponent below (above) threshold, μ: the surface tension exponent, β/sub Q/: the backbone density exponent and zeta: the chemical distance exponent. Note that all of these inequalities are mean-field bounds, and that they relate the exponent nu defined from below the percolation threshold to exponents defined from above threshold. Furthermore, we combine the strategy of the proofs these inequalities with notions of finite-size scaling to derive: max (d nu, d nu') ≥ 1 + β/sub Q/, where d is the lattice dimension. Since β/sub Q/ ≥ 2β, where β is the percolation density exponent, the final bound implies that, below six dimensions, the standard order parameter and correlation length exponents cannot simultaneously assume their mean-field values; hence an implicit bound on the upper critical dimension: d/sub c/ ≥ 6

Extending the biosynthetic repertoires of cyanobacteria and chloroplasts.

Science.gov (United States)

Nielsen, Agnieszka Zygadlo; Mellor, Silas Busck; Vavitsas, Konstantinos; Wlodarczyk, Artur Jacek; Gnanasekaran, Thiyagarajan; Perestrello Ramos H de Jesus, Maria; King, Brian Christopher; Bakowski, Kamil; Jensen, Poul Erik

2016-07-01

Chloroplasts in plants and algae and photosynthetic microorganisms such as cyanobacteria are emerging hosts for sustainable production of valuable biochemicals, using only inorganic nutrients, water, CO2 and light as inputs. In the past decade, many bioengineering efforts have focused on metabolic engineering and synthetic biology in the chloroplast or in cyanobacteria for the production of fuels, chemicals and complex, high-value bioactive molecules. Biosynthesis of all these compounds can be performed in photosynthetic organelles/organisms by heterologous expression of the appropriate pathways, but this requires optimization of carbon flux and reducing power, and a thorough understanding of regulatory pathways. Secretion or storage of the compounds produced can be exploited for the isolation or confinement of the desired compounds. In this review, we explore the use of chloroplasts and cyanobacteria as biosynthetic compartments and hosts, and we estimate the levels of production to be expected from photosynthetic hosts in light of the fraction of electrons and carbon that can potentially be diverted from photosynthesis. The supply of reducing power, in the form of electrons derived from the photosynthetic light reactions, appears to be non-limiting, but redirection of the fixed carbon via precursor molecules presents a challenge. We also discuss the available synthetic biology tools and the need to expand the molecular toolbox to facilitate cellular reprogramming for increased production yields in both cyanobacteria and chloroplasts. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

Current Percolation in Medium with Boundaries under Quantum Hall Effect Conditions

Directory of Open Access Journals (Sweden)

M. U. Malakeeva

2012-01-01

Full Text Available The current percolation has been considered in the medium with boundaries under quantum Hall effect conditions. It has been shown that in that case the effective Hall conductivity has a nonzero value due to percolation of the Hall current through the finite number of singular points (in our model these are corners at the phase joints.

Walking on fractals: diffusion and self-avoiding walks on percolation clusters

International Nuclear Information System (INIS)

Blavatska, V; Janke, W

2009-01-01

We consider random walks (RWs) and self-avoiding walks (SAWs) on disordered lattices directly at the percolation threshold. Applying numerical simulations, we study the scaling behavior of the models on the incipient percolation cluster in space dimensions d = 2, 3, 4. Our analysis yields estimates of universal exponents, governing the scaling laws for configurational properties of RWs and SAWs

Mirrorless lasing from light emitters in percolating clusters

Science.gov (United States)

Burlak, Gennadiy; Rubo, Y. G.

2015-07-01

We describe the lasing effect in the three-dimensional percolation system, where the percolating cluster is filled by active media composed by light emitters excited noncoherently. We show that, due to the presence of a topologically nontrivial photonic structure, the stimulated emission is modified with respect to both conventional and random lasers. The time dynamics and spectra of the lasing output are studied numerically with finite-difference time-domain approach. The Fermat principle and Monte Carlo approach are applied to characterize the optimal optical path and interconnection between the radiating emitters. The spatial structure of the laser mode is found by a long-time FDTD simulation.

Ising percolation in a three-state majority vote model

Energy Technology Data Exchange (ETDEWEB)

Balankin, Alexander S., E-mail: abalankin@ipn.mx [Grupo Mecánica Fractal, ESIME, Instituto Politécnico Nacional, México D.F., 07738 (Mexico); Martínez-Cruz, M.A.; Gayosso Martínez, Felipe [Grupo Mecánica Fractal, ESIME, Instituto Politécnico Nacional, México D.F., 07738 (Mexico); Mena, Baltasar [Laboratorio de Ingeniería y Procesos Costeros, Instituto de Ingeniería, Universidad Nacional Autónoma de México, Sisal, Yucatán, 97355 (Mexico); Tobon, Atalo; Patiño-Ortiz, Julián; Patiño-Ortiz, Miguel; Samayoa, Didier [Grupo Mecánica Fractal, ESIME, Instituto Politécnico Nacional, México D.F., 07738 (Mexico)

2017-02-05

Highlights: • Three-state non-consensus majority voter model is introduced. • Phase transition in the absorbing state non-consensus is revealed. • The percolation transition belongs to the universality class of Ising percolation. • The effect of an updating rule for a tie between voter neighbors is highlighted. - Abstract: In this Letter, we introduce a three-state majority vote model in which each voter adopts a state of a majority of its active neighbors, if exist, but the voter becomes uncommitted if its active neighbors are in a tie, or all neighbors are the uncommitted. Numerical simulations were performed on square lattices of different linear size with periodic boundary conditions. Starting from a random distribution of active voters, the model leads to a stable non-consensus state in which three opinions coexist. We found that the “magnetization” of the non-consensus state and the concentration of uncommitted voters in it are governed by an initial composition of system and are independent of the lattice size. Furthermore, we found that a configuration of the stable non-consensus state undergoes a second order percolation transition at a critical concentration of voters holding the same opinion. Numerical simulations suggest that this transition belongs to the same universality class as the Ising percolation. These findings highlight the effect of an updating rule for a tie between voter neighbors on the critical behavior of models obeying the majority vote rule whenever a strict majority exists.

Ising percolation in a three-state majority vote model

International Nuclear Information System (INIS)

Balankin, Alexander S.; Martínez-Cruz, M.A.; Gayosso Martínez, Felipe; Mena, Baltasar; Tobon, Atalo; Patiño-Ortiz, Julián; Patiño-Ortiz, Miguel; Samayoa, Didier

2017-01-01

Highlights: • Three-state non-consensus majority voter model is introduced. • Phase transition in the absorbing state non-consensus is revealed. • The percolation transition belongs to the universality class of Ising percolation. • The effect of an updating rule for a tie between voter neighbors is highlighted. - Abstract: In this Letter, we introduce a three-state majority vote model in which each voter adopts a state of a majority of its active neighbors, if exist, but the voter becomes uncommitted if its active neighbors are in a tie, or all neighbors are the uncommitted. Numerical simulations were performed on square lattices of different linear size with periodic boundary conditions. Starting from a random distribution of active voters, the model leads to a stable non-consensus state in which three opinions coexist. We found that the “magnetization” of the non-consensus state and the concentration of uncommitted voters in it are governed by an initial composition of system and are independent of the lattice size. Furthermore, we found that a configuration of the stable non-consensus state undergoes a second order percolation transition at a critical concentration of voters holding the same opinion. Numerical simulations suggest that this transition belongs to the same universality class as the Ising percolation. These findings highlight the effect of an updating rule for a tie between voter neighbors on the critical behavior of models obeying the majority vote rule whenever a strict majority exists.

Interlocking-induced stiffness in stochastically microcracked materials beyond the transport percolation threshold

Science.gov (United States)

Picu, R. C.; Pal, A.; Lupulescu, M. V.

2016-04-01

We study the mechanical behavior of two-dimensional, stochastically microcracked continua in the range of crack densities close to, and above, the transport percolation threshold. We show that these materials retain stiffness up to crack densities much larger than the transport percolation threshold due to topological interlocking of sample subdomains. Even with a linear constitutive law for the continuum, the mechanical behavior becomes nonlinear in the range of crack densities bounded by the transport and stiffness percolation thresholds. The effect is due to the fractal nature of the fragmentation process and is not linked to the roughness of individual cracks.

A new approach for multicriticality in directed and diode percolation

International Nuclear Information System (INIS)

Tsallis, C.; Boston Univ., MA; Redner, S.

1983-01-01

A new and very simple model for treating directed and more general diode percolation problems is presented, by allowing neighboring sites to be joined by up to two independent bonds of opposite orientations. A generalized 'break-collapse' method is developed to calculate renormalization group recursion relations. On the square lattice, a very symmetric phase diagram is obtained which displays multicritical percolation phenomena, and a variety of interesting conductivity transitions are predicted. (Author) [pt

Percolation temperature and the 'instability' of the effective potential

International Nuclear Information System (INIS)

Carvalho, C.A. de; Bazeia Filho, D.; Eboli, O.J.P.; Marques, G.C.; Silva, A.J. da; Ventura, I.

1984-01-01

It is shown that in spontaneously broken lambda phi 4 theory the percolation temperature coincides with the temperature at which the semiclassical (loop) expansion of the effective potential (free energy) of the system around a uniform field configuration fails. This allows us to extract the percolation temperature directly from the effective potential. The addition of fermions or gauge fields does not alter the result as long as they are weakly coupled to the scalars. The coincidence holds in the high temperature limit at every order in the loop expansion. (Author) [pt

Generalized bond percolation and statistical mechanics

International Nuclear Information System (INIS)

Tsallis, C.

1978-05-01

A generalization of traditional bond percolation is performed, in the sens that bonds have now the possibility of partially transmitting the information (a fact which leads to the concept of 'fidelity' of the bond), and also in the sens that, besides the normal tendency to equiprobability, the bonds are allowed to substantially change the information. Furthermore the fidelity is allowed, to become an aleatory variable, and the operational rules concerning the associated distribution laws are determined. Thermally quenched random bonds and the whole body of Statistical Mechanics become particular cases of this formalism, which is in general adapted to the treatment of all problems whose main characteristic is to preserve a part of the information through a long path or array (critical phenomena, regime changements, thermal random models, etc). Operationally it provides a quick method for the calculation of the equivalent probability of complex clusters within the traditional bond percolation problem [pt

Percolation systems away from the critical point

Indian Academy of Sciences (India)

DEEPAK DHAR. Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India ... There is more to percolation theory than the critical exponents. Of course, an experi- .... simple qualitative arguments. In the summation ...

Endurance Pump Test with MIL-PRF-83282 Hydraulic Fluid, Purified with Malabar Purifier

National Research Council Canada - National Science Library

Sharma, Shashi

2004-01-01

.... Endurance aircraft hydraulic pump tests under carefully controlled conditions were previously conducted using hydraulic fluid purified with a rotating-disk and vacuum type purifier, the portable...

Deep percolation in greenhouse-cultivated celery using the technique of subsurface film strips placement

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Zhida Du

2014-05-01

Full Text Available To reduce the deep percolation during greenhouse vegetable cultivation, the technique of subsurface film strips placement was tested. Four treatments with two kinds of cross-sections (flat and U-shaped and two different spacings (10 cm and 40 cm of subsurface film strips were arranged in a greenhouse before planting celery. At the same time, a non-film treatment was arranged for comparison. Soil water content was measured and irrigation time was adjusted according to the soil water content. Evapotranspiration of celery during growth was calculated by the method of energy balance and the deep percolation was calculated by the equation of water balance. Deep percolation was reduced in all experimental treatments. Greater reduction in deep percolation was observed when using U-shaped cross-section strips compared with that using the flat cross-section strips. In addition, greater reduction in deep percolation was observed when the spacing between the film strips was smaller. The results of this test showed that the technique of subsurface film strips placement can reduce deep percolation and conserve irrigation water for greenhouse vegetables cultivation. However, the optimal layout variables for the use of the technique of subsurface film strips placement need further experimental and numerical analysis.

Percolation for a model of statistically inhomogeneous random media

International Nuclear Information System (INIS)

Quintanilla, J.; Torquato, S.

1999-01-01

We study clustering and percolation phenomena for a model of statistically inhomogeneous two-phase random media, including functionally graded materials. This model consists of inhomogeneous fully penetrable (Poisson distributed) disks and can be constructed for any specified variation of volume fraction. We quantify the transition zone in the model, defined by the frontier of the cluster of disks which are connected to the disk-covered portion of the model, by defining the coastline function and correlation functions for the coastline. We find that the behavior of these functions becomes largely independent of the specific choice of grade in volume fraction as the separation of length scales becomes large. We also show that the correlation function behaves in a manner similar to that of fractal Brownian motion. Finally, we study fractal characteristics of the frontier itself and compare to similar properties for two-dimensional percolation on a lattice. In particular, we show that the average location of the frontier appears to be related to the percolation threshold for homogeneous fully penetrable disks. copyright 1999 American Institute of Physics

Multiscale volatility duration characteristics on financial multi-continuum percolation dynamics

Science.gov (United States)

Wang, Min; Wang, Jun

A random stock price model based on the multi-continuum percolation system is developed to investigate the nonlinear dynamics of stock price volatility duration, in an attempt to explain various statistical facts found in financial data, and have a deeper understanding of mechanisms in the financial market. The continuum percolation system is usually referred to be a random coverage process or a Boolean model, it is a member of a class of statistical physics systems. In this paper, the multi-continuum percolation (with different values of radius) is employed to model and reproduce the dispersal of information among the investors. To testify the rationality of the proposed model, the nonlinear analyses of return volatility duration series are preformed by multifractal detrending moving average analysis and Zipf analysis. The comparison empirical results indicate the similar nonlinear behaviors for the proposed model and the actual Chinese stock market.

The selected models of the mesostructure of composites percolation, clusters, and force fields

CERN Document Server

Herega, Alexander

2018-01-01

This book presents the role of mesostructure on the properties of composite materials. A complex percolation model is developed for the material structure containing percolation clusters of phases and interior boundaries. Modeling of technological cracks and the percolation in the Sierpinski carpet are described. The interaction of mesoscopic interior boundaries of the material, including the fractal nature of interior boundaries, the oscillatory nature of it interaction and also the stochastic model of the interior boundaries’ interaction, the genesis, structure, and properties are discussed. One of part of the book introduces the percolation model of the long-range effect which is based on the notion on the multifractal clusters with transforming elements, and the theorem on the field interaction of multifractals is described. In addition small clusters, their characteristic properties and the criterion of stability are presented.

Effect of particle size ratio on the conducting percolation threshold of granular conductive-insulating composites

International Nuclear Information System (INIS)

He Da; Ekere, N N

2004-01-01

In this paper, we apply Monte Carlo simulation to investigate the conductive percolation threshold of granular composite of conductive and insulating powders with amorphous structure. We focus on the effect of insulating to conductive particle size ratio λ = d i /d c on the conducting percolation threshold p c (the volume fraction of the conductive powder). Simulation results show that, for λ = 1, the percolation threshold p c lies between simple cubic and body centred cubic site percolation thresholds, and that as λ increases the percolation threshold decreases. We also use the structural information obtained by the simulation to study the nonlinear current-voltage characteristics of composite with solid volume fraction of conductive powder below p c in terms of electron tunnelling for nanoscale powders, dielectric breakdown for microscale or larger powders, and pressing induced conduction for non-rigid insulating powders

SKL1 Is Essential for Chloroplast Development in Arabidopsis

Directory of Open Access Journals (Sweden)

Huimin Xu

2018-02-01

Full Text Available The Arabidopsis shikimate kinase-like 1 (skl1-8 mutant is characterized by a pigment-defective phenotype. Although the related phenotypical defect mainly has been attributed to the blocking of chloroplast development, the molecular functions of SKL1 remain largely unknown. In this study, we combined multiple approaches to investigate the potential functions of SKL1. Results showed that the skl1-8 mutant exhibited an albino phenotype and had dramatically reduced chlorophyll content as a consequence of a single nuclear recessive gene mutation. Chemical complementation analysis indicated that SKL1 does not function as SK enzyme in the shikimate pathway. In addition, by chlorophyll fluorescence parameters and immunoblot analysis, the levels of photosynthetic proteins are substantially reduced. Moreover, by transcriptome analysis, specific groups of nuclear genes involved in photosynthesis, such as light-harvesting complex, pigment metabolism, carbon metabolism, and chloroplast gene expression, were down-regulated, whereas several defense and oxidative stress responsive genes were up-regulated in the skl1-8 mutant compared with the wide type. Furthermore, we found the expression of genes related to auxin transport and response was repressed in the skl1-8 mutant, probable suggesting that SKL1 is involved in auxin-related pathways during chloroplast development. Together, these results provide a useful reference for characterization of SKL1 function during chloroplast biogenesis and development.

Protein disorder in plants: a view from the chloroplast

Directory of Open Access Journals (Sweden)

Yruela Inmaculada

2012-09-01

Full Text Available Abstract Background The intrinsically unstructured state of some proteins, observed in all living organisms, is essential for basic cellular functions. In this field the available information from plants is limited but it has been reached a point where these proteins can be comprehensively classified on the basis of disorder, function and evolution. Results Our analysis of plant genomes confirms that nuclear-encoded proteins follow the same trend than other multi-cellular eukaryotes; however, chloroplast- and mitochondria- encoded proteins conserve the patterns of Archaea and Bacteria, in agreement with their phylogenetic origin. Based on current knowledge about gene transference from the chloroplast to the nucleus, we report a strong correlation between the rate of disorder of transferred and nuclear-encoded proteins, even for polypeptides that play functional roles back in the chloroplast. We further investigate this trend by reviewing the set of chloroplast ribosomal proteins, one of the most representative transferred gene clusters, finding that the ribosomal large subunit, assembled from a majority of nuclear-encoded proteins, is clearly more unstructured than the small one, which integrates mostly plastid-encoded proteins. Conclusions Our observations suggest that the evolutionary dynamics of the plant nucleus adds disordered segments to genes alike, regardless of their origin, with the notable exception of proteins currently encoded in both genomes, probably due to functional constraints.

Transcriptome analysis of ectopic chloroplast development in green curd cauliflower (Brassica oleracea L. var. botrytis

Directory of Open Access Journals (Sweden)

Zhou Xiangjun

2011-11-01

Full Text Available Abstract Background Chloroplasts are the green plastids where photosynthesis takes place. The biogenesis of chloroplasts requires the coordinate expression of both nuclear and chloroplast genes and is regulated by developmental and environmental signals. Despite extensive studies of this process, the genetic basis and the regulatory control of chloroplast biogenesis and development remain to be elucidated. Results Green cauliflower mutant causes ectopic development of chloroplasts in the curd tissue of the plant, turning the otherwise white curd green. To investigate the transcriptional control of chloroplast development, we compared gene expression between green and white curds using the RNA-seq approach. Deep sequencing produced over 15 million reads with lengths of 86 base pairs from each cDNA library. A total of 7,155 genes were found to exhibit at least 3-fold changes in expression between green and white curds. These included light-regulated genes, genes encoding chloroplast constituents, and genes involved in chlorophyll biosynthesis. Moreover, we discovered that the cauliflower ELONGATED HYPOCOTYL5 (BoHY5 was expressed higher in green curds than white curds and that 2616 HY5-targeted genes, including 1600 up-regulated genes and 1016 down-regulated genes, were differently expressed in green in comparison to white curd tissue. All these 1600 up-regulated genes were HY5-targeted genes in the light. Conclusions The genome-wide profiling of gene expression by RNA-seq in green curds led to the identification of large numbers of genes associated with chloroplast development, and suggested the role of regulatory genes in the high hierarchy of light signaling pathways in mediating the ectopic chloroplast development in the green curd cauliflower mutant.

Transcriptome analysis of ectopic chloroplast development in green curd cauliflower (Brassica oleracea L. var. botrytis).

Science.gov (United States)

Zhou, Xiangjun; Fei, Zhangjun; Thannhauser, Theodore W; Li, Li

2011-11-23

Chloroplasts are the green plastids where photosynthesis takes place. The biogenesis of chloroplasts requires the coordinate expression of both nuclear and chloroplast genes and is regulated by developmental and environmental signals. Despite extensive studies of this process, the genetic basis and the regulatory control of chloroplast biogenesis and development remain to be elucidated. Green cauliflower mutant causes ectopic development of chloroplasts in the curd tissue of the plant, turning the otherwise white curd green. To investigate the transcriptional control of chloroplast development, we compared gene expression between green and white curds using the RNA-seq approach. Deep sequencing produced over 15 million reads with lengths of 86 base pairs from each cDNA library. A total of 7,155 genes were found to exhibit at least 3-fold changes in expression between green and white curds. These included light-regulated genes, genes encoding chloroplast constituents, and genes involved in chlorophyll biosynthesis. Moreover, we discovered that the cauliflower ELONGATED HYPOCOTYL5 (BoHY5) was expressed higher in green curds than white curds and that 2616 HY5-targeted genes, including 1600 up-regulated genes and 1016 down-regulated genes, were differently expressed in green in comparison to white curd tissue. All these 1600 up-regulated genes were HY5-targeted genes in the light. The genome-wide profiling of gene expression by RNA-seq in green curds led to the identification of large numbers of genes associated with chloroplast development, and suggested the role of regulatory genes in the high hierarchy of light signaling pathways in mediating the ectopic chloroplast development in the green curd cauliflower mutant.

Percolation Model of Adhesion at Polymer Interfaces

Science.gov (United States)

Wool, Richard P.

1998-03-01

Adhesion at polymer interfaces is treated as a percolation problem, where an areal density of chains Σ, of length L, contribute a number of entanglements to the interface of thickness X. The fracture energy G, is determined by the fraction of entanglements P, fractured or disentangled in the deformation zone preceding the crack tip, via G ~ P-P_c, where Pc is the percolation threshold, given by Pc = 1- M_e/Mc . For incompatible A/B interfaces reinforced with Σ diblocks or random A-B copolymers of effective length L'(L' ~ 0 for brushes and strongly adsorbed chains), we obtain P ~ ΣL/X, Pc ~ Σ _cL/X, such that G = K(Σ - Σ _c)+ G_o, where K and Go ~ 1 J/m^2 are constants. Note that Log G vs Log Σ will have an apparent slope of about 2, incorrectly suggesting that G ~ Σ ^2. For cohesive fracture, disentanglement dominates at M M*, G = G*[1-M_c/M]. For fatigue crack propagation da/dN, at welding interfaces, we obtain da/dN ~ M-5/2(t/Tr)-5/4, where t is the welding time and Tr is the reptation time. For polymer-solid interfaces, G ~ (X/R)^2. where X is the conformational width of the first layer of chains of random coil size R. The fractal nature of the percolation process is relevant to the fracture mechanism and fractography.

Cities and regions in Britain through hierarchical percolation

Science.gov (United States)

Arcaute, Elsa; Molinero, Carlos; Hatna, Erez; Murcio, Roberto; Vargas-Ruiz, Camilo; Masucci, A. Paolo; Batty, Michael

2016-04-01

Urban systems present hierarchical structures at many different scales. These are observed as administrative regional delimitations which are the outcome of complex geographical, political and historical processes which leave almost indelible footprints on infrastructure such as the street network. In this work, we uncover a set of hierarchies in Britain at different scales using percolation theory on the street network and on its intersections which are the primary points of interaction and urban agglomeration. At the larger scales, the observed hierarchical structures can be interpreted as regional fractures of Britain, observed in various forms, from natural boundaries, such as National Parks, to regional divisions based on social class and wealth such as the well-known North-South divide. At smaller scales, cities are generated through recursive percolations on each of the emerging regional clusters. We examine the evolution of the morphology of the system as a whole, by measuring the fractal dimension of the clusters at each distance threshold in the percolation. We observe that this reaches a maximum plateau at a specific distance. The clusters defined at this distance threshold are in excellent correspondence with the boundaries of cities recovered from satellite images, and from previous methods using population density.

Conflict amongst chloroplast DNA sequences obscures the phylogeny of a group of Asplenium ferns.

Science.gov (United States)

Shepherd, Lara D; Holland, Barbara R; Perrie, Leon R

2008-07-01

A previous study of the relationships amongst three subgroups of the Austral Asplenium ferns found conflicting signal between the two chloroplast loci investigated. Because organelle genomes like those of chloroplasts and mitochondria are thought to be non-recombining, with a single evolutionary history, we sequenced four additional chloroplast loci with the expectation that this would resolve these relationships. Instead, the conflict was only magnified. Although tree-building analyses favoured one of the three possible trees, one of the alternative trees actually had one more supporting site (six versus five) and received greater support in spectral and neighbor-net analyses. Simulations suggested that chance alone was unlikely to produce strong support for two of the possible trees and none for the third. Likelihood permutation tests indicated that the concatenated chloroplast sequence data appeared to have experienced recombination. However, recombination between the chloroplast genomes of different species would be highly atypical, and corollary supporting observations, like chloroplast heteroplasmy, are lacking. Wider taxon sampling clarified the composition of the Austral group, but the conflicting signal meant analyses (e.g., morphological evolution, biogeographic) conditional on a well-supported phylogeny could not be performed.

Fractal properties of percolation clusters in Euclidian neural networks

International Nuclear Information System (INIS)

Franovic, Igor; Miljkovic, Vladimir

2009-01-01

The process of spike packet propagation is observed in two-dimensional recurrent networks, consisting of locally coupled neuron pools. Local population dynamics is characterized by three key parameters - probability for pool connectedness, synaptic strength and neuron refractoriness. The formation of dynamic attractors in our model, synfire chains, exhibits critical behavior, corresponding to percolation phase transition, with probability for non-zero synaptic strength values representing the critical parameter. Applying the finite-size scaling method, we infer a family of critical lines for various synaptic strengths and refractoriness values, and determine the Hausdorff-Besicovitch fractal dimension of the percolation clusters.

The complete chloroplast genomes of two Wisteria species, W. floribunda and W. sinensis (Fabaceae).

Science.gov (United States)

Kim, Na-Rae; Kim, Kyunghee; Lee, Sang-Choon; Lee, Jung-Hoon; Cho, Seong-Hyun; Yu, Yeisoo; Kim, Young-Dong; Yang, Tae-Jin

2016-11-01

Wisteria floribunda and Wisteria sinensis are ornamental woody vines in the Fabaceae. The complete chloroplast genome sequences of the two species were generated by de novo assembly using whole genome next generation sequences. The chloroplast genomes of W. floribunda and W. sinensis were 130 960 bp and 130 561 bp long, respectively, and showed inverted repeat (IR)-lacking structures as those reported in IRLC in the Fabaceae. The chloroplast genomes of both species contained same number of protein-coding sequences (77), tRNA genes (30), and rRNA genes (4). The phylogenetic analysis with the reported chloroplast genomes confirmed close taxonomical relationship of W. floribunda and W. sinensis.

Computer simulation of current percolation in polycrystalline high-temperature superconductors

Energy Technology Data Exchange (ETDEWEB)

Zeimetz, B [Department of Materials Science and Interdisciplinary Research Centre in Superconductivity, Cambridge University, Pembroke Street, Cambridge (United Kingdom); Rutter, N A; Glowacki, B A; Evetts, J E [Department of Materials Science and Interdisciplinary Research Centre in Superconductivity, Cambridge University, Pembroke Street, Cambridge (United Kingdom)

2001-09-01

YBCO-coated conductors were modelled in a computer simulation using a resistor network concept, with the resistors representing the grain boundaries. Dissipation above the critical current, accompanied by flux penetration into the grain boundaries, was described by a linear (flux-flow) resistivity. The model allowed calculation of the combined percolation of current and magnetic flux. Current-voltage data showed scaling in agreement with percolation theory for two-dimensional systems. The influence of grain alignment and electromagnetic parameters on conductor performance was investigated. (author)

Real-space renormalization group; application to site percolation in square lattice

International Nuclear Information System (INIS)

Tsallis, C.; Schwachheim, G.

1978-05-01

The real-space renormalization group proposed by Reynolds, Klein and Stanley 1977 to treat the site percolation is analysed and extended . The best among 3 possible definitions of 'percolating' configurations and among 5 possible methods to weight these configurations, are established for percolation in square lattices. The use of n xn square clusters leads, for n = 2 (RKS), n = 3 and n = 4, to √ sub (p) approximately equal to 1.635, √ sub(p) approximately equal to 1.533 and √ sub(p) approximately equal to 1.498, and also to P sub(c) approximately equal to 0.382, P sub(c) approximately equal to 0.388 and P sub(c) approximately equal to 0.398, exhibiting in this way the correct (but slow) tendency towards the best up to date values [pt

Handbook of purified gases

CERN Document Server

Schoen, Helmut

2015-01-01

Technical gases are used in almost every field of industry, science and medicine and also as a means of control by government authorities and institutions and are regarded as indispensable means of assistance. In this complete handbook of purified gases the physical foundations of purified gases and mixtures as well as their manufacturing, purification, analysis, storage, handling and transport are presented in a comprehensive way. This important reference work is accompanied with a large number of Data Sheets dedicated to the most important purified gases.  

Percolation and cooperation with mobile agents: geometric and strategy clusters.

Science.gov (United States)

Vainstein, Mendeli H; Brito, Carolina; Arenzon, Jeferson J

2014-08-01

We study the conditions for persistent cooperation in an off-lattice model of mobile agents playing the Prisoner's Dilemma game with pure, unconditional strategies. Each agent has an exclusion radius r(P), which accounts for the population viscosity, and an interaction radius r(int), which defines the instantaneous contact network for the game dynamics. We show that, differently from the r(P)=0 case, the model with finite-sized agents presents a coexistence phase with both cooperators and defectors, besides the two absorbing phases, in which either cooperators or defectors dominate. We provide, in addition, a geometric interpretation of the transitions between phases. In analogy with lattice models, the geometric percolation of the contact network (i.e., irrespective of the strategy) enhances cooperation. More importantly, we show that the percolation of defectors is an essential condition for their survival. Differently from compact clusters of cooperators, isolated groups of defectors will eventually become extinct if not percolating, independently of their size.

Dissecting the chloroplast proteome of chickpea (Cicer arietinum L.) provides new insights into classical and non-classical functions.

Science.gov (United States)

Lande, Nilesh Vikram; Subba, Pratigya; Barua, Pragya; Gayen, Dipak; Keshava Prasad, T S; Chakraborty, Subhra; Chakraborty, Niranjan

2017-08-08

Chloroplast, the energy organelle unique to plant cells, is a dynamic entity which integrates an array of metabolic pathways and serves as first level for energy conversion for the entire ecological hierarchy. Increasing amount of sequence data and evolution of mass spectrometric approaches has opened up new avenues for opportune exploration of the global proteome of this organelle. In our study, we aimed at generation of a comprehensive catalogue of chloroplast proteins in a grain legume, chickpea and provided a reference proteome map. To accurately assign the identified proteins, purity of chloroplast-enriched fraction was stringently monitored by multiple chemical and immunological indexes, besides pigment and enzyme analyses. The proteome analysis led to the identification of 2451 proteins, including 27 isoforms, which include predicted and novel chloroplast constituents. The identified proteins were validated through their sequence analysis. Extensive sequence based localization prediction revealed more than 50% proteins to be chloroplast resident by at least two different algorithms. Chromosomal distribution of identified proteins across nuclear and chloroplast genome unveiled the presence of 55 chloroplast encoded gene. In depth comparison of our dataset with the non-redundant set of chloroplast proteins identified so far across other species revealed novel as well as overlapping candidates. Pulses add large amount of nitrogen to the soil and has very low water footprint and therefore, contributes to fortification of sustainable agriculture. Chickpea is one of the earliest cultivated legumes and serves as an energy and protein source for humans and animals. Chloroplasts are the unique organelles which conduct photosynthesis. Investigation on chloroplast proteome is of particular significance, especially to plant biologists, as it would allow a better understanding of chloroplast function in plants. Generation of a saturated proteome map would not only

Discrete redox signaling pathways regulate photosynthetic light-harvesting and chloroplast gene transcription.

Directory of Open Access Journals (Sweden)

John F Allen

Full Text Available In photosynthesis in chloroplasts, two related regulatory processes balance the actions of photosystems I and II. These processes are short-term, post-translational redistribution of light-harvesting capacity, and long-term adjustment of photosystem stoichiometry initiated by control of chloroplast DNA transcription. Both responses are initiated by changes in the redox state of the electron carrier, plastoquinone, which connects the two photosystems. Chloroplast Sensor Kinase (CSK is a regulator of transcription of chloroplast genes for reaction centres of the two photosystems, and a sensor of plastoquinone redox state. We asked whether CSK is also involved in regulation of absorbed light energy distribution by phosphorylation of light-harvesting complex II (LHC II. Chloroplast thylakoid membranes isolated from a CSK T-DNA insertion mutant and from wild-type Arabidopsis thaliana exhibit similar light- and redox-induced (32P-labelling of LHC II and changes in 77 K chlorophyll fluorescence emission spectra, while room-temperature chlorophyll fluorescence emission transients from Arabidopsis leaves are perturbed by inactivation of CSK. The results indicate indirect, pleiotropic effects of reaction centre gene transcription on regulation of photosynthetic light-harvesting in vivo. A single, direct redox signal is transmitted separately to discrete transcriptional and post-translational branches of an integrated cytoplasmic regulatory system.

Do diatoms percolate through soil and can they be used for tracing the origin of runoff?

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De Graaf, Lenka; Cammeraat, Erik; Pfister, Laurent; Wetzel, Carlos; Klaus, Julian; Hissler, Christophe

2015-04-01

Tracers are widely used to study the movement of water in a catchment. Because of depletion of scientific possibilities with most common tracer types, we proposed the use of diatoms as a natural tracer. Paradoxical results on the contribution of surface runoff to the storm hydrograph were obtained in pioneer research on this idea. Diatom transport via the subsurface flow to the stream would explain this paradox. Prerequisite for this is vertical transport of diatoms through soils, which is the topic of this study. Emphasis is on percolation behavior (speed of percolation, speed of percolation over time, and species distribution) of Pseudostaurosira sp. and Melosira sp. (Bacillariophyceae) through undisturbed soil columns of contrasting substrates. Co-objective is to study the flowpaths of water through the soil columns. Natural undisturbed soil columns were sampled in the Attert basin (Luxembourg) on schist, marl and sandstone substrates. Rain simulation experiments were performed to study vertical diatom transport. Rhodamine dye experiments were carried out to gain insight in the active flowpaths of water, and breakthrough experiments were performed to study the responses of the soil columns to applied water. Diatoms were transported through the soil columns of the three substrates. A vast majority of diatom percolation took place within the first 15 minutes, percolation hereafter was marginal but nevertheless present. Peaks in diatom percolation corresponded with a high flux caused by the addition of the diatom culture, but seepage of diatoms along the sides is unlikely according to the species distribution and the rhodamine dye experiment. Pseudostaurosira sp. percolated significantly better than Melosira sp. Significantly more diatoms percolated through the marl columns compared to the schist columns and variance within the sandstone group was very high. Absolute differences between substrates however, were marginal. Most preferential flowpaths were observed in

RNA transcription in isolated chloroplasts during senescence and rejuvenation of intact cotyledons of CUCURBITA PEPO L. (ZUCCHINI)

International Nuclear Information System (INIS)

Mishev, K.; Ananiev, E.; Denev, L.; Radeva, G.

2006-01-01

RNA transcription was studied in intact chloroplasts isolated from cotyledons of Cucurbita pepoL. (zucchini) during their growth and development including natural senescence and rejuvenation. Rejuvenation of cotyledons was studied after decapitation of the epicotyl above the senescing yellow cotyledons. Maximal incorporation of [32P] UTP into overall chloroplast RNA was measured two days after exposure of seedlings to light (day 6 th after the onset of germination), followed by a gradual decrease reaching minimal values at the age of 25-28 days when cotyledons began to yellow and eventually die. Rejuvenation of cotyledons completely restored chloroplast RNA synthesis and fifteen days after decapitation (at the age of 40 days), the values of chloroplast transcription even exceeded that of the maximal transcriptional activity in young cotyledons. Inhibitory analysis with tagetitoxin (a specific inhibitor of plastid encoded chloroplast RNA polymerase (PEP)) showed that in young and rejuvenated cotyledons about 85% of chloroplast RNA polymerase activity was due to PEP and only 15% corresponded to the nuclear encoded plastid RNA polymerase (NEP). Definite regions of two chloroplast encoded genes were amplified by means of PCR technique using specific DNA primers for Rubisco large subunit gene (rbcL) and the housekeeping gene for chloroplast 16S rRNA as well as chloroplast DNA as a template. The appropriate lengths of the amplified DNA fragments were checked by restriction analysis

Percolation in Heterogeneous Media

International Nuclear Information System (INIS)

Vocka, Radim

1999-01-01

This work is a theoretical reflection on the problematic of the modeling of heterogeneous media, that is on the way of their simple representation conserving their characteristic features. Two particular problems are addressed in this thesis. Firstly, we study the transport in porous media, that is in a heterogeneous media which structure is quenched. A pore space is represented in a simple way - a pore is symbolized as a tube of a given length and a given diameter. The fact that the correlations in the distribution of pore sizes are taken into account by a construction of a hierarchical network makes possible the modeling of porous media with a porosity distributed over several length scales. The transport in the hierarchical network shows qualitatively different phenomena from those observed in simpler models. A comparison of numerical results with experimental data shows that the hierarchical network gives a good qualitative representation of the structure of real porous media. Secondly, we study a problem of the transport in a heterogeneous media which structure is evolving during the time. The models where the evolution of the structure is not influenced by the transport are studied in detail. These models present a phase transition of the same nature as that observed on the percolation networks. We propose a new theoretical description of this transition, and we express critical exponents describing the evolution of the conductivity as a function of fundamental exponents of percolation theory. (author) [fr

Chloroplast-Derived Vaccine Antigens and Biopharmaceuticals: Expression, Folding, Assembly and Functionality

Science.gov (United States)

Chebolu, S.; Daniell, H.

2009-01-01

Chloroplast genetic engineering offers several advantages, including high levels of transgene expression, transgene containment via maternal inheritance, and multi-gene expression in a single transformation event. Oral delivery is facilitated by hyperexpression of vaccine antigens against cholera, tetanus, anthrax, plague, or canine parvovirus (4%–31% of total soluble protein, TSP) in transgenic chloroplasts (leaves) or non-green plastids (carrots, tomato) as well as the availability of antibiotic free selectable markers or the ability to excise selectable marker genes. Hyperexpression of several therapeutic proteins, including human serum albumin (11.1% TSP), somatotropin (7% TSP), interferon-alpha (19% TSP), interferon-gamma (6% TSP), and antimicrobial peptide (21.5% TSP), facilitates efficient and economic purification. Also, the presence of chaperones and enzymes in chloroplasts facilitates assembly of complex multisubunit proteins and correct folding of human blood proteins with proper disulfide bonds. Functionality of chloroplast-derived vaccine antigens and therapeutic proteins has been demonstrated by several assays, including the macrophage lysis assay, GM1-ganglioside binding assay, protection of HeLA cells or human lung carcinoma cells against encephalomyocarditis virus, systemic immune response, protection against pathogen challenge, and growth or inhibition of cell cultures. Purification of human proinsulin has been achieved using novel purification strategies (inverse temperature transition property) that do not require expensive column chromatography techniques. Thus, transgenic chloroplasts are ideal bioreactors for production of functional human and animal therapeutic proteins in an environmentally friendly manner. PMID:19401820

Formation and scavenging of superoxide in chloroplasts, with relation to injury by sulfur dioxide

Energy Technology Data Exchange (ETDEWEB)

Asada, K

1980-01-01

Injury of plant leaf cells by sulfur dioxide-exposure is greater in day time than in night. A hypothesis is proposed that the free radical chain oxidation of sulfite is initiated by the superoxide radicals (O/sub 2//sup -/) produced in illuminated chloroplasts, and that the resulting amplified production of O/sub 2//sup -/, the hydroxyl radicals and the bisulfite radicals causes the injury of leaf tissues. In this review, the production of O/sub 2//sup -/ in illuminated chloroplasts and scavenging of O/sub 2//sup -/ by superoxide dismutase and their relation to oxidation of sulfite in chloroplasts are discussed. Superoxide dismutase in chloroplasts plays an important role in protecting leaf cells from injury by sulfur dioxide.

Comparative analyses of chloroplast genome data representing nine green algae in Sphaeropleales (Chlorophyceae, Chlorophyta

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Karolina Fučíková

2016-06-01

Full Text Available The chloroplast genomes of green algae are highly variable in their architecture. In this article we summarize gene content across newly obtained and published chloroplast genomes in Chlorophyceae, including new data from nine of species in Sphaeropleales (Chlorophyceae, Chlorophyta. We present genome architecture information, including genome synteny analysis across two groups of species. Also, we provide a phylogenetic tree obtained from analysis of gene order data for species in Chlorophyceae with fully sequenced chloroplast genomes. Further analyses and interpretation of the data can be found in “Chloroplast phylogenomic data from the green algal order Sphaeropleales (Chlorophyceae, Chlorophyta reveal complex patterns of sequence evolution” (Fučíková et al., In review [1].

Using a dynamic point-source percolation model to simulate bubble growth

International Nuclear Information System (INIS)

Zimmerman, Jonathan A.; Zeigler, David A.; Cowgill, Donald F.

2004-01-01

Accurate modeling of nucleation, growth and clustering of helium bubbles within metal tritide alloys is of high scientific and technological importance. Of interest is the ability to predict both the distribution of these bubbles and the manner in which these bubbles interact at a critical concentration of helium-to-metal atoms to produce an accelerated release of helium gas. One technique that has been used in the past to model these materials, and again revisited in this research, is percolation theory. Previous efforts have used classical percolation theory to qualitatively and quantitatively model the behavior of interstitial helium atoms in a metal tritide lattice; however, higher fidelity models are needed to predict the distribution of helium bubbles and include features that capture the underlying physical mechanisms present in these materials. In this work, we enhance classical percolation theory by developing the dynamic point-source percolation model. This model alters the traditionally binary character of site occupation probabilities by enabling them to vary depending on proximity to existing occupied sites, i.e. nucleated bubbles. This revised model produces characteristics for one and two dimensional systems that are extremely comparable with measurements from three dimensional physical samples. Future directions for continued development of the dynamic model are also outlined

Unusual percolation in simple small-world networks.

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Cohen, Reuven; Dawid, Daryush Jonathan; Kardar, Mehran; Bar-Yam, Yaneer

2009-06-01

We present an exact solution of percolation in a generalized class of Watts-Strogatz graphs defined on a one-dimensional underlying lattice. We find a nonclassical critical point in the limit of the number of long-range bonds in the system going to zero, with a discontinuity in the percolation probability and a divergence in the mean finite-cluster size. We show that the critical behavior falls into one of three regimes depending on the proportion of occupied long-range to unoccupied nearest-neighbor bonds, with each regime being characterized by different critical exponents. The three regimes can be united by a single scaling function around the critical point. These results can be used to identify the number of long-range links necessary to secure connectivity in a communication or transportation chain. As an example, we can resolve the communication problem in a game of "telephone."

Cooperation percolation in spatial prisoner's dilemma game

International Nuclear Information System (INIS)

Yang, Han-Xin; Rong, Zhihai; Wang, Wen-Xu

2014-01-01

The paradox of cooperation among selfish individuals still puzzles scientific communities. Although a large amount of evidence has demonstrated that the cooperator clusters in spatial games are effective in protecting the cooperators against the invasion of defectors, we continue to lack the condition for the formation of a giant cooperator cluster that ensures the prevalence of cooperation in a system. Here, we study the dynamical organization of the cooperator clusters in spatial prisoner's dilemma game to offer the condition for the dominance of cooperation, finding that a phase transition characterized by the emergence of a large spanning cooperator cluster occurs when the initial fraction of the cooperators exceeds a certain threshold. Interestingly, the phase transition belongs to different universality classes of percolation determined by the temptation to defect b. Specifically, on square lattices, 1 < b < 4/3 leads to a phase transition pertaining to the class of regular site percolation, whereas 3/2 < b < 2 gives rise to a phase transition subject to invasion percolation with trapping. Our findings offer a deeper understanding of cooperative behavior in nature and society. (paper)

Low cost tuberculosis vaccine antigens in capsules: expression in chloroplasts, bio-encapsulation, stability and functional evaluation in vitro.

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Priya Saikumar Lakshmi

Full Text Available Tuberculosis (TB caused by Mycobacterium tuberculosis is one of the leading fatal infectious diseases. The development of TB vaccines has been recognized as a major public health priority by the World Health Organization. In this study, three candidate antigens, ESAT-6 (6 kDa early secretory antigenic target and Mtb72F (a fusion polyprotein from two TB antigens, Mtb32 and Mtb39 fused with cholera toxin B-subunit (CTB and LipY (a cell wall protein were expressed in tobacco and/or lettuce chloroplasts to facilitate bioencapsulation/oral delivery. Site-specific transgene integration into the chloroplast genome was confirmed by Southern blot analysis. In transplastomic leaves, CTB fusion proteins existed in soluble monomeric or multimeric forms of expected sizes and their expression levels varied depending upon the developmental stage and time of leaf harvest, with the highest-level of accumulation in mature leaves harvested at 6PM. The CTB-ESAT6 and CTB-Mtb72F expression levels reached up to 7.5% and 1.2% of total soluble protein respectively in mature tobacco leaves. Transplastomic CTB-ESAT6 lettuce plants accumulated up to 0.75% of total leaf protein. Western blot analysis of lyophilized lettuce leaves stored at room temperature for up to six months showed that the CTB-ESAT6 fusion protein was stable and preserved proper folding, disulfide bonds and assembly into pentamers for prolonged periods. Also, antigen concentration per gram of leaf tissue was increased 22 fold after lyophilization. Hemolysis assay with purified CTB-ESAT6 protein showed partial hemolysis of red blood cells and confirmed functionality of the ESAT-6 antigen. GM1-binding assay demonstrated that the CTB-ESAT6 fusion protein formed pentamers to bind with the GM1-ganglioside receptor. The expression of functional Mycobacterium tuberculosis antigens in transplastomic plants should facilitate development of a cost-effective and orally deliverable TB booster vaccine with potential

Low cost tuberculosis vaccine antigens in capsules: expression in chloroplasts, bio-encapsulation, stability and functional evaluation in vitro.

Science.gov (United States)

Lakshmi, Priya Saikumar; Verma, Dheeraj; Yang, Xiangdong; Lloyd, Bethany; Daniell, Henry

2013-01-01

Tuberculosis (TB) caused by Mycobacterium tuberculosis is one of the leading fatal infectious diseases. The development of TB vaccines has been recognized as a major public health priority by the World Health Organization. In this study, three candidate antigens, ESAT-6 (6 kDa early secretory antigenic target) and Mtb72F (a fusion polyprotein from two TB antigens, Mtb32 and Mtb39) fused with cholera toxin B-subunit (CTB) and LipY (a cell wall protein) were expressed in tobacco and/or lettuce chloroplasts to facilitate bioencapsulation/oral delivery. Site-specific transgene integration into the chloroplast genome was confirmed by Southern blot analysis. In transplastomic leaves, CTB fusion proteins existed in soluble monomeric or multimeric forms of expected sizes and their expression levels varied depending upon the developmental stage and time of leaf harvest, with the highest-level of accumulation in mature leaves harvested at 6PM. The CTB-ESAT6 and CTB-Mtb72F expression levels reached up to 7.5% and 1.2% of total soluble protein respectively in mature tobacco leaves. Transplastomic CTB-ESAT6 lettuce plants accumulated up to 0.75% of total leaf protein. Western blot analysis of lyophilized lettuce leaves stored at room temperature for up to six months showed that the CTB-ESAT6 fusion protein was stable and preserved proper folding, disulfide bonds and assembly into pentamers for prolonged periods. Also, antigen concentration per gram of leaf tissue was increased 22 fold after lyophilization. Hemolysis assay with purified CTB-ESAT6 protein showed partial hemolysis of red blood cells and confirmed functionality of the ESAT-6 antigen. GM1-binding assay demonstrated that the CTB-ESAT6 fusion protein formed pentamers to bind with the GM1-ganglioside receptor. The expression of functional Mycobacterium tuberculosis antigens in transplastomic plants should facilitate development of a cost-effective and orally deliverable TB booster vaccine with potential for long

Insights from the complete chloroplast genome into the evolution of Sesamum indicum L.

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Haiyang Zhang

Full Text Available Sesame (Sesamum indicum L. is one of the oldest oilseed crops. In order to investigate the evolutionary characters according to the Sesame Genome Project, apart from sequencing its nuclear genome, we sequenced the complete chloroplast genome of S. indicum cv. Yuzhi 11 (white seeded using Illumina and 454 sequencing. Comparisons of chloroplast genomes between S. indicum and the 18 other higher plants were then analyzed. The chloroplast genome of cv. Yuzhi 11 contains 153,338 bp and a total of 114 unique genes (KC569603. The number of chloroplast genes in sesame is the same as that in Nicotiana tabacum, Vitis vinifera and Platanus occidentalis. The variation in the length of the large single-copy (LSC regions and inverted repeats (IR in sesame compared to 18 other higher plant species was the main contributor to size variation in the cp genome in these species. The 77 functional chloroplast genes, except for ycf1 and ycf2, were highly conserved. The deletion of the cp ycf1 gene sequence in cp genomes may be due either to its transfer to the nuclear genome, as has occurred in sesame, or direct deletion, as has occurred in Panax ginseng and Cucumis sativus. The sesame ycf2 gene is only 5,721 bp in length and has lost about 1,179 bp. Nucleotides 1-585 of ycf2 when queried in BLAST had hits in the sesame draft genome. Five repeats (R10, R12, R13, R14 and R17 were unique to the sesame chloroplast genome. We also found that IR contraction/expansion in the cp genome alters its rate of evolution. Chloroplast genes and repeats display the signature of convergent evolution in sesame and other species. These findings provide a foundation for further investigation of cp genome evolution in Sesamum and other higher plants.

Conformal Field Theory of Percolation (1)

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CERN. Geneva

2015-01-01

This series of 5 lectures will describe what is known about the Logarithmic CFT describing the critical point of percolation. The subsequent lectures will take place in TH Conference room on: (2) Wednesday Sep 16 at 10am (3) Thursday Sep 17 at 10am (4) Thursday Sep 17 at 2pm (5) Friday Sep 18 at 10am

Identification and Characterization of a Chloroplast-Targeted Obg GTPase in Dendrobium officinale.

Science.gov (United States)

Chen, Ji; Deng, Feng; Deng, Mengsheng; Han, Jincheng; Chen, Jianbin; Wang, Li; Yan, Shen; Tong, Kai; Liu, Fan; Tian, Mengliang

2016-12-01

Bacterial homologous chloroplast-targeted Obg GTPases (ObgCs) belong to the plant-typical Obg group, which is involved in diverse physiological processes during chloroplast development. However, the evolutionarily conserved function of ObgC in plants remains elusive and requires further investigation. In this study, we identified DoObgC from an epiphytic plant Dendrobium officinale and demonstrated the characteristics of DoObgC. Sequence analysis indicated that DoObgC is highly conserved with other plant ObgCs, which contain the chloroplast transit peptide (cTP), Obg fold, G domain, and OCT regions. The C terminus of DoObgC lacking the chloroplast-targeting cTP region, DoObgC Δ1-160 , showed strong similarity to ObgE and other bacterial Obgs. Overexpression of DoObgC Δ1-160 in Escherichia coli caused slow cell growth and an increased number of elongated cells. This phenotype was consistent with the phenotype of cells overexpressing ObgE. Furthermore, the expression of recombinant DoObgC Δ1-160 enhanced the cell persistence of E. coli to streptomycin. Results of transient expression assays revealed that DoObgC was localized to chloroplasts. Moreover, we demonstrated that DoObgC could rescue the embryotic lethal phenotype of the Arabidopsis obgc-t mutant, suggesting that DoObgC is a functional homolog to Arabidopsis AtObgC in D. officinale. Gene expression profiles showed that DoObgC was expressed in leaf-specific and light-dependent patterns and that DoObgC responded to wounding treatments. Our previous and present studies reveal that ObgC has an evolutionarily conserved role in ribosome biogenesis to adapt chloroplast development to the environment.

Light-stimulated accumulation of transcripts of nuclear and chloroplast genes for ribulosebisphosphate carboxylase

Energy Technology Data Exchange (ETDEWEB)

Smith, S M; Ellis, R J

1981-01-01

The chloroplast enzyme, ribulosebisphosphate carboxylase, consists of large subunit polypeptides encoded in the chloroplast genome and small subunit polypeptides encoded in the nuclear genome. Cloned DNA complementary to the small subunit mRNA hybridizes to a single RNA species of 900-1000 nucleotides in both total and poly(A)-containing RNA from leaves of Pisum sativum, but does not hybridize to chloroplast RNA. Small subunit cDNA hybridizes to at least three RNA species from nuclei, two of which are of higher molecular weight than the mature mRNA. A cloned large subunit DNA sequence hybridizes to a single species of Pisum chloroplast RNA containing approximately 1700 nucleotides, but does not hybridize to nuclear RNA. The light-stimulation of carboxylase accumulation reflects increases in the amounts of transcripts for both subunits in total leaf RNA. Transcripts of the small subunit gene are more abundant in nuclear RNA from light-grown leaves than in that from dark-grown leaves. These results suggest that the stimulation of carboxylase accumulation by light is mediated at the level of either transcription or RNA turnover in both nucleus and chloroplast.

The abundance threshold for plague as a critical percolation phenomenon

DEFF Research Database (Denmark)

Davis, S; Trapman, P; Leirs, H

2008-01-01

. However, no natural examples have been reported. The central question of interest in percolation theory 4 , the possibility of an infinite connected cluster, corresponds in infectious disease to a positive probability of an epidemic. Archived records of plague (infection with Yersinia pestis....... Abundance thresholds are the theoretical basis for attempts to manage infectious disease by reducing the abundance of susceptibles, including vaccination and the culling of wildlife 6, 7, 8 . This first natural example of a percolation threshold in a disease system invites a re-appraisal of other invasion...

Percolation model of excess electrical noise in transition-edge sensors

International Nuclear Information System (INIS)

Lindeman, M.A.; Anderson, M.B.; Bandler, S.R.; Bilgri, N.; Chervenak, J.; Gwynne Crowder, S.; Fallows, S.; Figueroa-Feliciano, E.; Finkbeiner, F.; Iyomoto, N.; Kelley, R.; Kilbourne, C.A.; Lai, T.; Man, J.; McCammon, D.; Nelms, K.L.; Porter, F.S.; Rocks, L.E.; Saab, T.; Sadleir, J.; Vidugiris, G.

2006-01-01

We present a geometrical model to describe excess electrical noise in transition-edge sensors (TESs). In this model, a network of fluctuating resistors represents the complex dynamics inside a TES. The fluctuations can cause several resistors in series to become superconducting. Such events short out part of the TES and generate noise because much of the current percolates through low resistance paths. The model predicts that excess white noise increases with decreasing TES bias resistance (R/R N ) and that perpendicular zebra stripes reduce noise and alpha of the TES by reducing percolation

Quasiuniversal Connectedness Percolation of Polydisperse Rod Systems

NARCIS (Netherlands)

Nigro, B.; Grimaldi, C.; Chatterjee, A.P.; van der Schoot, P. P. A. M.

2013-01-01

The connectedness percolation threshold (ηc) and critical coordination number (Zc) of systems of penetrable spherocylinders characterized by a length polydispersity are studied by way of Monte Carlo simulations for several aspect ratio distributions. We find that (i) ηc is a nearly universal

Phase transition approach to bursting in neuronal cultures: quorum percolation models

Science.gov (United States)

Monceau, P.; Renault, R.; Métens, S.; Bottani, S.; Fardet, T.

2017-10-01

The Quorum Percolation model has been designed in the context of neurobiology to describe bursts of activity occurring in neuronal cultures from the point of view of statistical physics rather than from a dynamical synchronization approach. It is based upon information propagation on a directed graph with a threshold activation rule; this leads to a phase diagram which exhibits a giant percolation cluster below some critical value mC of the excitability. We describe the main characteristics of the original model and derive extensions according to additional relevant biological features. Firstly, we investigate the effects of an excitability variability on the phase diagram and show that the percolation transition can be destroyed by a sufficient amount of such a disorder; we stress the weakly averaging character of the order parameter and show that connectivity and excitability can be seen as two overlapping aspects of the same reality. Secondly, we elaborate a discrete time stochastic model taking into account the decay originating from ionic leakage through the membrane of neurons and synaptic depression; we give evidence that the decay softens and shifts the transition, and conjecture than decay destroys the transition in the thermodynamical limit. We were able to develop mean-field theories associated with each of the two effects; we discuss the framework of their agreement with Monte Carlo simulations. It turns out that the the critical point mC from which information on the connectivity of the network can be inferred is affected by each of these additional effects. Lastly, we show how dynamical simulations of bursts with an adaptive exponential integrateand- fire model can be interpreted in terms of Quorum Percolation. Moreover, the usefulness of the percolation model including the set of sophistication we investigated can be extended to many scientific fields involving information propagation, such as the spread of rumors in sociology, ethology, ecology.

Chloroplast microsatellites reveal population genetic diversity in red pine, Pinus resinosa Ait

Science.gov (United States)

Craig S. Echt; L.L. DeVerno; M. Anzidei; G.G. Vendramin

1998-01-01

Variation in paternally inherited chloroplast microsatellite (cpSSR) DNA was used to study population genetic structure in red pine (Pinus resinosa Ait.), a species characterized by morphological uniformity, no allozyme variation, and limited RAPD variation. Using nine cpSSR loci, a total of 23 chloroplast haplotypes and 25 cpSSR alleles were were...

Enzymic synthesis of γ-coniceine in Conium maculatum chloroplasts and mitochondria.

Science.gov (United States)

Roberts, M F

1981-08-01

Further studies of the transaminase responsible for the first committed step in alkaloid formation in Conium maculatum have shown the L-alanine: 5-ketooctanal transaminase to occur in both the mitochondria and chloroplast. Experiments suggest that these enzymes are the isoenzymes Transaminase A and B respectively previously isolated by the author. It is suggested that the chloroplast enzyme is normally responsible for alkaloid production.

Chloroplast Signaling Gates Thermotolerance in Arabidopsis

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Patrick J. Dickinson

2018-02-01

Full Text Available Temperature is a key environmental variable influencing plant growth and survival. Protection against high temperature stress in eukaryotes is coordinated by heat shock factors (HSFs, transcription factors that activate the expression of protective chaperones such as HEAT SHOCK PROTEIN 70 (HSP70; however, the pathway by which temperature is sensed and integrated with other environmental signals into adaptive responses is not well understood. Plants are exposed to considerable diurnal variation in temperature, and we have found that there is diurnal variation in thermotolerance in Arabidopsis thaliana, with maximal thermotolerance coinciding with higher HSP70 expression during the day. In a forward genetic screen, we identified a key role for the chloroplast in controlling this response, suggesting that light-induced chloroplast signaling plays a key role. Consistent with this, we are able to globally activate binding of HSFA1a to its targets by altering redox status in planta independently of a heat shock.

The field theory approach to percolation processes

International Nuclear Information System (INIS)

Janssen, Hans-Karl; Taeuber, Uwe C.

2005-01-01

We review the field theory approach to percolation processes. Specifically, we focus on the so-called simple and general epidemic processes that display continuous non-equilibrium active to absorbing state phase transitions whose asymptotic features are governed, respectively, by the directed (DP) and dynamic isotropic percolation (dIP) universality classes. We discuss the construction of a field theory representation for these Markovian stochastic processes based on fundamental phenomenological considerations, as well as from a specific microscopic reaction-diffusion model realization. Subsequently we explain how dynamic renormalization group (RG) methods can be applied to obtain the universal properties near the critical point in an expansion about the upper critical dimensions d c = 4 (DP) and 6 (dIP). We provide a detailed overview of results for critical exponents, scaling functions, crossover phenomena, finite-size scaling, and also briefly comment on the influence of long-range spreading, the presence of a boundary, multispecies generalizations, coupling of the order parameter to other conserved modes, and quenched disorder

Noncoding RNA mediated traffic of foreign mRNA into chloroplasts reveals a novel signaling mechanism in plants.

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Gustavo Gómez

Full Text Available Communication between chloroplasts and the nucleus is one of the milestones of the evolution of plants on earth. Proteins encoded by ancestral chloroplast-endogenous genes were transferred to the nucleus during the endosymbiotic evolution and originated this communication, which is mainly dependent on specific transit-peptides. However, the identification of nuclear-encoded proteins targeted to the chloroplast lacking these canonical signals suggests the existence of an alternative cellular pathway tuning this metabolic crosstalk. Non-coding RNAS (NcRNAs are increasingly recognized as regulators of gene expression as they play roles previously believed to correspond to proteins. Avsunviroidae family viroids are the only noncoding functional RNAs that have been reported to traffic inside the chloroplasts. Elucidating mechanisms used by these pathogens to enter this organelle will unearth novel transport pathways in plant cells. Here we show that a viroid-derived NcRNA acting as a 5'UTR-end mediates the functional import of Green Fluorescent Protein (GFP mRNA into chloroplast. This claim is supported by the observation at confocal microscopy of a selective accumulation of GFP in the chloroplast of the leaves expressing the chimeric vd-5'UTR/GFP and by the detection of the GFP mRNA in chloroplasts isolated from cells expressing this construct. These results support the existence of an alternative signaling mechanism in plants between the host cell and chloroplasts, where an ncRNA functions as a key regulatory molecule to control the accumulation of nuclear-encoded proteins in this organelle. In addition, our findings provide a conceptual framework to develop new biotechnological tools in systems using plant chloroplast as bioreactors. Finally, viroids of the family Avsunviroidae have probably evolved to subvert this signaling mechanism to regulate their differential traffic into the chloroplast of infected cells.

A model for tetrapyrrole synthesis as the primary mechanism for plastid-to-nucleus signaling during chloroplast biogenesis

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Matthew J. Terry

2013-02-01

Full Text Available Chloroplast biogenesis involves the co-ordinated expression of the chloroplast and nuclear genomes, requiring information to be sent from the developing chloroplasts to the nucleus. This is achieved through retrograde signaling pathways and can be demonstrated experimentally using the photobleaching herbicide, Norflurazon, which results in chloroplast damage and the reduced expression of many photosynthesis-related, nuclear genes in seedlings. Genetic analysis of this pathway points to a major role for tetrapyrrole synthesis in retrograde signaling, as well as a strong interaction with light-signaling pathways. Currently, the best model to explain the genetic data is that a specific heme pool generated by flux through ferrochelatase-1 functions as a positive signal to promote the expression of genes required for chloroplast development. We propose that this heme-related signal is the primary positive signal during chloroplast biogenesis, and that treatments and mutations affecting chloroplast transcription, RNA editing, translation, or protein import all impact on the synthesis and/or processing of this signal. A positive signal is consistent with the need to provide information on chloroplast status at all times. We further propose that GUN1 normally serves to restrict the production of the heme signal. In addition to a positive signal re-enforcing chloroplast development under normal conditions, aberrant chloroplast development may produce a negative signal due to accumulation of unbound chlorophyll biosynthesis intermediates, such as Mg-porphyrins. Under these conditions a rapid shut-down of tetrapyrrole synthesis is required. We propose that accumulation of these intermediates results in a rapid light-dependent inhibition of nuclear gene expression that is most likely mediated via singlet oxygen generated by photo-excitation of Mg-porphyrins. Thus, the tetrapyrrole pathway may provide both positive and inhibitory signals to control

Expression and Chloroplast Targeting of Cholesterol Oxidase in Transgenic Tobacco Plants

Science.gov (United States)

Corbin, David R.; Grebenok, Robert J.; Ohnmeiss, Thomas E.; Greenplate, John T.; Purcell, John P.

2001-01-01

Cholesterol oxidase represents a novel type of insecticidal protein with potent activity against the cotton boll weevil (Anthonomus grandis grandis Boheman). We transformed tobacco (Nicotiana tabacum) plants with the cholesterol oxidase choM gene and expressed cytosolic and chloroplast-targeted versions of the ChoM protein. Transgenic leaf tissues expressing cholesterol oxidase exerted insecticidal activity against boll weevil larvae. Our results indicate that cholesterol oxidase can metabolize phytosterols in vivo when produced cytosolically or when targeted to chloroplasts. The transgenic plants exhibiting cytosolic expression accumulated low levels of saturated sterols known as stanols, and displayed severe developmental aberrations. In contrast, the transgenic plants expressing chloroplast-targeted cholesterol oxidase maintained a greater accumulation of stanols, and appeared phenotypically and developmentally normal. These results are discussed within the context of plant sterol distribution and metabolism. PMID:11457962

Explosive percolation on directed networks due to monotonic flow of activity

Science.gov (United States)

Waagen, Alex; D'Souza, Raissa M.; Lu, Tsai-Ching

2017-07-01

An important class of real-world networks has directed edges, and in addition, some rank ordering on the nodes, for instance the popularity of users in online social networks. Yet, nearly all research related to explosive percolation has been restricted to undirected networks. Furthermore, information on such rank-ordered networks typically flows from higher-ranked to lower-ranked individuals, such as follower relations, replies, and retweets on Twitter. Here we introduce a simple percolation process on an ordered, directed network where edges are added monotonically with respect to the rank ordering. We show with a numerical approach that the emergence of a dominant strongly connected component appears to be discontinuous. Large-scale connectivity occurs at very high density compared with most percolation processes, and this holds not just for the strongly connected component structure but for the weakly connected component structure as well. We present analysis with branching processes, which explains this unusual behavior and gives basic intuition for the underlying mechanisms. We also show that before the emergence of a dominant strongly connected component, multiple giant strongly connected components may exist simultaneously. By adding a competitive percolation rule with a small bias to link uses of similar rank, we show this leads to formation of two distinct components, one of high-ranked users, and one of low-ranked users, with little flow between the two components.

Structure of cells chloroplasts and mitochondria of cotton leaves following gamma irradiation

Energy Technology Data Exchange (ETDEWEB)

Arslanova, S V [AN Uzbekskoj SSR, Tashkent. Inst. Ehksperimental' noj Biologii Rastenij

1975-01-01

The article investigates the structural changes in the plastides and mitochondria of cotton leaf cells after irradiation. Cotton seeds that had been moistened for 24 hours were irradiated by a gamma source with a dose of 10 kR (intensity: 19 R/s.). For the study of the plastides and mitochondria of the leaf cells samples were taken in the cotyledonous leaf and flowering phases of the cotton. The cells of the cotton leaf mesophillum in the standard consists of chloroplast with developed interior structures. Study of the ultrastructure of the cells of the mesophilic tissue of the cotyledonous leaf in irradiated cotton plants showed that the chloroplastide membranes are not damaged. A change in the form of the chloroplasts, an accumulation of starch and plastic substances in the chloroplasts, and a reduction in the number of inter-grain bonds were noted. It was discovered that gamma irradiation produces an excessive build-up of starch in the chloroplasts. The mitochondria are often located close to the plastides. The optical density is typical of the matrix of the mitochondria in non-irradiated plants. After cotton seeds that have sprouted are irradiated with a dose of 10 kR in the cotyledonous leaf phase, part of the mitochondria swells. The matrix becomes more transparent, and the number of chrysts decreases. Part of the mitochondria remains intact. The optical density and internal membranes of the mitochondria remain the same as in the control group. The disturbances of the chloroplast and the mitochondria are also observed in the budding and flowering phases (under conditions of a natural day). It was noted that a shortened day facilitated to some extent a normalization of metabolism, and this produced in turn a normal development of the chloroplasts, leaf mitochondria and ATF generation, which reduces the final biological effect of the radiation.

Regulation of chloroplast biogenesis: the immutans mutant of Arabidopsis

Energy Technology Data Exchange (ETDEWEB)

Rodermel, Steven

2015-11-16

The immutans (im) variegation mutant of Arabidopsis is an ideal model to gain insight into factors that control chloroplast biogenesis. im defines the gene for PTOX, a plastoquinol terminal oxidase that participates in control of thylakoid redox. Here, we report that the im defect can be suppressed during the late stages of plant development by gigantea (gi2), which defines the gene for GIGANTEA (GI), a central component of the circadian clock that plays a poorly-understood role in diverse plant developmental processes. imgi2 mutants are late-flowering and display other well-known phenotypes associated with gi2, such as starch accumulation and resistance to oxidative stress. We show that the restoration of chloroplast biogenesis in imgi2 is caused by a developmental-specific de-repression of cytokinin signaling that involves crosstalk with signaling pathways mediated by gibberellin (GA) and SPINDLY (SPY), a GA response inhibitor. Suppression of the plastid defect in imgi2 is likely caused by a relaxation of excitation pressures in developing plastids by factors contributed by gi2, including enhanced rates of photosynthesis and increased resistance to oxidative stress. Interestingly, the suppression phenotype of imgi can be mimicked by crossing im with the starch accumulation mutant, sex1, perhaps because sex1 utilizes pathways similar to gi. We conclude that our studies provide a direct genetic linkage between GIGANTEA and chloroplast biogenesis, and we construct a model of interactions between signaling pathways mediated by gi, GA, SPY, cytokinins, and sex1 that are required for chloroplast biogenesis.

Delaying chloroplast turnover increases water-deficit stress tolerance through the enhancement of nitrogen assimilation in rice.

Science.gov (United States)

Sade, Nir; Umnajkitikorn, Kamolchanok; Rubio Wilhelmi, Maria Del Mar; Wright, Matthew; Wang, Songhu; Blumwald, Eduardo

2018-02-12

Abiotic stress-induced senescence in crops is a process particularly affecting the photosynthetic apparatus, decreasing photosynthetic activity and inducing chloroplast degradation. A pathway for stress-induced chloroplast degradation that involves the CHLOROPLAST VESICULATION (CV) gene was characterized in rice (Oryza sativa) plants. OsCV expression was up-regulated with the age of the plants and when plants were exposed to water-deficit conditions. The down-regulation of OsCV expression contributed to the maintenance of the chloroplast integrity under stress. OsCV-silenced plants displayed enhanced source fitness (i.e. carbon and nitrogen assimilation) and photorespiration, leading to water-deficit stress tolerance. Co-immunoprecipitation, intracellular co-localization, and bimolecular fluorescence demonstrated the in vivo interaction between OsCV and chloroplastic glutamine synthetase (OsGS2), affecting source-sink relationships of the plants under stress. Our results would indicate that the OsCV-mediated chloroplast degradation pathway is involved in the regulation of nitrogen assimilation during stress-induced plant senescence. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Fibrillar organization in tendons: A pattern revealed by percolation characteristics of the respective geometric network

Directory of Open Access Journals (Sweden)

Daniel Andres Dos Santos

2014-06-01

Full Text Available Since the tendon is composed by collagen fibrils of various sizes connected between them through molecular cross-links, it sounds logical to model it via a heterogeneous network of fibrils. Using cross sectional images, that network is operatively inferred from the respective Gabriel graph of the fibril mass centers. We focus on network percolation characteristics under an ordered activation of fibrils (progressive recruitment going from the smallest to the largest fibril. Analyses of percolation were carried out on a repository of images of digital flexor tendons obtained from samples of lizards and frogs. Observed percolation thresholds were compared against values derived from hypothetical scenarios of random activation of nodes. Strikingly, we found a significant delay for the occurrence of percolation in actual data. We interpret this finding as the consequence of some non-random packing of fibrillar units into a size-constrained geometric pattern. We erect an ideal geometric model of balanced interspersion of polymorphic units that accounts for the delayed percolating instance. We also address the circumstance of being percolation curves mirrored by the empirical curves of stress-strain obtained from the same studied tendons. By virtue of this isomorphism, we hypothesize that the inflection points of both curves are different quantitative manifestations of a common transitional process during mechanical load transference.

Comparative proteomics of chloroplasts envelopes from bundle sheath and mesophyll chloroplasts reveals novel membrane proteins with a possible role in C4-related metabolite fluxes and development.

Directory of Open Access Journals (Sweden)

Kalpana eManandhar-Shrestha

2013-03-01

Full Text Available As the world population grows, our need for food increases drastically. Limited amounts of arable land lead to a competition between food and fuel crops, while changes in the global climate may impact future crop yields. Thus, a second green revolution will need a better understanding of the processes essential for plant growth and development. One approach toward the solution of this problem is to better understand regulatory and transport processes in C4 plants. C4 plants display an up to 10-fold higher apparent CO2 assimilation and higher yields while maintaining high water use efficiency. This requires differential regulation of mesophyll (M and bundle sheath (BS chloroplast development as well as higher metabolic fluxes of photosynthetic intermediates between cells and across chloroplast envelopes. While previous analyses of overall chloroplast membranes have yielded significant insight, our comparative proteomics approach using enriched BS and M chloroplast envelopes of Zea mays allowed us to identify 37 proteins of unknown function that have not been seen in these earlier studies. We identified 280 proteins, 84% of which are known/predicted to be present in chloroplasts (cp. 74% have a known or predicted membrane association. 21 membrane proteins were 2-15 times more abundant in BS cells, while 36 proteins were more abundant in M cp envelopes. These proteins could represent additional candidates of proteins essential for development or metabolite transport processes in C4 plants. RT-PCR confirmed differential expression of thirteen candidate genes. Cp association was confirmed using GFP labeling. Genes for a PIC-like protein and an ER-AP-like protein show an early transient increase in gene expression during the transition to light. In addition, PIC gene expression is increased in the immature part of the leaf and was lower in the fully developed parts of the leaf, suggesting a need for/incorporation of the protein during chloroplast

Generalized model for k -core percolation and interdependent networks

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Panduranga, Nagendra K.; Gao, Jianxi; Yuan, Xin; Stanley, H. Eugene; Havlin, Shlomo

2017-09-01

Cascading failures in complex systems have been studied extensively using two different models: k -core percolation and interdependent networks. We combine the two models into a general model, solve it analytically, and validate our theoretical results through extensive simulations. We also study the complete phase diagram of the percolation transition as we tune the average local k -core threshold and the coupling between networks. We find that the phase diagram of the combined processes is very rich and includes novel features that do not appear in the models studying each of the processes separately. For example, the phase diagram consists of first- and second-order transition regions separated by two tricritical lines that merge and enclose a two-stage transition region. In the two-stage transition, the size of the giant component undergoes a first-order jump at a certain occupation probability followed by a continuous second-order transition at a lower occupation probability. Furthermore, at certain fixed interdependencies, the percolation transition changes from first-order → second-order → two-stage → first-order as the k -core threshold is increased. The analytic equations describing the phase boundaries of the two-stage transition region are set up, and the critical exponents for each type of transition are derived analytically.

The KAC family of kinesin-like proteins is essential for the association of chloroplasts with the plasma membrane in land plants.

Science.gov (United States)

Suetsugu, Noriyuki; Sato, Yoshikatsu; Tsuboi, Hidenori; Kasahara, Masahiro; Imaizumi, Takato; Kagawa, Takatoshi; Hiwatashi, Yuji; Hasebe, Mitsuyasu; Wada, Masamitsu

2012-11-01

Chloroplasts require association with the plasma membrane for movement in response to light and for appropriate positioning within the cell to capture photosynthetic light efficiently. In Arabidopsis, CHLOROPLAST UNUSUAL POSITIONING 1 (CHUP1), KINESIN-LIKE PROTEIN FOR ACTIN-BASED CHLOROPLAST MOVEMENT 1 (KAC1) and KAC2 are required for both the proper movement of chloroplasts and the association of chloroplasts with the plasma membrane, through the reorganization of short actin filaments located on the periphery of the chloroplasts. Here, we show that KAC and CHUP1 orthologs (AcKAC1, AcCHUP1A and AcCHUP1B, and PpKAC1 and PpKAC2) play important roles in chloroplast positioning in the fern Adiantum capillus-veneris and the moss Physcomitrella patens. The knockdown of AcKAC1 and two AcCHUP1 genes induced the aggregation of chloroplasts around the nucleus. Analyses of A. capillus-veneris mutants containing perinuclear-aggregated chloroplasts confirmed that AcKAC1 is required for chloroplast-plasma membrane association. In addition, P. patens lines in which two KAC genes had been knocked out showed an aggregated chloroplast phenotype similar to that of the fern kac1 mutants. These results indicate that chloroplast positioning and movement are mediated through the activities of KAC and CHUP1 proteins, which are conserved in land plants.

Percolation picture of disintegration of nuclei in the proton-nucleus interaction

International Nuclear Information System (INIS)

Botvina, A.S.; Lanin, L.V.

1992-01-01

Breakup of nuclei into fragments in the proton-nucleus interaction is studied. It is assumed that breakup occurs in two stages. During the first stage the incident particle interacts with individual nucleons of the nucleus, and high-energy reaction products are emitted from the nucleus. This stage is described by means of the intranuclear-cascade model. During the second stage some of the nuclei, whose excitation energy is high, or whose density is very inhomogeneous, break up. This breakup is described by means of a percolation model which takes into account the spatial distribution of nucleons in the nucleus and which generalizes the percolation description of the 'liquid-gas' phase transition for finite nuclei. Features of this breakup mechanism are studied. The analysis of the experimental data indicates that it is not sufficient to consider percolation only in the coordinate space, and that the momentum distribution of the nucleons in the nucleus must be taken into account

Influence of the growth process on some laws deduced from percolation theory

International Nuclear Information System (INIS)

Hachi, M.; Olivier, G.

1985-09-01

A brutal application of the percolation theory to some physical problems can lead to erroneous interpretation of the experimental results. Among these problems, the influence of the growth process on the percolation laws is studied. The behaviour of nsub(s)(t), the number of clusters of size s, at time t, is analyzed and linked to a macroscopic property of the system for a comparison to experimental laws. (author)

Destruction of pigments and lipids in isolated chloroplasts under the effect of visible radiation

International Nuclear Information System (INIS)

Merzlyak, M.N.; Pogosyan, S.I.

1988-01-01

The results of experiments on the effect of light radiation on lipid and pigment destruction in isolated chloroplasts are generalized. Substrates and products of oxidation destruction of lipid and pigments, the role of photosynthetic electron transport in photodestruction, the participation of activated oxygen and free-radical intermediate forms in it are considered. The role of antioxidants, carotenoids and enzymatic systems in protection of chloroplast membranes from destructive light effect is discussed. A general scheme of possible ways of photodestruction in chloroplasts is presented. 53 refs

Enzyme-Triggered Defined Protein Nanoarrays: Efficient Light-Harvesting Systems to Mimic Chloroplasts.

Science.gov (United States)

Zhao, Linlu; Zou, Haoyang; Zhang, Hao; Sun, Hongcheng; Wang, Tingting; Pan, Tiezheng; Li, Xiumei; Bai, Yushi; Qiao, Shanpeng; Luo, Quan; Xu, Jiayun; Hou, Chunxi; Liu, Junqiu

2017-01-24

The elegance and efficiency by which chloroplasts harvest solar energy and conduct energy transfer have been a source of inspiration for chemists to mimic such process. However, precise manipulation to obtain orderly arranged antenna chromophores in constructing artificial chloroplast mimics was a great challenge, especially from the structural similarity and bioaffinity standpoints. Here we reported a design strategy that combined covalent and noncovalent interactions to prepare a protein-based light-harvesting system to mimic chloroplasts. Cricoid stable protein one (SP1) was utilized as a building block model. Under enzyme-triggered covalent protein assembly, mutant SP1 with tyrosine (Tyr) residues at the designated sites can couple together to form nanostructures. Through controlling the Tyr sites on the protein surface, we can manipulate the assembly orientation to respectively generate 1D nanotubes and 2D nanosheets. The excellent stability endowed the self-assembled protein architectures with promising applications. We further integrated quantum dots (QDs) possessing optical and electronic properties with the 2D nanosheets to fabricate chloroplast mimics. By attaching different sized QDs as donor and acceptor chromophores to the negatively charged surface of SP1-based protein nanosheets via electrostatic interactions, we successfully developed an artificial light-harvesting system. The assembled protein nanosheets structurally resembled the natural thylakoids, and the QDs can achieve pronounced FRET phenomenon just like the chlorophylls. Therefore, the coassembled system was meaningful to explore the photosynthetic process in vitro, as it was designed to mimic the natural chloroplast.

First-passage percolation on the random graph

NARCIS (Netherlands)

Hofstad, van der R.W.; Hooghiemstra, G.; Van Mieghem, P.

2001-01-01

We study first-passage percolation on the random graph Gp(N) with exponentially distributed weights on the links. For the special case of the complete graph, this problem can be described in terms of a continuous-time Markov chain and recursive trees. The Markov chain X(t) describes the number of

Production of biopharmaceuticals and vaccines in plants via the chloroplast genome.

Science.gov (United States)

Daniell, Henry

2006-10-01

Transgenic plants offer many advantages, including low cost of production (by elimination of fermenters), storage and transportation; heat stability; and absence of human pathogens. When therapeutic proteins are orally delivered, plant cells protect antigens in the stomach through bioencapsulation and eliminate the need for expensive purification and sterile injections, in addition to development of both systemic and mucosal immunity. Chloroplast genetic engineering offers several advantages, including high levels of transgene expression, transgene containment via maternal inheritance and multi-gene expression in a single transformation event. Hyper-expression of vaccine antigens against cholera, tetanus, anthrax, plague or canine parvovirus (4-31% of total soluble protein, tsp) in transgenic chloroplasts (leaves) or non-green plastids (carrots, tomato), as well as the availability of antibiotic-free selectable markers or the ability to excise selectable marker genes, facilitate oral delivery. Hyper-expression of several therapeutic proteins, including human serum albumin (11.1% tsp), somatotropin (7% tsp), interferon-gamma (6% tsp), anti-microbial peptide (21.5% tsp), facilitates efficient and economic purification. Also, the presence of chaperones and enzymes in chloroplasts facilitate assembly of complex multi-subunit proteins and correct folding of human blood proteins with proper disulfide bonds. Functionality of chloroplast-derived vaccine antigens and therapeutic proteins has been demonstrated by several assays, including the macrophage lysis assay, GM1-ganglioside binding assay, protection of HeLa cells or human lung carcinoma cells against encephalomyocarditis virus, systemic immune response, protection against pathogen challenge, and growth or inhibition of cell cultures. Thus, transgenic chloroplasts are ideal bioreactors for production of functional human and animal therapeutic proteins in an environmentally friendly manner.

A dynamic phase microscopic study of optical characteristics of individual chloroplasts.

Science.gov (United States)

Tychinsky, V P; Kretushev, A V; Vyshenskaya, T V; Tikhonov, A N

2004-10-11

Dynamic phase microscopy (DPM) allows the monitoring of optical path difference (or phase height), h(x,y,t) approximately integraln(x,y,z,t)dz, an integral refractive index projection of the medium, n(x,y,z,t), in optically transparent biological specimens at high spatial and temporal resolutions. In this study, DPM was used for the analysis of fluctuations in the optical characteristics of individual bean chloroplasts in various metabolic states. A "phase image" of an individual chloroplast, which represents a three-dimensional plot of the "phase height", was obtained for the first time, and the frequency spectra of the fluctuations of h(x,y,t) were investigated. The fluctuation patterns, i.e., the intensity and the frequency spectra of phase height fluctuations in bean chloroplasts (Class B) were found to depend on their metabolic state. Under conditions of noncyclic (or pseudocyclic) electron transport, the fluctuations displayed characteristic frequencies in the range of 0.25-0.6 Hz and were space-time-correlated in the chloroplast domains with the cross sizes of approximately 2 microm. The fluctuation intensity decreased in the presence of uncouplers (nigericin and valinomycin, 20 microM). A stronger (in comparison with 20 microM valinomycin) effect of 20 microM nigericin suggests that the light-induced generation of the transmembrane pH difference (DeltapH) makes the main contribution to the increment of space-correlated fluctuations of h(x,y,t). Studies of chloroplasts incubated in media of various osmolarity (50-500 mM sucrose) have shown that structural changes in thylakoids are among other factors responsible for phase height fluctuations.

Robust expression of a bioactive mammalian protein in chlamydomonas chloroplast

Science.gov (United States)

Mayfield, Stephen P.

2010-03-16

Methods and compositions are disclosed to engineer chloroplast comprising heterologous mammalian genes via a direct replacement of chloroplast Photosystem II (PSII) reaction center protein coding regions to achieve expression of recombinant protein above 5% of total protein. When algae is used, algal expressed protein is produced predominantly as a soluble protein where the functional activity of the peptide is intact. As the host algae is edible, production of biologics in this organism for oral delivery or proteins/peptides, especially gut active proteins, without purification is disclosed.

Observation of feature ripening inversion effect at the percolation threshold for the growth of thin silver films

Energy Technology Data Exchange (ETDEWEB)

Nehm, Frederik, E-mail: frederik.nehm@iapp.de; Schubert, Sylvio; Müller-Meskamp, Lars; Leo, Karl

2014-04-01

The growth behavior of thin silver films on organic layers is investigated during deposition by means of simultaneous in-situ monitoring of sheet resistance and transmittance. Thermally evaporated films up to 11 nm show a distinct percolation behavior with strong resistance drop at the percolation thickness. Additionally, evaporations are divided into a sequence of one nanometer steps. In the deposition breaks, the films exhibit a ripening effect with an inversion at the percolation thickness, by changing from an increasing to decreasing sheet resistance over time. Scanning electron micrographs suggest same ripening mechanisms for islands below the percolation thickness as for holes above. - Highlights: • Fundamental understanding of metal thin film growth is presented. • Optical and electrical in-situ measurements used for optimizing transparent electrodes • Stepwise Ag deposition reveals extraordinary ripening effects. • Feature ripening inversion is discovered at the percolation threshold.

Observation of feature ripening inversion effect at the percolation threshold for the growth of thin silver films

International Nuclear Information System (INIS)

Nehm, Frederik; Schubert, Sylvio; Müller-Meskamp, Lars; Leo, Karl

2014-01-01

The growth behavior of thin silver films on organic layers is investigated during deposition by means of simultaneous in-situ monitoring of sheet resistance and transmittance. Thermally evaporated films up to 11 nm show a distinct percolation behavior with strong resistance drop at the percolation thickness. Additionally, evaporations are divided into a sequence of one nanometer steps. In the deposition breaks, the films exhibit a ripening effect with an inversion at the percolation thickness, by changing from an increasing to decreasing sheet resistance over time. Scanning electron micrographs suggest same ripening mechanisms for islands below the percolation thickness as for holes above. - Highlights: • Fundamental understanding of metal thin film growth is presented. • Optical and electrical in-situ measurements used for optimizing transparent electrodes • Stepwise Ag deposition reveals extraordinary ripening effects. • Feature ripening inversion is discovered at the percolation threshold

Spin dynamics on percolating networks

International Nuclear Information System (INIS)

Aeppli, G.; Guggenheim, H.; Uemura, Y.J.

1985-01-01

We have used inelastic neutron scattering to measure the order parameter relaxation rate GAMMA in the dilute, two-dimensional Ising antiferromagnet Rb 2 CoMg/sub 1-c/F 4 with c very close to the magnetic percolation threshold. Where kappa is the inverse magnetic correlation length, GAMMA approx. kappa/sup z/ with z = 2.4/sub -0.1//sup +0.2/. Our results are discussed in terms of current ideas about spin relaxation on fractals. 13 refs., 1 fig

Fatty acid synthesis by spinach chloroplasts, 2. The path from PGA to fatty acids

Energy Technology Data Exchange (ETDEWEB)

Yamada, Mitsuhiro; Nakamura, Yasunori [Tokyo Univ. (Japan). Coll. of General Education

1975-02-01

By incorporation of /sup 3/H/sub 2/O into the fatty acid chain in the presence of unlabelled precursor, we showed that fatty acids are synthesized from PGA, PEP and pyruvate by intact spinach chloroplasts in the light. /sup 13/C-tracer experiments confirmed that 1-C of pyruvate is decarboxylated and 2-C is incorporated into fatty acids by the chloroplasts. The patterns of fatty acids synthesized from PGA and pyruvate were the same as that from acetate. The highest rate of fatty acid synthesis was reached at the physiological concentration of PGA (3 mM) and pyruvate (1 mM). These results indicate the operation of the following path in the chloroplasts in light: PGA..-->..PEP..-->..pyruvate..-->..acetylCoA..-->..fatty acids. Since citrate and OAA were much less active and malate and glyoxylate were inert as precursors for fatty acid synthesis, PEP or pyruvate carboxylation, citrate lyase reaction and malate synthetase reaction are not involved in the formation of acetylCoA and fatty acids. Since pyruvate was much more effective as a substrate for fatty acid synthesis than lactate, acetaldehyde or acetate, direct decarboxylation path is considered to be the primary path from pyruvate to acetylCoA. The insignificant effect of chloroplast-washing on fatty acid synthesis from PGA and pyruvate indicates that the glycolytic path from PGA to pyruvate is associated with the chloroplasts. Since pyruvate was more effectively incorporated into fatty acids than acetylCoA, it is unlikely that pyruvate decarboxylation to acetylCoA is due to mitochondria contaminating the chloroplast preparation. On the basis of measurements of /sup 3/H/sub 2/O incorporation in the light and dark, the activity of fatty acid synthesis in spincah leaves appears to be shared by the activities in chloroplasts (87%) and other organelles (13%).

Application of Percolation Theory to Complex Interconnected Networks in Advanced Functional Composites

Science.gov (United States)

Hing, P.

2011-11-01

Percolation theory deals with the behaviour of connected clusters in a system. Originally developed for studying the flow of liquid in a porous body, the percolation theory has been extended to quantum computation and communication, entanglement percolation in quantum networks, cosmology, chaotic situations, properties of disordered solids, pandemics, petroleum industry, finance, control of traffic and so on. In this paper, the application of various models of the percolation theory to predict and explain the properties of a specially developed family of dense sintered and highly refractory Al2O3-W composites for potential application in high intensity discharge light sources such as high pressure sodium lamps and ceramic metal halide lamps are presented and discussed. The low cost, core-shell concept can be extended to develop functional composite materials with unusual dielectric, electrical, magnetic, superconducting, and piezoelectric properties starting from a classical insulator. The core shell concept can also be applied to develop catalysts with high specific surface areas with minimal amount of expensive platinium, palladium or rare earth nano structured materials for light harvesting, replicating natural photosynthesis, in synthetic zeolite composites for the cracking and separation of crude oil. There is also possibility of developing micron and nanosize Faraday cages for quantum devices, nano electronics and spintronics. The possibilities are limitless.

Specific and efficient targeting of cyanobacterial bicarbonate transporters to the inner envelope membrane of chloroplasts in Arabidopsis

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Susumu eUehara

2016-02-01

Full Text Available Installation of cyanobacterial bicarbonate transporters to the inner envelope membrane (IEM of chloroplasts in C3 plants has been thought to improve photosynthetic performance. However, the method to deliver cyanobacterial bicarbonate transporters to the chloroplast IEM remains to be established. In this study, we provide evidence that the cyanobacterial bicarbonate transporters, BicA and SbtA, can be specifically installed into the chloroplast IEM using the chloroplast IEM targeting signal in conjunction with the transit peptide. We fused the transit peptide and the mature portion of Cor413im1, whose targeting mechanism to the IEM has been characterized in detail, to either BicA or SbtA isolated from Synechocystis sp. PCC6803. Among the seven chimeric constructs tested, we confirmed that four chimeric bicarbonate transporters, designated as BicAI, BicAII, SbtAII, and SbtAIII, were expressed in Arabidopsis. Furthermore, these chimeric transporters were specifically targeted to the chloroplast IEM. They were also resistant to alkaline extraction but can be solubilized by Triton X-100, indicating that they are integral membrane proteins in the chloroplast IEM. One of the transporters, BicA, could reside in the chloroplast IEM even after removal of the IEM targeting signal. Taken together, our results indicate that the addition of IEM targeting signal, as well as the transit peptide, to bicarbonate transporters allows us to efficiently target nuclear-encoded chimeric bicarbonate transporters to the chloroplast IEM.

Influence of fractal substructures of the percolating cluster on transferring processes in macroscopically disordered environments

Science.gov (United States)

Kolesnikov, B. P.

2017-11-01

The presented work belongs to the issue of searching for the effective kinetic properties of macroscopically disordered environments (MDE). These properties characterize MDE in general on the sizes which significantly exceed the sizes of macro inhomogeneity. The structure of MDE is considered as a complex of interpenetrating percolating and finite clusters consolidated from homonymous components, topological characteristics of which influence on the properties of the whole environment. The influence of percolating clusters’ fractal substructures (backbone, skeleton of backbone, red bonds) on the transfer processes during crossover (a structure transition from fractal to homogeneous condition) is investigated based on the offered mathematical approach for finding the effective conductivity of MDEs and on the percolating cluster model. The nature of the change of the critical conductivity index t during crossover from the characteristic value for the area close to percolation threshold to the value corresponded to homogeneous condition is demonstrated. The offered model describes the transfer processes in MDE with the finite conductivity relation of «conductive» and «low conductive» phases above and below percolation threshold and in smearing area (an analogue of a blur area of the second-order phase transfer).

Chloroplast-derived vaccine antigens and biopharmaceuticals: protocols for expression, purification, or oral delivery and functional evaluation.

Science.gov (United States)

Singh, N Dolendro; Ding, Yi; Daniell, Henry

2009-01-01

Many vaccine antigens and biopharmaceutical proteins have been expressed at high levels via the chloroplast genome and their functionality has been evaluated using in vitro assays in cell cultures (i.e., macrophage lysis assay, inhibition of vesicular stomatitis virus-induced cytopathicity in baby hamster kidney cells, or inhibition of human HIV infection in TZM-BL cells) as well as protection after challenge with bacterial or viral pathogens or antitumor assays or delay the onset of insulitis in suitable animal models. Production of therapeutic proteins in chloroplasts eliminates the expensive fermentation technology. Moreover, oral delivery of chloroplast-derived therapeutic proteins eliminates expensive purification steps, cold storage, cold transportation, and delivery via sterile needles, thereby further decreasing their cost. In this chapter, we describe detailed protocols for chloroplast transformation including the construction of chloroplast transformation vectors, delivery of DNA into plant cells using particle bombardment, selection and regeneration of transformants by tissue culture, confirmation of transgene integration into the chloroplast genome and homoplasmy, evaluation of foreign gene expression, purification of foreign protein, or oral delivery via bioencapsulation, functional evaluation using in vitro and in vivo assays, and evaluation of immunity after challenge with pathogens in suitable animal models.

The complete chloroplast genome of a medicinal plant Epimedium koreanum Nakai (Berberidaceae).

Science.gov (United States)

Lee, Jung-Hoon; Kim, Kyunghee; Kim, Na-Rae; Lee, Sang-Choon; Yang, Tae-Jin; Kim, Young-Dong

2016-11-01

Epimedium koreanum is a perennial medicinal plant distributed in Eastern Asia. The complete chloroplast genome sequences of E. koreanum was obtained by de novo assembly using whole genome next-generation sequences. The chloroplast genome of E. koreanum was 157 218 bp in length and separated into four distinct regions such as large single copy region (89 600 bp), small single copy region (17 222 bp) and a pair of inverted repeat regions (25 198 bp). The genome contained a total of 112 genes including 78 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Phylogenetic analysis with the reported chloroplast genomes revealed that E. koreanum is most closely related to Berberis bealei, a traditional medicinal plant in the Berberidaceae family.

Genetic polymorphism in Gymnodinium galatheanum chloroplast DNA sequences and development of a molecular detection assay.

Science.gov (United States)

Tengs, T; Bowers, H A; Ziman, A P; Stoecker, D K; Oldach, D W

2001-02-01

Nuclear and chloroplast-encoded small subunit ribosomal DNA sequences were obtained from several strains of the toxic dinoflagellate Gymnodinium galatheanum. Phylogenetic analyses and comparison of sequences indicate that the chloroplast sequences show a higher degree of sequence divergence than the nuclear homologue. The chloroplast sequences were chosen as targets for the development of a 5'--3' exonuclease assay for detection of the organism. The assay has a very high degree of specificity and has been used to screen environmental water samples from a fish farm where the presence of this dinoflagellate species has previously been associated with fish kills. Various hypotheses for the derived nature of the chloroplast sequences are discussed, as well as what is known about the toxicity of the species.

The action spectrum in chloroplast translocation in multilayer leaf cells

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Zbigniew Lechowski

2015-01-01

Full Text Available By measurement of light transmittance through a leaf as criterion of chloroplast translocation, the action spectrum of Ajuga reptans was established. In the spectrum obtained, a correction was introduced for leaf autoabsorption calculated on the basis of the Beer-Lambert law. The action spectrum has two maxima: at λ= 375 nm and λ= 481 nm. The range above 502 nm has no significant effect on chloroplast translocation. Comparison with other objects examined demonstrated that in multilayer leaf cells riboflavin seems also to be a photoreceptor active in this process.

Combined analysis of the chloroplast genome and transcriptome of the Antarctic vascular plant Deschampsia antarctica Desv.

Science.gov (United States)

Lee, Jungeun; Kang, Yoonjee; Shin, Seung Chul; Park, Hyun; Lee, Hyoungseok

2014-01-01

Antarctic hairgrass (Deschampsia antarctica Desv.) is the only natural grass species in the maritime Antarctic. It has been researched as an important ecological marker and as an extremophile plant for studies on stress tolerance. Despite its importance, little genomic information is available for D. antarctica. Here, we report the complete chloroplast genome, transcriptome profiles of the coding/noncoding genes, and the posttranscriptional processing by RNA editing in the chloroplast system. The complete chloroplast genome of D. antarctica is 135,362 bp in length with a typical quadripartite structure, including the large (LSC: 79,881 bp) and small (SSC: 12,519 bp) single-copy regions, separated by a pair of identical inverted repeats (IR: 21,481 bp). It contains 114 unique genes, including 81 unique protein-coding genes, 29 tRNA genes, and 4 rRNA genes. Sequence divergence analysis with other plastomes from the BEP clade of the grass family suggests a sister relationship between D. antarctica, Festuca arundinacea and Lolium perenne of the Poeae tribe, based on the whole plastome. In addition, we conducted high-resolution mapping of the chloroplast-derived transcripts. Thus, we created an expression profile for 81 protein-coding genes and identified ndhC, psbJ, rps19, psaJ, and psbA as the most highly expressed chloroplast genes. Small RNA-seq analysis identified 27 small noncoding RNAs of chloroplast origin that were preferentially located near the 5'- or 3'-ends of genes. We also found >30 RNA-editing sites in the D. antarctica chloroplast genome, with a dominance of C-to-U conversions. We assembled and characterized the complete chloroplast genome sequence of D. antarctica and investigated the features of the plastid transcriptome. These data may contribute to a better understanding of the evolution of D. antarctica within the Poaceae family for use in molecular phylogenetic studies and may also help researchers understand the characteristics of the chloroplast

The Central Limit Theorem for Supercritical Oriented Percolation in Two Dimensions

Science.gov (United States)

Tzioufas, Achillefs

2018-04-01

We consider the cardinality of supercritical oriented bond percolation in two dimensions. We show that, whenever the the origin is conditioned to percolate, the process appropriately normalized converges asymptotically in distribution to the standard normal law. This resolves a longstanding open problem pointed out to in several instances in the literature. The result applies also to the continuous-time analog of the process, viz. the basic one-dimensional contact process. We also derive general random-indices central limit theorems for associated random variables as byproducts of our proof.

Sequencing of chloroplast genome using whole cellular DNA and Solexa sequencing technology

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Jian eWu

2012-11-01

Full Text Available Sequencing of the chloroplast genome using traditional sequencing methods has been difficult because of its size (>120 kb and the complicated procedures required to prepare templates. To explore the feasibility of sequencing the chloroplast genome using DNA extracted from whole cells and Solexa sequencing technology, we sequenced whole cellular DNA isolated from leaves of three Brassica rapa accessions with one lane per accession. In total, 246 Mb, 362Mb, 361 Mb sequence data were generated for the three accessions Chiifu-401-42, Z16 and FT, respectively. Microreads were assembled by reference-guided assembly using the cpDNA sequences of B. rapa, Arabidopsis thaliana, and Nicotiana tabacum. We achieved coverage of more than 99.96% of the cp genome in the three tested accessions using the B. rapa sequence as the reference. When A. thaliana or N. tabacum sequences were used as references, 99.7–99.8% or 95.5–99.7% of the B. rapa chloroplast genome was covered, respectively. These results demonstrated that sequencing of whole cellular DNA isolated from young leaves using the Illumina Genome Analyzer is an efficient method for high-throughput sequencing of chloroplast genome.

Critical points for spread-out self-avoiding walk, percolation and the contact process above the upper critical dimensions

NARCIS (Netherlands)

Hofstad, van der R.W.; Sakai, A.

2005-01-01

We consider self-avoiding walk and percolation in d, oriented percolation in d×+, and the contact process in d, with p D(·) being the coupling function whose range is proportional to L. For percolation, for example, each bond is independently occupied with probability p D(y–x). The above models are

Genetic analysis of a Microseris douglasii (Asteraceae) population polymorphic for an alien chloroplast type

NARCIS (Netherlands)

Roelofs, Dick; Bachmann, Konrad

1997-01-01

Recent evidence suggests chloroplast introgression from Microseris bigelovii into M. douglasii. We have examined 23 plants from a population of M. douglasii polymorphic for M. douglasii and M. bigelovii chloroplast types. All 23 plants were completely homozygous for morphological and RAPD markers,

Longevity of guard cell chloroplasts in falling leaves: implication for stomatal function and cellular aging.

Science.gov (United States)

Zeiger, E; Schwartz, A

1982-11-12

Guard cell chloroplasts in senescing leaves from 12 species of perennial trees and three species of annual plants survived considerably longer than their mesophyll counterparts. In Ginkgo biloba, stomata from yellow leaves opened during the day and closed at night; guard cell chloroplasts from these leaves showed fluorescence transients associated with electron transport and photophosphorylation. These findings indicate that guard cell chloroplasts are highly conserved throughout the life-span of the leaf and that leaves retain stomatal control during senescence.

Emergent Percolation Length and Localization in Random Elastic Networks

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Ariel Amir

2013-06-01

Full Text Available We study, theoretically and numerically, a minimal model for phonons in a disordered system. For sufficient disorder, the vibrational modes of this classical system can become Anderson localized, yet this problem has received significantly less attention than its electronic counterpart. We find rich behavior in the localization properties of the phonons as a function of the density, frequency, and spatial dimension. We use a percolation analysis to argue for a Debye spectrum at low frequencies for dimensions higher than one, and for a localization-delocalization transition (at a critical frequency above two dimensions. We show that in contrast to the behavior in electronic systems, the transition exists for arbitrarily large disorder, albeit with an exponentially small critical frequency. The structure of the modes reflects a divergent percolation length that arises from the disorder in the springs without being explicitly present in the definition of our model. Within the percolation approach, we calculate the speed of sound of the delocalized modes (phonons, which we corroborate with numerics. We find the critical frequency of the localization transition at a given density and find good agreement of these predictions with numerical results using a recursive Green-function method that was adapted for this problem. The connection of our results to recent experiments on amorphous solids is discussed.

Percolation bounds for decoding thresholds with correlated erasures in quantum LDPC codes

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Hamilton, Kathleen; Pryadko, Leonid

Correlations between errors can dramatically affect decoding thresholds, in some cases eliminating the threshold altogether. We analyze the existence of a threshold for quantum low-density parity-check (LDPC) codes in the case of correlated erasures. When erasures are positively correlated, the corresponding multi-variate Bernoulli distribution can be modeled in terms of cluster errors, where qubits in clusters of various size can be marked all at once. In a code family with distance scaling as a power law of the code length, erasures can be always corrected below percolation on a qubit adjacency graph associated with the code. We bound this correlated percolation transition by weighted (uncorrelated) percolation on a specially constructed cluster connectivity graph, and apply our recent results to construct several bounds for the latter. This research was supported in part by the NSF Grant PHY-1416578 and by the ARO Grant W911NF-14-1-0272.

Release of proteins from intact chloroplasts induced by reactive oxygen species during biotic and abiotic stress.

Science.gov (United States)

Kwon, Kwang-Chul; Verma, Dheeraj; Jin, Shuangxia; Singh, Nameirakpam D; Daniell, Henry

2013-01-01

Plastids sustain life on this planet by providing food, feed, essential biomolecules and oxygen. Such diverse metabolic and biosynthetic functions require efficient communication between plastids and the nucleus. However, specific factors, especially large molecules, released from plastids that regulate nuclear genes have not yet been fully elucidated. When tobacco and lettuce transplastomic plants expressing GFP within chloroplasts, were challenged with Erwinia carotovora (biotic stress) or paraquat (abiotic stress), GFP was released into the cytoplasm. During this process GFP moves gradually towards the envelope, creating a central red zone of chlorophyll fluorescence. GFP was then gradually released from intact chloroplasts into the cytoplasm with an intact vacuole and no other visible cellular damage. Different stages of GFP release were observed inside the same cell with a few chloroplasts completely releasing GFP with detection of only red chlorophyll fluorescence or with no reduction in GFP fluorescence or transitional steps between these two phases. Time lapse imaging by confocal microscopy clearly identified sequence of these events. Intactness of chloroplasts during this process was evident from chlorophyll fluorescence emanated from thylakoid membranes and in vivo Chla fluorescence measurements (maximum quantum yield of photosystem II) made before or after infection with pathogens to evaluate their photosynthetic competence. Hydrogen peroxide and superoxide anion serve as signal molecules for generation of reactive oxygen species and Tiron, scavenger of superoxide anion, blocked release of GFP from chloroplasts. Significant increase in ion leakage in the presence of paraquat and light suggests changes in the chloroplast envelope to facilitate protein release. Release of GFP-RC101 (an antimicrobial peptide), which was triggered by Erwinia infection, ceased after conferring protection, further confirming this export phenomenon. These results suggest a

Release of proteins from intact chloroplasts induced by reactive oxygen species during biotic and abiotic stress.

Directory of Open Access Journals (Sweden)

Kwang-Chul Kwon

Full Text Available Plastids sustain life on this planet by providing food, feed, essential biomolecules and oxygen. Such diverse metabolic and biosynthetic functions require efficient communication between plastids and the nucleus. However, specific factors, especially large molecules, released from plastids that regulate nuclear genes have not yet been fully elucidated. When tobacco and lettuce transplastomic plants expressing GFP within chloroplasts, were challenged with Erwinia carotovora (biotic stress or paraquat (abiotic stress, GFP was released into the cytoplasm. During this process GFP moves gradually towards the envelope, creating a central red zone of chlorophyll fluorescence. GFP was then gradually released from intact chloroplasts into the cytoplasm with an intact vacuole and no other visible cellular damage. Different stages of GFP release were observed inside the same cell with a few chloroplasts completely releasing GFP with detection of only red chlorophyll fluorescence or with no reduction in GFP fluorescence or transitional steps between these two phases. Time lapse imaging by confocal microscopy clearly identified sequence of these events. Intactness of chloroplasts during this process was evident from chlorophyll fluorescence emanated from thylakoid membranes and in vivo Chla fluorescence measurements (maximum quantum yield of photosystem II made before or after infection with pathogens to evaluate their photosynthetic competence. Hydrogen peroxide and superoxide anion serve as signal molecules for generation of reactive oxygen species and Tiron, scavenger of superoxide anion, blocked release of GFP from chloroplasts. Significant increase in ion leakage in the presence of paraquat and light suggests changes in the chloroplast envelope to facilitate protein release. Release of GFP-RC101 (an antimicrobial peptide, which was triggered by Erwinia infection, ceased after conferring protection, further confirming this export phenomenon. These

Phaseolin expression in tobacco chloroplast reveals an autoregulatory mechanism in heterologous protein translation.

Science.gov (United States)

De Marchis, Francesca; Bellucci, Michele; Pompa, Andrea

2016-02-01

Plastid DNA engineering is a well-established research area of plant biotechnology, and plastid transgenes often give high expression levels. However, it is still almost impossible to predict the accumulation rate of heterologous protein in transplastomic plants, and there are many cases of unsuccessful transgene expression. Chloroplasts regulate their proteome at the post-transcriptional level, mainly through translation control. One of the mechanisms to modulate the translation has been described in plant chloroplasts for the chloroplast-encoded subunits of multiprotein complexes, and the autoregulation of the translation initiation of these subunits depends on the availability of their assembly partners [control by epistasy of synthesis (CES)]. In Chlamydomonas reinhardtii, autoregulation of endogenous proteins recruited in the assembly of functional complexes has also been reported. In this study, we revealed a self-regulation mechanism triggered by the accumulation of a soluble recombinant protein, phaseolin, in the stroma of chloroplast-transformed tobacco plants. Immunoblotting experiments showed that phaseolin could avoid this self-regulation mechanism when targeted to the thylakoids in transplastomic plants. To inhibit the thylakoid-targeted phaseolin translation as well, this protein was expressed in the presence of a nuclear version of the phaseolin gene with a transit peptide. Pulse-chase and polysome analysis revealed that phaseolin mRNA translation on plastid ribosomes was repressed due to the accumulation in the stroma of the same soluble polypeptide imported from the cytosol. We suggest that translation autoregulation in chloroplast is not limited to heteromeric protein subunits but also involves at least some of the foreign soluble recombinant proteins, leading to the inhibition of plastome-encoded transgene expression in chloroplast. © 2015 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

Confocal laser scanning microscopy detection of chlorophylls and carotenoids in chloroplasts and chromoplasts of tomato fruit.

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D'Andrea, Lucio; Amenós, Montse; Rodríguez-Concepción, Manuel

2014-01-01

Plant cells are unique among eukaryotic cells because of the presence of plastids, including chloroplasts and chromoplasts. Chloroplasts are found in green tissues and harbor the photosynthetic machinery (including chlorophyll molecules), while chromoplasts are present in non-photosynthetic tissues and accumulate large amounts of carotenoids. During tomato fruit development, chloroplasts are converted into chromoplasts that accumulate high levels of lycopene, a linear carotenoid responsible for the characteristic red color of ripe fruit. Here, we describe a simple and fast method to detect both types of fully differentiated plastids (chloroplasts and chromoplasts), as well as intermediate stages, in fresh tomato fruits. The method is based on the differential autofluorescence of chlorophylls and carotenoids (lycopene) detected by Confocal Laser Scanning Microscopy.

Density of phonon-fracton states of disordered solids in the vicinity of percolation phase transitions

International Nuclear Information System (INIS)

Korzhenevskii, A.L.; Luzhkov, A.A.

1991-01-01

The development of a theory of phase transitions in disordered materials is still one of the central problems in solid-state physics. The model of a percolation phase transition plays the same role among the models put forward to account for phase transitions in disordered media as does the Ising model for second-order phase transitions in ideal crystals. In addition to the clear picture of the processes occurring in the course of a percolation phase transition, a scaling theory has been developed and various techniques have been used to calculate the critical exponents describing the thermodynamics of a medium in the vicinity of the percolation threshold. The authors adopt a field-theoretic approach in a study of acoustic properties of disordered solids undergoing percolation phase transitions characterized by h ∼ 1. Among these transitions they concentrate on the case with the simplest type of striction interaction when the solution of a stochastic vector differential equation of motion describing the behavior of an elastic medium in the critical region can be reduced to a scalar equation. The results of their calculations by the field renormalization group method confirmed the existence of the scaling relationships between the critical exponents and also the conclusion on the nature of short- and long-wavelength vibrations near the percolation threshold, which follow from phenomenological considerations of the scaling theory. The values of the upper critical dimensionality and of the critical exponents of the problem are shown to differ from the values applicable to percolation phase transitions characterized by h much-lt 1

Complex dynamic behaviors of oriented percolation-based financial time series and Hang Seng index

International Nuclear Information System (INIS)

Niu, Hongli; Wang, Jun

2013-01-01

Highlights: • We develop a financial time series model by two-dimensional oriented percolation system. • We investigate the statistical behaviors of returns for HSI and the financial model by chaos-exploring methods. • We forecast the phase point of reconstructed phase space by RBF neural network. -- Abstract: We develop a financial price model by the two-dimensional oriented (directed) percolation system. The oriented percolation model is a directed variant of ordinary (isotropic) percolation, and it is applied to describe the fluctuations of stock prices. In this work, we assume that the price fluctuations result from the participants’ investment attitudes toward the market, and we investigate the information spreading among the traders and the corresponding effect on the price fluctuations. We study the complex dynamic behaviors of return time series of the model by using the multiaspect chaos-exploring methods. And we also explore the corresponding behaviors of the actual market index (Hang Seng Index) for comparison. Further, we introduce the radial basic function (RBF) neural network to train and forecast the phase point of reconstructed phase space

Electrical percolation threshold of magnetostrictive inclusions in a piezoelectric matrix composite as a function of relative particle size

Science.gov (United States)

Barbero, Ever J.; Bedard, Antoine Joseph

2018-04-01

Magnetoelectric composites can be produced by embedding magnetostrictive particles in a piezoelectric matrix derived from a piezoelectric powder precursor. Ferrite magnetostrictive particles, if allowed to percolate, can short the potential difference generated in the piezoelectric phase. Modeling a magnetoelectric composite as an aggregate of bi-disperse hard shells, molecular dynamics was used to explore relationships among relative particle size, particle affinity, and electrical percolation with the goal of maximizing the percolation threshold. It is found that two factors raise the percolation threshold, namely the relative size of magnetostrictive to piezoelectric particles, and the affinity between the magnetostrictive and piezoelectric particles.

Topological interlocking provides stiffness to stochastically micro-cracked materials beyond the transport percolation limit

Science.gov (United States)

Pal, Anirban; Picu, Catalin; Lupulescu, Marian V.

We study the mechanical behavior of two-dimensional, stochastically microcracked continua in the range of crack densities close to, and above the transport percolation threshold. We show that these materials retain stiffness up to crack densities much larger than the transport percolation threshold, due to topological interlocking of sample sub-domains. Even with a linear constitutive law for the continuum, the mechanical behavior becomes non-linear in the range of crack densities bounded by the transport and stiffness percolation thresholds. The effect is due to the fractal nature of the fragmentation process and is not linked to the roughness of individual cracks. We associate this behavior to that of itacolumite, a sandstone that exhibits unusual flexibility.

Directed polymers versus directed percolation

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Halpin-Healy, Timothy

1998-10-01

Universality plays a central role within the rubric of modern statistical mechanics, wherein an insightful continuum formulation rises above irrelevant microscopic details, capturing essential scaling behaviors. Nevertheless, occasions do arise where the lattice or another discrete aspect can constitute a formidable legacy. Directed polymers in random media, along with its close sibling, directed percolation, provide an intriguing case in point. Indeed, the deep blood relation between these two models may have sabotaged past efforts to fully characterize the Kardar-Parisi-Zhang universality class, to which the directed polymer belongs.

White Light Generation and Anisotropic Damage in Gold Films near Percolation Threshold

DEFF Research Database (Denmark)

Novikov, Sergey M.; Frydendahl, Christian; Beermann, Jonas

2017-01-01

in vanishingly small gaps between gold islands in thin films near the electrically determined percolation threshold. Optical explorations using two-photon luminescence (TPL) and near-field microscopies reveals supercubic TPL power dependencies with white-light spectra, establishing unequivocally...... that the strongest TPL signals are generated close to the percolation threshold films, and occurrence of extremely confined (similar to 30 nm) and strongly enhanced (similar to 100 times) fields at the illumination wavelength. For linearly polarized and sufficiently powerful light, we observe pronounced optical...

Experimental observation of percolation-enhanced nonlinear light scattering from semicontinuous metal films

Science.gov (United States)

Breit, M.; Podolskiy, V. A.; Grésillon, S.; von Plessen, G.; Feldmann, J.; Rivoal, J. C.; Gadenne, P.; Sarychev, Andrey K.; Shalaev, Vladimir M.

2001-09-01

Strongly enhanced second-harmonic generation (SHG), which is characterized by a nearly isotropic intensity distribution, is observed for gold-glass films near the percolation threshold. The diffuselike SHG scattering, which can be thought of as nonlinear critical opalescence, is in sharp contrast with highly collimated linear reflection and transmission from these nanostructured semicontinuous metal films. Our observations, which can be explained by giant fluctuations of local nonlinear sources for SHG due to plasmon localization, verify recent predictions of percolation-enhanced nonlinear scattering.

Weak link behaviour in YBa2Cu3O7-δ system studied by a site percolation model

International Nuclear Information System (INIS)

Arulgnanam, A.; Balasubramanian, A.

1992-01-01

The superconductivity in the YBaCuO system can be explained in terms of the superconducting percolation of 90 K orthorhombic microdomain. Kubo et al. have studied the percolation behaviour of the 123 system and estimated the total critical oxygen occupancy P c to be 0.75 for the orthorhombic I structure using at 150x180 lattice model. In this paper, we report our work on the percolative behaviour of the 123 system, using a Monte Carlo method. We have studied the effect on P c of increasing the lattice dimension up to 500x500. For P c ≤0.60 no percolative behaviour was observed, suggesting the tetragonal phase. Few times percolation was observed for 0.60≤P≤0.65 indicating the phase transformation from tetragonal to orthorhombic. For 0.65≤P≤0.77 (or 0.230≤δ≤0.35) weak percolative behaviour was observed suggesting the formation of orthorhombic II structure, which is in good agreement with the value observed by Cava et al. For 0.77≤P≤1.0 strong percolation was exhibited indicating the formation of orthorhombic I phase. We have explained the weak link region observed for 0.60≤P≤0.77. We estimated the total critical oxygen occupancy P c =0.766 for an orthorhombic I structure for the lattice. (orig.)

The novel chloroplast outer membrane kinase KOC1 is a required component of the plastid protein import machinery.

Science.gov (United States)

Zufferey, Mónica; Montandon, Cyrille; Douet, Véronique; Demarsy, Emilie; Agne, Birgit; Baginsky, Sacha; Kessler, Felix

2017-04-28

The biogenesis and maintenance of cell organelles such as mitochondria and chloroplasts require the import of many proteins from the cytosol, a process that is controlled by phosphorylation. In the case of chloroplasts, the import of hundreds of different proteins depends on translocons at the outer and inner chloroplast membrane (TOC and TIC, respectively) complexes. The essential protein TOC159 functions thereby as an import receptor. It has an N-terminal acidic (A-) domain that extends into the cytosol, controls receptor specificity, and is highly phosphorylated in vivo However, kinases that phosphorylate the TOC159 A-domain to enable protein import have remained elusive. Here, using co-purification with TOC159 from Arabidopsis , we discovered a novel component of the chloroplast import machinery, the regulatory kinase at the outer chloroplast membrane 1 (KOC1). We found that KOC1 is an integral membrane protein facing the cytosol and stably associates with TOC. Moreover, KOC1 phosphorylated the A-domain of TOC159 in vitro , and in mutant koc1 chloroplasts, preprotein import efficiency was diminished. koc1 Arabidopsis seedlings had reduced survival rates after transfer from the dark to the light in which protein import into plastids is required to rapidly complete chloroplast biogenesis. In summary, our data indicate that KOC1 is a functional component of the TOC machinery that phosphorylates import receptors, supports preprotein import, and contributes to efficient chloroplast biogenesis. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Optimization of flow modeling in fractured media with discrete fracture network via percolation theory

Science.gov (United States)

Donado-Garzon, L. D.; Pardo, Y.

2013-12-01

Fractured media are very heterogeneous systems where occur complex physical and chemical processes to model. One of the possible approaches to conceptualize this type of massifs is the Discrete Fracture Network (DFN). Donado et al., modeled flow and transport in a granitic batholith based on this approach and found good fitting with hydraulic and tracer tests, but the computational cost was excessive due to a gigantic amount of elements to model. We present in this work a methodology based on percolation theory for reducing the number of elements and in consequence, to reduce the bandwidth of the conductance matrix and the execution time of each network. DFN poses as an excellent representation of all the set of fractures of the media, but not all the fractures of the media are part of the conductive network. Percolation theory is used to identify which nodes or fractures are not conductive, based on the occupation probability or percolation threshold. In a fractured system, connectivity determines the flow pattern in the fractured rock mass. This volume of fluid is driven through connection paths formed by the fractures, when the permeability of the rock is negligible compared to the fractures. In a population of distributed fractures, each of this that has no intersection with any connected fracture do not contribute to generate a flow field. This algorithm also permits us to erase these elements however they are water conducting and hence, refine even more the backbone of the network. We used 100 different generations of DFN that were optimized in this study using percolation theory. In each of the networks calibrate hydrodynamic parameters as hydraulic conductivity and specific storage coefficient, for each of the five families of fractures, yielding a total of 10 parameters to estimate, at each generation. Since the effects of the distribution of fault orientation changes the value of the percolation threshold, but not the universal laws of classical

On Equivalence between Critical Probabilities of Dynamic Gossip Protocol and Static Site Percolation

Science.gov (United States)

Ishikawa, Tetsuya; Hayakawa, Tomohisa

The relationship between the critical probability of gossip protocol on the square lattice and the critical probability of site percolation on the square lattice is discussed. Specifically, these two critical probabilities are analytically shown to be equal to each other. Furthermore, we present a way of evaluating the critical probability of site percolation by approximating the saturation of gossip protocol. Finally, we provide numerical results which support the theoretical analysis.

Finite-Size Effects for Some Bootstrap Percolation Models

NARCIS (Netherlands)

Enter, A.C.D. van; Adler, Joan; Duarte, J.A.M.S.

The consequences of Schonmann's new proof that the critical threshold is unity for certain bootstrap percolation models are explored. It is shown that this proof provides an upper bound for the finite-size scaling in these systems. Comparison with data for one case demonstrates that this scaling

Comparative analysis of complete chloroplast genome sequence and inversion variation in Lasthenia burkei (Madieae, Asteraceae).

Science.gov (United States)

Walker, Joseph F; Zanis, Michael J; Emery, Nancy C

2014-04-01

Complete chloroplast genome studies can help resolve relationships among large, complex plant lineages such as Asteraceae. We present the first whole plastome from the Madieae tribe and compare its sequence variation to other chloroplast genomes in Asteraceae. We used high throughput sequencing to obtain the Lasthenia burkei chloroplast genome. We compared sequence structure and rates of molecular evolution in the small single copy (SSC), large single copy (LSC), and inverted repeat (IR) regions to those for eight Asteraceae accessions and one Solanaceae accession. The chloroplast sequence of L. burkei is 150 746 bp and contains 81 unique protein coding genes and 4 coding ribosomal RNA sequences. We identified three major inversions in the L. burkei chloroplast, all of which have been found in other Asteraceae lineages, and a previously unreported inversion in Lactuca sativa. Regions flanking inversions contained tRNA sequences, but did not have particularly high G + C content. Substitution rates varied among the SSC, LSC, and IR regions, and rates of evolution within each region varied among species. Some observed differences in rates of molecular evolution may be explained by the relative proportion of coding to noncoding sequence within regions. Rates of molecular evolution vary substantially within and among chloroplast genomes, and major inversion events may be promoted by the presence of tRNAs. Collectively, these results provide insight into different mechanisms that may promote intramolecular recombination and the inversion of large genomic regions in the plastome.

Electrical percolation in the presence of attractive interactions: An effective medium lattice approach applied to microemulsion systems

Science.gov (United States)

Hattori, Y.; Ushiki, H.; Engl, W.; Courbin, L.; Panizza, P.

2005-08-01

Within the framework of an effective medium approach and a mean-field approximation, we present a simple lattice model to treat electrical percolation in the presence of attractive interactions. We show that the percolation line depends on the magnitude of interactions. In 2 dimensions, the percolation line meets the binodal line at the critical point. A good qualitative agreement is observed with experimental results on a ternary AOT-based water-in-oil microemulsion system.

Is chloroplast import of photosynthesis proteins facilitated by an actin-TOC-TIC-VIPP1 complex?

Science.gov (United States)

Jouhet, Juliette; Gray, John C

2009-10-01

Actin filaments are major components of the cytoskeleton that interact with chloroplast envelope membranes to allow chloroplast positioning and movement, stromule mobility and gravitropism perception. We recently reported that Toc159, a component of the TOC complex of the chloroplast protein import apparatus, interacts directly with actin. The interaction of Toc159 and actin was identified by co-immunoprecipitation and co-sedimentation experiments with detergent-solubilised pea chloroplast envelope membranes. In addition, many of the components of the TOC-TIC protein import apparatus and VIPP1 (vesicle-inducing protein in plastids 1) were identified by mass spectroscopy in the material co-immunoprecipitated with antibodies to actin. Toc159 is the receptor for the import of photosynthesis proteins and VIPP1 is involved in thylakoid membrane formation by inducing vesicle formation from the chloroplast inner envelope membrane, suggesting we may have identified an actin-TOC-TIC-VIPP1 complex that may provide a means of channeling cytosolic preproteins to the thylakoid membrane. The interaction of Toc159 with actin may facilitate exchange between the putative soluble and membrane forms of Toc159 and promote the interaction of cytosolic preproteins with the TOC complex.

Percolation Diffusion into Self-Assembled Mesoporous Silica Microfibres

Directory of Open Access Journals (Sweden)

John Canning

2014-03-01

Full Text Available Percolation diffusion into long (11.5 cm self-assembled, ordered mesoporous microfibres is studied using optical transmission and laser ablation inductive coupled mass spectrometry (LA-ICP-MS. Optical transmission based diffusion studies reveal rapid penetration (<5 s, D > 80 μm2∙s−1 of Rhodamine B with very little percolation of larger molecules such as zinc tetraphenylporphyrin (ZnTPP observed under similar loading conditions. The failure of ZnTPP to enter the microfibre was confirmed, in higher resolution, using LA-ICP-MS. In the latter case, LA-ICP-MS was used to determine the diffusion of zinc acetate dihydrate, D~3 × 10−4 nm2∙s−1. The large differences between the molecules are accounted for by proposing ordered solvent and structure assisted accelerated diffusion of the Rhodamine B based on its hydrophilicity relative to the zinc compounds. The broader implications and applications for filtration, molecular sieves and a range of devices and uses are described.

Modeling Percolation in Polymer Nanocomposites by Stochastic Microstructuring

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Matias Soto

2015-09-01

Full Text Available A methodology was developed for the prediction of the electrical properties of carbon nanotube-polymer nanocomposites via Monte Carlo computational simulations. A two-dimensional microstructure that takes into account waviness, fiber length and diameter distributions is used as a representative volume element. Fiber interactions in the microstructure are identified and then modeled as an equivalent electrical circuit, assuming one-third metallic and two-thirds semiconductor nanotubes. Tunneling paths in the microstructure are also modeled as electrical resistors, and crossing fibers are accounted for by assuming a contact resistance associated with them. The equivalent resistor network is then converted into a set of linear equations using nodal voltage analysis, which is then solved by means of the Gauss–Jordan elimination method. Nodal voltages are obtained for the microstructure, from which the percolation probability, equivalent resistance and conductivity are calculated. Percolation probability curves and electrical conductivity values are compared to those found in the literature.

FtsZ-less prokaryotic cell division as well as FtsZ- and dynamin-less chloroplast and non-photosynthetic plastid division

Directory of Open Access Journals (Sweden)

Shin-Ya eMiyagishima

2014-09-01

Full Text Available The chloroplast division machinery is a mixture of a stromal FtsZ-based complex descended from a cyanobacterial ancestor of chloroplasts and a cytosolic dynamin-related protein (DRP 5B-based complex derived from the eukaryotic host. Molecular genetic studies have shown that each component of the division machinery is normally essential for normal chloroplast division. However, several exceptions have been found. In the absence of the FtsZ ring, nonphotosynthetic plastids are able to proliferate, likely by elongation and budding. Depletion of DRP5B impairs, but does not stop chloroplast division. Chloroplasts in glaucophytes, which possesses a peptidoglycan (PG layer, divide without DRP5B. Certain parasitic eukaryotes possess nonphotosynthetic plastids of secondary endosymbiotic origin, but neither FtsZ nor DRP5B is encoded in their genomes. Elucidation of the FtsZ- and/or DRP5B-less chloroplast division mechanism will lead to a better understanding of the function and evolution of the chloroplast division machinery and the finding of the as-yet-unknown mechanism that is likely involved in chloroplast division. Recent studies have shown that FtsZ was lost from a variety of prokaryotes, many of which lost PG by regressive evolution. In addition, even some of the FtsZ-bearing bacteria are able to divide when FtsZ and PG are depleted experimentally. In some cases, alternative mechanisms for cell division, such as budding by an increase of the cell surface-to-volume ratio, are proposed. Although PG is believed to have been lost from chloroplasts other than in glaucophytes, there is some indirect evidence for the existence of PG in chloroplasts. Such information is also useful for understanding how nonphotosynthetic plastids are able to divide in FtsZ-depleted cells and the reason for the retention of FtsZ in chloroplast division. Here we summarize information to facilitate analyses of FtsZ- and/or DRP5B-less chloroplast and nonphotosynthetic plastid

Quantitative characterization of the formation of an interpenetrating phase composite in polystyrene from the percolation of multiwalled carbon nanotubes

International Nuclear Information System (INIS)

Kota, Arun K; Cipriano, Bani H; Powell, Dan; Raghavan, Srinivasa R; Bruck, Hugh A

2007-01-01

For the first time, an interpenetrating phase polymer nanocomposite formed by the percolation of multiwalled carbon nanotubes (MWCNTs) in polystyrene (PS) has been quantitatively characterized through electrical conductivity measurements and melt rheology. Both sets of measurements, in conjunction with scanning electron microscopy (SEM) images, indicate the presence of a continuous phase of percolated MWCNTs appearing at particle concentrations exceeding 2 vol% MWCNTs in PS. To quantify the amount of this continuous phase present in the PS/MWCNT composite, electrical conductivity data at various MWCNT concentrations, β, are correlated with a proposed degree of percolation, C-bar(β), developed using a conventional power-law formula with and without a percolation threshold. To quantify the properties of the interpenetrating phase polymer nanocomposite, the PS/MWCNT composite is treated as a combination of two phases: a continuous phase consisting of a pseudo-solid-like network of percolated MWCNTs, and a continuous PS phase reinforced by non-interacting MWCNTs. The proposed degree of percolation is used to quantify the distribution of MWCNTs among the phases, and is then used in a rule-of-mixtures formulation for the storage modulus, G'(β, C-bar(β), ω), and the loss modulus, G''(β, C-bar(β), ω), to quantify the properties of the continuous phase consisting of percolated MWCNTs and the continuous PS phase reinforced by non-interacting MWCNTs from the experimental melt rheology data. The properties of the continuous phase of percolated MWCNTs are indicative of a scaffold-like microstructure exhibiting an elastic behavior with a complex modulus of 360 kPa at lower frequencies and viscoplastic behavior with a complex viscosity of 6 kPa s rad -1 at higher frequencies, most likely due to a stick-slip friction mechanism at the interface of the percolated MWCNTs. Additional evidence of this microstructure was obtained via scanning electron microscopy. This research

Biparental chloroplast inheritance leads to rescue from cytonuclear incompatibility.

Science.gov (United States)

Barnard-Kubow, Karen B; McCoy, Morgan A; Galloway, Laura F

2017-02-01

Although organelle inheritance is predominantly maternal across animals and plants, biparental chloroplast inheritance has arisen multiple times in the angiosperms. Biparental inheritance has the potential to impact the evolutionary dynamics of cytonuclear incompatibility, interactions between nuclear and organelle genomes that are proposed to be among the earliest types of genetic incompatibility to arise in speciation. We examine the interplay between biparental inheritance and cytonuclear incompatibility in Campanulastrum americanum, a plant species exhibiting both traits. We first determine patterns of chloroplast inheritance in genetically similar and divergent crosses, and then associate inheritance with hybrid survival across multiple generations. There is substantial biparental inheritance in C. americanum. The frequency of biparental inheritance is greater in divergent crosses and in the presence of cytonuclear incompatibility. Biparental inheritance helps to mitigate cytonuclear incompatibility, leading to increased fitness of F 1 hybrids and recovery in the F 2 generation. This study demonstrates the potential for biparental chloroplast inheritance to rescue cytonuclear compatibility, reducing cytonuclear incompatibility's contribution to reproductive isolation and potentially slowing speciation. The efficacy of rescue depended upon the strength of incompatibility, with a greater persistence of weak incompatibilities in later generations. These findings suggest that incompatible plastids may lead to selection for biparental inheritance. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Electrical percolation, morphological and dispersion properties of MWCNT/PMMA nanocomposites

Energy Technology Data Exchange (ETDEWEB)

Coelho, Paulo Henrique da Silva Leite; Marchesin, Marcel Silva; Morales, Ana Rita; Bartoli, Julio Roberto, E-mail: piyke.coelho@gmail.com [Universidade de Campinas (UNICAMP), SP (Brazil). Escola de Engenharia Quimica

2014-08-15

Nanocomposites of poly (methyl methacrylate) (PMMA) and carbon nanotubes have a high potential for applications where conductivity and low specific weight are required. This piece of work concerns investigations of the level of dispersion and morphology on the electrical properties of in situ polymerized nanocomposites in different concentrations of multi-walled carbon nanotubes (MWCNT) in a PMMA matrix. The electrical conductivity was measured by the four point probe. The morphology and dispersion was analyzed by Transmission Electron Microscopy (TEM) and Small Angle X-ray Scattering (SAXS). The correlation between electrical conductivity and the MWCNT amount, presented a typical percolation behavior, whose electrical percolation threshold determined by power law relationship was 0.2 vol. (%) The exponent t from the percolation power law indicated the formation of a 3D network of randomly arranged MWCNT. SAXS detected that the structures are intermediate to disks or spheres indicating fractal geometry for the MWCNT aggregates instead of isolated rods. HR-TEM images allowed us to observe the MWCNT individually dispersed into the matrix, revealing their distribution without preferential space orientation and absence of significant damage to the walls. The combined results of SAXS and HR-TEM suggest that MWCNT into the polymeric matrix might present interconnected aggregates and some dispersed single structures. (author)

Electrical percolation, morphological and dispersion properties of MWCNT/PMMA nanocomposites

International Nuclear Information System (INIS)

Coelho, Paulo Henrique da Silva Leite; Marchesin, Marcel Silva; Morales, Ana Rita; Bartoli, Julio Roberto

2014-01-01

Nanocomposites of poly (methyl methacrylate) (PMMA) and carbon nanotubes have a high potential for applications where conductivity and low specific weight are required. This piece of work concerns investigations of the level of dispersion and morphology on the electrical properties of in situ polymerized nanocomposites in different concentrations of multi-walled carbon nanotubes (MWCNT) in a PMMA matrix. The electrical conductivity was measured by the four point probe. The morphology and dispersion was analyzed by Transmission Electron Microscopy (TEM) and Small Angle X-ray Scattering (SAXS). The correlation between electrical conductivity and the MWCNT amount, presented a typical percolation behavior, whose electrical percolation threshold determined by power law relationship was 0.2 vol. (%) The exponent t from the percolation power law indicated the formation of a 3D network of randomly arranged MWCNT. SAXS detected that the structures are intermediate to disks or spheres indicating fractal geometry for the MWCNT aggregates instead of isolated rods. HR-TEM images allowed us to observe the MWCNT individually dispersed into the matrix, revealing their distribution without preferential space orientation and absence of significant damage to the walls. The combined results of SAXS and HR-TEM suggest that MWCNT into the polymeric matrix might present interconnected aggregates and some dispersed single structures. (author)

Transcriptome and proteomic analyses reveal multiple differences associated with chloroplast development in the spaceflight-induced wheat albino mutant mta.

Directory of Open Access Journals (Sweden)

Kui Shi

Full Text Available Chloroplast development is an integral part of plant survival and growth, and occurs in parallel with chlorophyll biosynthesis. However, little is known about the mechanisms underlying chloroplast development in hexaploid wheat. Here, we obtained a spaceflight-induced wheat albino mutant mta. Chloroplast ultra-structural observation showed that chloroplasts of mta exhibit abnormal morphology and distribution compared to wild type. Photosynthetic pigments content was also significantly decreased in mta. Transcriptome and chloroplast proteome profiling of mta and wild type were done to identify differentially expressed genes (DEGs and proteins (DEPs, respectively. In total 4,588 DEGs including 1,980 up- and 2,608 down-regulated, and 48 chloroplast DEPs including 15 up- and 33 down-regulated were identified in mta. Classification of DEGs revealed that most were involved in chloroplast development, chlorophyll biosynthesis, or photosynthesis. Besides, transcription factors such as PIF3, GLK and MYB which might participate in those pathways were also identified. The correlation analysis between DEGs and DEPs revealed that the transcript-to-protein in abundance was functioned into photosynthesis and chloroplast relevant groups. Real time qPCR analysis validated that the expression level of genes encoding photosynthetic proteins was significantly decreased in mta. Together, our results suggest that the molecular mechanism for albino leaf color formation in mta is a thoroughly regulated and complicated process. The combined analysis of transcriptome and proteome afford comprehensive information for further research on chloroplast development mechanism in wheat. And spaceflight provides a potential means for mutagenesis in crop breeding.

Chloroplast-derived vaccine antigens confer dual immunity against cholera and malaria by oral or injectable delivery.

Science.gov (United States)

Davoodi-Semiromi, Abdoreza; Schreiber, Melissa; Nalapalli, Samson; Verma, Dheeraj; Singh, Nameirakpam D; Banks, Robert K; Chakrabarti, Debopam; Daniell, Henry

2010-02-01

Cholera and malaria are major diseases causing high mortality. The only licensed cholera vaccine is expensive; immunity is lost in children within 3 years and adults are not fully protected. No vaccine is yet available for malaria. Therefore, in this study, the cholera toxin-B subunit (CTB) of Vibrio cholerae fused to malarial vaccine antigens apical membrane antigen-1 (AMA1) and merozoite surface protein-1 (MSP1) was expressed in lettuce and tobacco chloroplasts. Southern blot analysis confirmed homoplasmy and stable integration of transgenes. CTB-AMA1 and CTB-MSP1 fusion proteins accumulated up to 13.17% and 10.11% (total soluble protein, TSP) in tobacco and up to 7.3% and 6.1% (TSP) in lettuce, respectively. Nine groups of mice (n = 10/group) were immunized subcutaneously (SQV) or orally (ORV) with purified antigens or transplastomic tobacco leaves. Significant levels of antigen-specific antibody titres of immunized mice completely inhibited proliferation of the malarial parasite and cross-reacted with the native parasite proteins in immunoblots and immunofluorescence studies. Protection against cholera toxin challenge in both ORV (100%) and SQV (89%) mice correlated with CTB-specific titres of intestinal, serum IgA and IgG1 in ORV and only IgG1 in SQV mice, but no other immunoglobulin. Increasing numbers of interleukin-10(+) T cell but not Foxp3(+) regulatory T cells, suppression of interferon-gamma and absence of interleukin-17 were observed in protected mice, suggesting that immunity is conferred via the Tr1/Th2 immune response. Dual immunity against two major infectious diseases provided by chloroplast-derived vaccine antigens for long-term (>300 days, 50% of mouse life span) offers a realistic platform for low cost vaccines and insight into mucosal and systemic immunity.

Electrical and percolative behavior of Sr2YSbO6-YBa2Cu3O7-δ composites

International Nuclear Information System (INIS)

Ortiz-Diaz, O.; Landinez Tellez, D.A.; Perez, F.; Tovar, H.; Roa-Rojas, J.

2007-01-01

We found that a mixture of materials Sr 2 YSbO 6 insulator with YBa 2 Cu 3 O 7-δ superconductor is a system where the particles of superconductor and insulator materials are found coexisting in a composite with two well-defined separate phases. Electrical transport properties and percolation behavior have been studied by electrical resistivity measurements at room temperature on several samples of composites with different vol.% of YBa 2 Cu 3 O 7-δ . Resistivity measurements agree with the equation which describes the conductivity in percolation theory. However, critical exponent t=6.65 is greater than universal value t∼2. Furthermore, there is a non-negligible conductivity below percolation threshold while it is expected to be zero in ideal percolative systems. Nevertheless, percolative behavior in this region was found and, critical exponent value s was determined to be s=0.75 in agreement with universal value

Separation of Chloroplast Pigments Using Reverse Phase Chromatography.

Science.gov (United States)

Reese, R. Neil

1997-01-01

Presents a protocol that uses reverse phase chromatography for the separation of chloroplast pigments. Provides a simple and relatively safe procedure for use in teaching laboratories. Discusses pigment extraction, chromatography, results, and advantages of the process. (JRH)

A nonsteady-state firn-densification model for the percolation zone of a glacier

DEFF Research Database (Denmark)

Reeh, Niels

2008-01-01

A simple steady state firn-densification model is modified to account for short-term time variations of accumulation rate and surface temperature. The temporal surface-elevation- and mass changes at two sites in the percolation zone of an ice sheet in response to various climate histories...... are determined. It is shown that a straight-forward translation of observed short-term ice-sheet surface-elevation variations into mass changes may be completely misleading, particularly for the percolation zone of the ice sheet, where temperature driven variations of melting/re-freezing rates have a strong...... impact on near surface density. In the lower percolation zone, the mass change associated with a temperature anomaly in respect to the mean climate may for example amount to as little as 10 percent of the observed, simultaneous surface elevation change. Moreover, significant surface elevation change may...

Photosynthesis-dependent H2O2 transfer from chloroplasts to nuclei provides a high-light signalling mechanism.

Science.gov (United States)

Exposito-Rodriguez, Marino; Laissue, Pierre Philippe; Yvon-Durocher, Gabriel; Smirnoff, Nicholas; Mullineaux, Philip M

2017-06-29

Chloroplasts communicate information by signalling to nuclei during acclimation to fluctuating light. Several potential operating signals originating from chloroplasts have been proposed, but none have been shown to move to nuclei to modulate gene expression. One proposed signal is hydrogen peroxide (H 2 O 2 ) produced by chloroplasts in a light-dependent manner. Using HyPer2, a genetically encoded fluorescent H 2 O 2 sensor, we show that in photosynthetic Nicotiana benthamiana epidermal cells, exposure to high light increases H 2 O 2 production in chloroplast stroma, cytosol and nuclei. Critically, over-expression of stromal ascorbate peroxidase (H 2 O 2 scavenger) or treatment with DCMU (photosynthesis inhibitor) attenuates nuclear H 2 O 2 accumulation and high light-responsive gene expression. Cytosolic ascorbate peroxidase over-expression has little effect on nuclear H 2 O 2 accumulation and high light-responsive gene expression. This is because the H 2 O 2 derives from a sub-population of chloroplasts closely associated with nuclei. Therefore, direct H 2 O 2 transfer from chloroplasts to nuclei, avoiding the cytosol, enables photosynthetic control over gene expression.Multiple plastid-derived signals have been proposed but not shown to move to the nucleus to promote plant acclimation to fluctuating light. Here the authors use a fluorescent hydrogen peroxide sensor to provide evidence that H 2 O 2 is transferred directly from chloroplasts to nuclei to control nuclear gene expression.

Overoxidation of chloroplast 2-Cys peroxiredoxins: balancing toxic and signaling activities of hydrogen peroxide

Directory of Open Access Journals (Sweden)

Leonor ePuerto-Galán

2013-08-01

Full Text Available Photosynthesis, the primary source of biomass and oxygen into the biosphere, involves the transport of electrons in the presence of oxygen and, therefore, chloroplasts constitute an important source of reactive oxygen species (ROS, including hydrogen peroxide. If accumulated at high level, hydrogen peroxide may exert a toxic effect; however, it is as well an important second messenger. In order to balance the toxic and signaling activities of hydrogen peroxide its level has to be tightly controlled. To this end, chloroplasts are equipped with different antioxidant systems such as 2-Cys peroxiredoxins (2-Cys Prxs, thiol-based peroxidases able to reduce hydrogen- and organic peroxides. At high peroxide concentrations the peroxidase function of 2-Cys Prxs may become inactivated through a process of overoxidation. This inactivation has been proposed to explain the signaling function of hydrogen peroxide in eukaryotes, whereas in prokaryotes, the 2-Cys Prxs of which were considered to be insensitive to overoxidation, the signaling activity of hydrogen peroxide is less relevant. Here we discuss the current knowledge about the mechanisms controlling 2-Cys Prx overoxidation in chloroplasts, organelles with an important signaling function in plants. Given the prokaryotic origin of chloroplasts, we discuss the occurrence of 2-Cys Prx overoxidation in cyanobacteria with the aim of identifying similarities between chloroplasts and their ancestors regarding their response to hydrogen peroxide.

Fast and Accurate Protein False Discovery Rates on Large-Scale Proteomics Data Sets with Percolator 3.0

Science.gov (United States)

The, Matthew; MacCoss, Michael J.; Noble, William S.; Käll, Lukas

2016-11-01

Percolator is a widely used software tool that increases yield in shotgun proteomics experiments and assigns reliable statistical confidence measures, such as q values and posterior error probabilities, to peptides and peptide-spectrum matches (PSMs) from such experiments. Percolator's processing speed has been sufficient for typical data sets consisting of hundreds of thousands of PSMs. With our new scalable approach, we can now also analyze millions of PSMs in a matter of minutes on a commodity computer. Furthermore, with the increasing awareness for the need for reliable statistics on the protein level, we compared several easy-to-understand protein inference methods and implemented the best-performing method—grouping proteins by their corresponding sets of theoretical peptides and then considering only the best-scoring peptide for each protein—in the Percolator package. We used Percolator 3.0 to analyze the data from a recent study of the draft human proteome containing 25 million spectra (PM:24870542). The source code and Ubuntu, Windows, MacOS, and Fedora binary packages are available from http://percolator.ms/ under an Apache 2.0 license.

Purifying hydrocarbons

Energy Technology Data Exchange (ETDEWEB)

Dunstan, A E

1918-06-03

Ligroin, kerosene, and other distillates from petroleum and shale oil, are purified by treatment with a solution of a hypochlorite containing an excess of alkali. The hydrocarbon may be poured into brine, the mixture stirred, and an electric current passed through. Heat may be applied.

Effect of micellar collisions and polyvinylpyrrolidone confinement on the electrical conductivity percolation parameters of water/AOT/isooctane reverse micelles

Science.gov (United States)

Guettari, Moez; Aferni, Ahmed E. L.; Tajouri, Tahar

2017-12-01

The main aim of this paper is the analysis of micellar collisions and polymer confinement effects on the electrical conductivity percolative behavior of water/sodium bis(2-ethylhexyl) sulfosuccinate (AOT)/isooctane reverse micelles. Firstly, we have performed conductance measurements of the system for three AOT to isooctane volume ratio, φm = 0.1 , 0.15 and 0.2 to examine the influence of micellar collisions on the percolation parameters. All the measurements were carried out over the 298.15 K-333.15 K temperature range at a fixed water to AOT molar ratio, W0 = 45 . We have assessed that the rise of micellar collisions frequency enhances the conductance percolation. Secondly, the confinement effect of a water-soluble polymer, polyvinylpyrrolidone (PVP), on the reverse micelles conductance behavior was investigated. Temperature-induced percolation, Tp , have shown a dependence on the polymer concentration, CPVP . It was also observed that for various PVP concentrations, the activation energy of percolation decreases. Finally, the values of the critical exponents determined in the presence and absence of PVP prove that the polymer affects the dynamic of percolation.

Nano-scale characterization of the dynamics of the chloroplast Toc translocon.

Science.gov (United States)

Reddick, L Evan; Chotewutmontri, Prakitchai; Crenshaw, Will; Dave, Ashita; Vaughn, Michael; Bruce, Barry D

2008-01-01

Translocons are macromolecular nano-scale machines that facilitate the selective translocation of proteins across membranes. Although common in function, different translocons have evolved diverse molecular mechanisms for protein translocation. Subcellular organelles of endosymbiotic origin such as the chloroplast and mitochondria had to evolve/acquire translocons capable of importing proteins whose genes were transferred to the host genome. These gene products are expressed on cytosolic ribosomes as precursor proteins and targeted back to the organelle by an N-terminal extension called the transit peptide or presequence. In chloroplasts the transit peptide is specifically recognized by the Translocon of the Outer Chloroplast membrane (Toc) which is composed of receptor GTPases that potentially function as gate-like switches, where GTP binding and hydrolysis somehow facilitate preprotein binding and translocation. Compared to other translocons, the dynamics of the Toc translocon are probably more complex and certainly less understood. We have developed biochemical/biophysical, imaging, and computational techniques to probe the dynamics of the Toc translocon at the nanoscale. In this chapter we provide detailed protocols for kinetic and binding analysis of precursor interactions in organeller, measurement of the activity and nucleotide binding of the Toc GTPases, native electrophoretic analysis of the assembly/organization of the Toc complex, visualization of the distribution and mobility of Toc apparatus on the surface of chloroplasts, and conclude with the identification and molecular modeling Toc75 POTRA domains. With these new methodologies we discuss future directions of the field.

Polyuridylylation and processing of transcripts from multiple gene minicircles in chloroplasts of the dinoflagellate Amphidinium carterae

KAUST Repository

Barbrook, Adrian C.; Dorrell, Richard G.; Burrows, Jennifer; Plenderleith, Lindsey J.; Nisbet, R. Ellen R.; Howe, Christopher J.

2012-01-01

-PCR to study transcription and transcript processing in the chloroplasts of Amphidinium carterae, a model peridinin-containing dinoflagellate. These organisms have a highly unusual chloroplast genome, with genes located on multiple small 'minicircle' elements

Large Dielectric Constant Enhancement in MXene Percolative Polymer Composites

KAUST Repository

Tu, Shao Bo; Jiang, Qiu; Zhang, Xixiang; Alshareef, Husam N.

2018-01-01

near the percolation limit of about 15.0 wt % MXene loading, which surpasses all previously reported composites made of carbon-based fillers in the same polymer. With up to 10 wt % MXene loading, the dielectric loss of the MXene

Pentacene field-effect transistors by in situ and real time electrical characterization: Comparison between purified and non-purified thin films

International Nuclear Information System (INIS)

Liu, Shun-Wei; Wen, Je-Min; Lee, Chih-Chien; Su, Wei-Cheng; Wang, Wei-Lun; Chen, Ho-Chien; Lin, Chun-Feng

2013-01-01

We present an electrical characterization of the organic field-effect transistor with purified and non-purified pentacene by using in situ and real time measurements. The field-effect phenomenon was observed at the thickness of 1.5 nm (approximately one monolayer of pentacene) for purified pentacene, as compared to 3.0 nm for the non-purified counterpart. Moreover, the hole mobility is improved from 0.13 to 0.23 cm 2 /V s after the sublimation process to purify the pentacene. With atomic force microscopic measurements, the purified pentacene thin film exhibits a larger grain size and film coverage, resulting in better crystallinity of the thin film structure due to the absence of the impurities. This is further confirmed by X-ray diffraction patterns, which show higher intensities for the purified pentacene. - Highlights: • We present in-situ characterization for pentacene field-effect transistors. • The hole mobility is improved after the sublimation process to purify the pentacene. • Purified pentacene thin film exhibits a larger grain size and film coverage. • Hole mobility of pentacene is improved from 0.13 to 0.23 cm 2 /V s. • The discontinuity of grain boundary may cause the shift of threshold voltage

Pentacene field-effect transistors by in situ and real time electrical characterization: Comparison between purified and non-purified thin films

Energy Technology Data Exchange (ETDEWEB)

Liu, Shun-Wei, E-mail: swliu@mail.mcut.edu.tw [Department of Electronic Engineering, Ming Chi University of Technology, New Taipei City 24301, Taiwan, ROC (China); Wen, Je-Min; Lee, Chih-Chien; Su, Wei-Cheng; Wang, Wei-Lun; Chen, Ho-Chien [Department of Electronic Engineering, National Taiwan University of Science and Technology, Taipei, 10607 Taiwan, ROC (China); Lin, Chun-Feng [Department of Electronic Engineering, Ming Chi University of Technology, New Taipei City 24301, Taiwan, ROC (China)

2013-05-01

We present an electrical characterization of the organic field-effect transistor with purified and non-purified pentacene by using in situ and real time measurements. The field-effect phenomenon was observed at the thickness of 1.5 nm (approximately one monolayer of pentacene) for purified pentacene, as compared to 3.0 nm for the non-purified counterpart. Moreover, the hole mobility is improved from 0.13 to 0.23 cm{sup 2}/V s after the sublimation process to purify the pentacene. With atomic force microscopic measurements, the purified pentacene thin film exhibits a larger grain size and film coverage, resulting in better crystallinity of the thin film structure due to the absence of the impurities. This is further confirmed by X-ray diffraction patterns, which show higher intensities for the purified pentacene. - Highlights: • We present in-situ characterization for pentacene field-effect transistors. • The hole mobility is improved after the sublimation process to purify the pentacene. • Purified pentacene thin film exhibits a larger grain size and film coverage. • Hole mobility of pentacene is improved from 0.13 to 0.23 cm{sup 2}/V s. • The discontinuity of grain boundary may cause the shift of threshold voltage.

The complete chloroplast genome sequence of Helwingia himalaica (Helwingiaceae, Aquifoliales) and a chloroplast phylogenomic analysis of the Campanulidae.

Science.gov (United States)

Yao, Xin; Liu, Ying-Ying; Tan, Yun-Hong; Song, Yu; Corlett, Richard T

2016-01-01

Complete chloroplast genome sequences have been very useful for understanding phylogenetic relationships in angiosperms at the family level and above, but there are currently large gaps in coverage. We report the chloroplast genome for Helwingia himalaica , the first in the distinctive family Helwingiaceae and only the second genus to be sequenced in the order Aquifoliales. We then combine this with 36 published sequences in the large (c. 35,000 species) subclass Campanulidae in order to investigate relationships at the order and family levels. The Helwingia genome consists of 158,362 bp containing a pair of inverted repeat (IR) regions of 25,996 bp separated by a large single-copy (LSC) region and a small single-copy (SSC) region which are 87,810 and 18,560 bp, respectively. There are 142 known genes, including 94 protein-coding genes, eight ribosomal RNA genes, and 40 tRNA genes. The topology of the phylogenetic relationships between Apiales, Asterales, and Dipsacales differed between analyses based on complete genome sequences and on 36 shared protein-coding genes, showing that further studies of campanulid phylogeny are needed.

Degree product rule tempers explosive percolation in the absence of global information

Science.gov (United States)

Trevelyan, Alexander J.; Tsekenis, Georgios; Corwin, Eric I.

2018-02-01

We introduce a guided network growth model, which we call the degree product rule process, that uses solely local information when adding new edges. For small numbers of candidate edges our process gives rise to a second-order phase transition, but becomes first order in the limit of global choice. We provide the set of critical exponents required to characterize the nature of this percolation transition. Such a process permits interventions which can delay the onset of percolation while tempering the explosiveness caused by cluster product rule processes.

The First Complete Chloroplast Genome Sequences in Actinidiaceae: Genome Structure and Comparative Analysis.

Science.gov (United States)

Yao, Xiaohong; Tang, Ping; Li, Zuozhou; Li, Dawei; Liu, Yifei; Huang, Hongwen

2015-01-01

Actinidia chinensis is an important economic plant belonging to the basal lineage of the asterids. Availability of a complete Actinidia chloroplast genome sequence is crucial to understanding phylogenetic relationships among major lineages of angiosperms and facilitates kiwifruit genetic improvement. We report here the complete nucleotide sequences of the chloroplast genomes for Actinidia chinensis and A. chinensis var deliciosa obtained through de novo assembly of Illumina paired-end reads produced by total DNA sequencing. The total genome size ranges from 155,446 to 157,557 bp, with an inverted repeat (IR) of 24,013 to 24,391 bp, a large single copy region (LSC) of 87,984 to 88,337 bp and a small single copy region (SSC) of 20,332 to 20,336 bp. The genome encodes 113 different genes, including 79 unique protein-coding genes, 30 tRNA genes and 4 ribosomal RNA genes, with 16 duplicated in the inverted repeats, and a tRNA gene (trnfM-CAU) duplicated once in the LSC region. Comparisons of IR boundaries among four asterid species showed that IR/LSC borders were extended into the 5' portion of the psbA gene and IR contraction occurred in Actinidia. The clap gene has been lost from the chloroplast genome in Actinidia, and may have been transferred to the nucleus during chloroplast evolution. Twenty-seven polymorphic simple sequence repeat (SSR) loci were identified in the Actinidia chloroplast genome. Maximum parsimony analyses of a 72-gene, 16 taxa angiosperm dataset strongly support the placement of Actinidiaceae in Ericales within the basal asterids.

Chloroplast RNA-Binding Protein RBD1 Promotes Chilling Tolerance through 23S rRNA Processing in Arabidopsis.

Directory of Open Access Journals (Sweden)

Shuai Wang

2016-05-01

Full Text Available Plants have varying abilities to tolerate chilling (low but not freezing temperatures, and it is largely unknown how plants such as Arabidopsis thaliana achieve chilling tolerance. Here, we describe a genome-wide screen for genes important for chilling tolerance by their putative knockout mutants in Arabidopsis thaliana. Out of 11,000 T-DNA insertion mutant lines representing half of the genome, 54 lines associated with disruption of 49 genes had a drastic chilling sensitive phenotype. Sixteen of these genes encode proteins with chloroplast localization, suggesting a critical role of chloroplast function in chilling tolerance. Study of one of these proteins RBD1 with an RNA binding domain further reveals the importance of chloroplast translation in chilling tolerance. RBD1 is expressed in the green tissues and is localized in the chloroplast nucleoid. It binds directly to 23S rRNA and the binding is stronger under chilling than at normal growth temperatures. The rbd1 mutants are defective in generating mature 23S rRNAs and deficient in chloroplast protein synthesis especially under chilling conditions. Together, our study identifies RBD1 as a regulator of 23S rRNA processing and reveals the importance of chloroplast function especially protein translation in chilling tolerance.

Pilot test of bacterial percolation leaching at Fuzhou uranium mine

International Nuclear Information System (INIS)

Fan Baotuan; Liu Jian; Jiang Yngqiong; Cai Chunhui; Jiang Lang; Zhou Renhua; Tong Changning; Zhang Hongli

2006-01-01

Total 18 t uranium ores of Fuzhou Uranium Mine packed in three or four columns in series were leached by bacterial percolation. The results show that without adding any other chemical oxidant such as sodium chlorate, the leaching rate measured by residue is 91.45%-94.48%, leaching time is 50-60 d, acid consumption is 6.17%-7.75%, and residue grade is 0.0149%-0.0208%. Compared with conventional percolation leaching process, the leaching rate is improved by 3%, leaching time is shorted by 26%, and acid consumption is saved by 34%. Accumulation pattern of ΣFe and F - in the process of leaching is discussed. Influence of F - on bacterial growth, regeneration of barren solution as well as correlative techniques are reviewed. (authors)

Conductivity percolation in loosely compacted microcrystalline cellulose: An in situ study by dielectric spectroscopy during densification.

Science.gov (United States)

Nilsson, Martin; Frenning, Göran; Gråsjö, Johan; Alderborn, Göran; Strømme, Maria

2006-10-19

The present study aims at contributing to a complete understanding of the water-induced ionic charge transport in cellulose. The behavior of this transport in loosely compacted microcrystalline cellulose (MCC) powder was investigated as a function of density utilizing a new type of measurement setup, allowing for dielectric spectroscopy measurement in situ during compaction. The ionic conductivity in MCC was found to increase with increasing density until a leveling-out was observed for densities above approximately 0.7 g/cm3. Further, it was shown that the ionic conductivity vs density followed a percolation type behavior signifying the percolation of conductive paths in a 3D conducting network. The density percolation threshold was found to be between approximately 0.2 and 0.4 g/cm3, depending strongly on the cellulose moisture content. The observed percolation behavior was attributed to the forming of interparticulate bonds in the MCC and the percolation threshold dependence on moisture was linked to the moisture dependence of particle rearrangement and plastic deformation in MCC during compaction. The obtained results add to the understanding of the density-dependent water-induced ionic transport in cellulose showing that, at given moisture content, the two major parameters determining the magnitude of the conductivity are the connectedness of the interparticluate bonds and the connectedness of pores with a diameter in the 5-20 nm size range. At densities between approximately 0.7 and 1.2 g/cm3 both the bond and the pore networks have percolated, facilitating charge transport through the MCC compact.

Finite-size effects for anisotropic bootstrap percolation : Logarithmic corrections

NARCIS (Netherlands)

van Enter, Aernout C. D.; Hulshof, Tim

In this note we analyse an anisotropic, two-dimensional bootstrap percolation model introduced by Gravner and Griffeath. We present upper and lower bounds on the finite-size effects. We discuss the similarities with the semi-oriented model introduced by Duarte.

Finite-size effects for anisotropic bootstrap percolation: logerithmic corrections

NARCIS (Netherlands)

Enter, van A.C.D.; Hulshof, T.

2007-01-01

In this note we analyse an anisotropic, two-dimensional bootstrap percolation model introduced by Gravner and Griffeath. We present upper and lower bounds on the finite-size effects. We discuss the similarities with the semi-oriented model introduced by Duarte.

The Complete Chloroplast Genome Sequences of the Medicinal Plant Forsythia suspensa (Oleaceae

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Wenbin Wang

2017-10-01

Full Text Available Forsythia suspensa is an important medicinal plant and traditionally applied for the treatment of inflammation, pyrexia, gonorrhea, diabetes, and so on. However, there is limited sequence and genomic information available for F. suspensa. Here, we produced the complete chloroplast genomes of F. suspensa using Illumina sequencing technology. F. suspensa is the first sequenced member within the genus Forsythia (Oleaceae. The gene order and organization of the chloroplast genome of F. suspensa are similar to other Oleaceae chloroplast genomes. The F. suspensa chloroplast genome is 156,404 bp in length, exhibits a conserved quadripartite structure with a large single-copy (LSC; 87,159 bp region, and a small single-copy (SSC; 17,811 bp region interspersed between inverted repeat (IRa/b; 25,717 bp regions. A total of 114 unique genes were annotated, including 80 protein-coding genes, 30 tRNA, and four rRNA. The low GC content (37.8% and codon usage bias for A- or T-ending codons may largely affect gene codon usage. Sequence analysis identified a total of 26 forward repeats, 23 palindrome repeats with lengths >30 bp (identity > 90%, and 54 simple sequence repeats (SSRs with an average rate of 0.35 SSRs/kb. We predicted 52 RNA editing sites in the chloroplast of F. suspensa, all for C-to-U transitions. IR expansion or contraction and the divergent regions were analyzed among several species including the reported F. suspensa in this study. Phylogenetic analysis based on whole-plastome revealed that F. suspensa, as a member of the Oleaceae family, diverged relatively early from Lamiales. This study will contribute to strengthening medicinal resource conservation, molecular phylogenetic, and genetic engineering research investigations of this species.

High-throughput sequencing of three Lemnoideae (duckweeds chloroplast genomes from total DNA.

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Wenqin Wang

Full Text Available BACKGROUND: Chloroplast genomes provide a wealth of information for evolutionary and population genetic studies. Chloroplasts play a particularly important role in the adaption for aquatic plants because they float on water and their major surface is exposed continuously to sunlight. The subfamily of Lemnoideae represents such a collection of aquatic species that because of photosynthesis represents one of the fastest growing plant species on earth. METHODS: We sequenced the chloroplast genomes from three different genera of Lemnoideae, Spirodela polyrhiza, Wolffiella lingulata and Wolffia australiana by high-throughput DNA sequencing of genomic DNA using the SOLiD platform. Unfractionated total DNA contains high copies of plastid DNA so that sequences from the nucleus and mitochondria can easily be filtered computationally. Remaining sequence reads were assembled into contiguous sequences (contigs using SOLiD software tools. Contigs were mapped to a reference genome of Lemna minor and gaps, selected by PCR, were sequenced on the ABI3730xl platform. CONCLUSIONS: This combinatorial approach yielded whole genomic contiguous sequences in a cost-effective manner. Over 1,000-time coverage of chloroplast from total DNA were reached by the SOLiD platform in a single spot on a quadrant slide without purification. Comparative analysis indicated that the chloroplast genome was conserved in gene number and organization with respect to the reference genome of L. minor. However, higher nucleotide substitution, abundant deletions and insertions occurred in non-coding regions of these genomes, indicating a greater genomic dynamics than expected from the comparison of other related species in the Pooideae. Noticeably, there was no transition bias over transversion in Lemnoideae. The data should have immediate applications in evolutionary biology and plant taxonomy with increased resolution and statistical power.

Preparation of rat gastric heavy and light microsomal membranes enriched in (H+-K+)-ATPase using 2H2O and Percoll gradients

International Nuclear Information System (INIS)

Im, W.B.; Davis, J.P.; Blakeman, D.P.

1985-01-01

Gastric heavy microsomal membranes highly enriched in (H + -K + )-ATPase were obtained from cimetidine- or carbachol-treated rats through 2 H 2 O and Percoll gradient centrifugations. Both the resting (cimetidine-treated) and the stimulated (carbachol-treated) heavy membranes which presumably represent the apical membrane of gastric parietal cells were enriched with the polypeptides of 81,000 and 45,000 besides that of 93,000 representing (H + -K + )-ATPase. No apparent differences could be detected between the resting and the stimulated heavy membranes in their polypeptide profiles or their specific activity of (H + -K + )-ATPase. Nevertheless, the level of 86 RbCl uptake was greater in the stimulated than the resting heavy microsomal membrane vesicles. The light gastric microsomes which abound in intracellular tubulovesicles containing reserve (H + -K + )-ATPase as isolated from cimetidine-treated rats were similarly purified with respect to (H + -K + )-ATPase. The purified light gastric membranes were largely devoid of the polypeptides of 81,000 and 45,000 found in the heavy gastric membranes. These observations further support the current hypothesis that secretagogues bring about changes in the environment of (H + -K + )-ATPase and induce KCl permeability in the apical membrane of the parietal cells, although at present the authors have been unable to identify the polypeptide(s) responsible for the KCl pathway

Formation and Change of Chloroplast-Located Plant Metabolites in Response to Light Conditions

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Yiyong Chen

2018-02-01

Full Text Available Photosynthesis is the central energy conversion process for plant metabolism and occurs within mature chloroplasts. Chloroplasts are also the site of various metabolic reactions involving amino acids, lipids, starch, and sulfur, as well as where the production of some hormones takes place. Light is one of the most important environmental factors, acting as an essential energy source for plants, but also as an external signal influencing their growth and development. Plants experience large fluctuations in the intensity and spectral quality of light, and many attempts have been made to improve or modify plant metabolites by treating them with different light qualities (artificial lighting or intensities. In this review, we discuss how changes in light intensity and wavelength affect the formation of chloroplast-located metabolites in plants.

Chloroplast evolution in the Pinus montezumae complex: a coalescent approach to hybridization.

Science.gov (United States)

Matos, J A; Schaal, B A

2000-08-01

This study addresses the evolutionary history of the chloroplast genomes of two closely related pine species, Pinus hartwegii Lindl. and P. montezumae Lamb (subsect. Ponderosae) using coalescent theory and some of the statistical tools that have been developed from it during the past two decades. Pinus hartwegii and P. montezumae are closely related species in the P. montezumae complex (subsect. Ponderosae) of Mexico and Central America. Pinus hartwegii is a high elevation species, whereas P. montezumae occurs at lower elevations. The two species occur on many of the same mountains throughout Mexico. A total of 350 individuals of P. hartwegii and P. montezumae were collected from Nevado de Colima (Jalisco), Cerro Potosí (Nuevo León), Iztaccihuatl/Popocatepetl (México), and Nevado de Toluca (México). The chloroplast genome of P. hartwegii and P. montezumae was mapped using eight restriction enzymes. Fifty-one different haplotypes were characterized; 38 of 160 restriction sites were polymorphic. Clades of most parsimoniously related chloroplast haplotypes are geographically localized and do not overlap in distribution, and the geographically localized clades of haplotypes include both P. hartwegii and P. montezumae. Some haplotypes in the clades occur in only one of the two species, whereas other haplotypes occur in both species. These data strongly suggest ancient and/or ongoing hybridization between P. hartwegii and P. montezumae and a shared chloroplast genome history within geographic regions of Mexico.

Light affects the chloroplast ultrastructure and post-storage photosynthetic performance of watermelon (Citrullus lanatus) plug seedlings.

Science.gov (United States)

Duan, Qingqing; Jiang, Wu; Ding, Ming; Lin, Ye; Huang, Danfeng

2014-01-01

Watermelon [Citrullus lanatus (Thunb.) Matsum. and Nakai] plug seedlings were stored at 15°C in the light at a photosynthetic photon flux density of 15 µmol·m(-2)·s(-1) or in darkness for 6 days, to evaluate their chloroplast ultrastructure, and associated photosynthetic characteristics. Storage in the dark caused swelling, disordered granal arrangement, and starch grain disappearance in the chloroplasts. In contrast, the chloroplasts stored in the light were relatively normal. As a result, the light-stored seedlings had a significantly higher chlorophyll content, Fv/Fm, and Pn than did dark-stored seedlings. Regardless of whether the seedlings were stored in light or darkness, the Gs and Ls of the seedlings significantly decreased, while the Ci obviously increased when the Pn decreased after 6 days of storage. This result suggests that the decreased Pn is not solely a stomatal effect, as the effects on the chloroplasts contributed to this photosynthetic inhibition. Six days after transplanting, seedlings that were stored in the light or darkness for 2 or 4 days showed complete recovery of chloroplast ultrastructure, chlorophyll content, Fv/Fm, Gs and Pn. When the storage period increased to 6 days, the dark-stored seedlings had a significantly lower Fv/Fm and Pn than the light-stored and control seedlings 6 days after transplanting, which was mainly ascribed to incomplete recovery of chloroplast ultrastructure. Furthermore, the light-stored seedlings exhibited a significantly higher shoot dry weight during storage and a higher percentage dry weight increase after transplanting than the dark-stored seedlings. These effects were enhanced by prolonged storage (4 to 6 days). This study demonstrated that dim light during storage is beneficial for maintaining chloroplast ultrastructure as well as photosynthetic efficiency in watermelon seedlings, thus contributing to the rapid recovery of post-storage photosynthetic performance, which ensures the transplant quality

Construction of a restriction map and gene map of the lettuce chloroplast small single-copy region using Southern cross-hybridization.

Science.gov (United States)

Mitchelson, K R

1996-01-01

The small single-copy region (SSCR) of the chloroplast genome of many higher plants typically contain ndh genes encoding proteins that share homology with subunits of the respiratory-chain reduced nicotinamide adenine dinucleotide (NADH) dehydrogenase complex of mitochondria. A map of the lettuce chloroplast SSCR has been determined by Southern cross-hybridization, taking advantage of the high degree of homology between a tobacco small single-copy fragment and a corresponding lettuce chloroplast fragment. The gene order of the SSCR of lettuce and tobacco chloroplasts is similar. The cross-hybridization method can rapidly create a primary gene map of unknown chloroplast fragments, thus providing detailed information of the localization and arrangement of genes and conserved open reading frame regions.

Rigidity percolation in dispersions with a structured viscoelastic matrix

NARCIS (Netherlands)

Wilbrink, M.W.L.; Michels, M.A.J.; Vellinga, W.P.; Meijer, H.E.H.

2005-01-01

This paper deals with rigidity percolation in composite materials consisting of a dispersion of mineral particles in a microstructured viscoelastic matrix. The viscoelastic matrix in this specific case is a hydrocarbon refinery residue. In a set of model random composites the mean interparticle

Polyuridylylation and processing of transcripts from multiple gene minicircles in chloroplasts of the dinoflagellate Amphidinium carterae

KAUST Repository

Barbrook, Adrian C.

2012-05-05

Although transcription and transcript processing in the chloroplasts of plants have been extensively characterised, the RNA metabolism of other chloroplast lineages across the eukaryotes remains poorly understood. In this paper, we use RT-PCR to study transcription and transcript processing in the chloroplasts of Amphidinium carterae, a model peridinin-containing dinoflagellate. These organisms have a highly unusual chloroplast genome, with genes located on multiple small \\'minicircle\\' elements, and a number of idiosyncratic features of RNA metabolism including transcription via a rolling circle mechanism, and 3′ terminal polyuridylylation of transcripts. We demonstrate that transcription occurs in A. carterae via a rolling circle mechanism, as previously shown in the dinoflagellate Heterocapsa, and present evidence for the production of both polycistronic and monocistronic transcripts from A. carterae minicircles, including several regions containing ORFs previously not known to be expressed. We demonstrate the presence of both polyuridylylated and non-polyuridylylated transcripts in A. carterae, and show that polycistronic transcripts can be terminally polyuridylylated. We present a model for RNA metabolism in dinoflagellate chloroplasts where long polycistronic precursors are processed to form mature transcripts. Terminal polyuridylylation may mark transcripts with the correct 3′ end. © 2012 Springer Science+Business Media B.V.

Numerical calculation of the conductivity of percolation clusters and the use of special purpose computers

International Nuclear Information System (INIS)

Herrmann, H.J.

1989-01-01

Electrical conductivity diffusion or phonons, have an anomalous behaviour on percolation clusters at the percolation threshold due to the fractality of these clusters. The results that have been found numerically for this anomalous behaviour are reviewed. A special purpose computer built for this purpose is described and the evaluation of the data from this machine is discussed

The complete chloroplast genome of Cinnamomum camphora and its comparison with related Lauraceae species

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Caihui Chen

2017-09-01

Full Text Available Cinnamomum camphora, a member of the Lauraceae family, is a valuable aromatic and timber tree that is indigenous to the south of China and Japan. All parts of Cinnamomum camphora have secretory cells containing different volatile chemical compounds that are utilized as herbal medicines and essential oils. Here, we reported the complete sequencing of the chloroplast genome of Cinnamomum camphora using illumina technology. The chloroplast genome of Cinnamomum camphora is 152,570 bp in length and characterized by a relatively conserved quadripartite structure containing a large single copy region of 93,705 bp, a small single copy region of 19,093 bp and two inverted repeat (IR regions of 19,886 bp. Overall, the genome contained 123 coding regions, of which 15 were repeated in the IR regions. An analysis of chloroplast sequence divergence revealed that the small single copy region was highly variable among the different genera in the Lauraceae family. A total of 40 repeat structures and 83 simple sequence repeats were detected in both the coding and non-coding regions. A phylogenetic analysis indicated that Calycanthus is most closely related to Lauraceae, both being members of Laurales, which forms a sister group to Magnoliids. The complete sequence of the chloroplast of Cinnamomum camphora will aid in in-depth taxonomical studies of the Lauraceae family in the future. The genetic sequence information will also have valuable applications for chloroplast genetic engineering.

Percolation analysis for cosmic web with discrete points

Science.gov (United States)

Zhang, Jiajun; Cheng, Dalong; Chu, Ming-Chung

2018-01-01

Percolation analysis has long been used to quantify the connectivity of the cosmic web. Most of the previous work is based on density fields on grids. By smoothing into fields, we lose information about galaxy properties like shape or luminosity. The lack of mathematical modeling also limits our understanding for the percolation analysis. To overcome these difficulties, we have studied percolation analysis based on discrete points. Using a friends-of-friends (FoF) algorithm, we generate the S -b b relation, between the fractional mass of the largest connected group (S ) and the FoF linking length (b b ). We propose a new model, the probability cloud cluster expansion theory to relate the S -b b relation with correlation functions. We show that the S -b b relation reflects a combination of all orders of correlation functions. Using N-body simulation, we find that the S -b b relation is robust against redshift distortion and incompleteness in observation. From the Bolshoi simulation, with halo abundance matching (HAM), we have generated a mock galaxy catalog. Good matching of the projected two-point correlation function with observation is confirmed. However, comparing the mock catalog with the latest galaxy catalog from Sloan Digital Sky Survey (SDSS) Data Release (DR)12, we have found significant differences in their S -b b relations. This indicates that the mock galaxy catalog cannot accurately retain higher-order correlation functions than the two-point correlation function, which reveals the limit of the HAM method. As a new measurement, the S -b b relation is applicable to a wide range of data types, fast to compute, and robust against redshift distortion and incompleteness and contains information of all orders of correlation functions.

Remarks on the percolation problem in anisotropic systems

International Nuclear Information System (INIS)

Chaves, C.M.G.F.; Oliveira, P.M.C. de; Queiroz, S.L.A. de; Riera, R.

1979-07-01

The bond percolation problem is discused in an anisotropic square lattice using the position space renormalization group. It is shown that, due to symmetry, this treatment reproduces known exact results for this problem. The phase diagram and the flow lines in parameter space are also shown. Results are in agreement with universality.(Author) [pt

The complete chloroplast DNA sequence of the green alga Oltmannsiellopsis viridis reveals a distinctive quadripartite architecture in the chloroplast genome of early diverging ulvophytes

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Lemieux Claude

2006-02-01

Full Text Available Abstract Background The phylum Chlorophyta contains the majority of the green algae and is divided into four classes. The basal position of the Prasinophyceae has been well documented, but the divergence order of the Ulvophyceae, Trebouxiophyceae and Chlorophyceae is currently debated. The four complete chloroplast DNA (cpDNA sequences presently available for representatives of these classes have revealed extensive variability in overall structure, gene content, intron composition and gene order. The chloroplast genome of Pseudendoclonium (Ulvophyceae, in particular, is characterized by an atypical quadripartite architecture that deviates from the ancestral type by a large inverted repeat (IR featuring an inverted rRNA operon and a small single-copy (SSC region containing 14 genes normally found in the large single-copy (LSC region. To gain insights into the nature of the events that led to the reorganization of the chloroplast genome in the Ulvophyceae, we have determined the complete cpDNA sequence of Oltmannsiellopsis viridis, a representative of a distinct, early diverging lineage. Results The 151,933 bp IR-containing genome of Oltmannsiellopsis differs considerably from Pseudendoclonium and other chlorophyte cpDNAs in intron content and gene order, but shares close similarities with its ulvophyte homologue at the levels of quadripartite architecture, gene content and gene density. Oltmannsiellopsis cpDNA encodes 105 genes, contains five group I introns, and features many short dispersed repeats. As in Pseudendoclonium cpDNA, the rRNA genes in the IR are transcribed toward the single copy region featuring the genes typically found in the ancestral LSC region, and the opposite single copy region harbours genes characteristic of both the ancestral SSC and LSC regions. The 52 genes that were transferred from the ancestral LSC to SSC region include 12 of those observed in Pseudendoclonium cpDNA. Surprisingly, the overall gene organization of

Effect of percolation rate on water-travel time in deep, partially saturated zones

International Nuclear Information System (INIS)

Peters, R.R.; Gauthier, J.H.; Dudley, A.L.

1986-01-01

The Nevada Nuclear Waste Storage Investigations (NNWSI) project is investigating Yucca Mountain, Nye County, Nevada, as a prospective site for a radioactive-waste repository. The Yucca Mountain site is unique among those currently being investigated by the US Department of Energy (DOE) in that the prospective repository location is in the unsaturated zone, approximately 300 m above the water table. A composite-porosity, continuum model was developed to model flow in a fractured, porous medium. Simulations using data from the Yucca Mountain site and this model in the one-dimensional code TOSPAC indicate that current estimates of the percolation rate result in water movement confined to the matrix and that the water-travel time from the repository to the water table in on the order of hundreds of thousands of years. This result is sensitive to the percolation rate; an increase in percolation rate of a factor of 10 may initiate water movement in the fractures, reducing the travel time significantly

Stable megadalton TOC-TIC supercomplexes as major mediators of protein import into chloroplasts.

Science.gov (United States)

Chen, Lih-Jen; Li, Hsou-Min

2017-10-01

Preproteins are believed to be imported into chloroplasts through membrane contact sites where the translocon complexes of the outer (TOC) and inner (TIC) envelope membranes are assembled together. However, a single TOC-TIC supercomplex containing preproteins undergoing active import has not yet been directly observed. We optimized the blue native polyacrylamide gel electrophoresis (PAGE) (BN-PAGE) system to detect and resolve megadalton (MD)-sized complexes. Using this optimized system, the outer-membrane channel Toc75 from pea chloroplasts was found in at least two complexes: the 880-kD TOC complex and a previously undetected 1-MD complex. Two-dimensional BN-PAGE immunoblots further showed that Toc75, Toc159, Toc34, Tic20, Tic56 and Tic110 were all located in the 880-kD to 1.3-MD region. During active preprotein import, preproteins were transported mostly through the 1-MD complex and a smaller amount of preproteins was also detected in a complex of 1.25 MD. Antibody-shift assays showed that the 1-MD complex is a TOC-TIC supercomplex containing at least Toc75, Toc159, Toc34 and Tic110. Results from crosslinking and import with Arabidopsis chloroplasts suggest that the 1.25-MD complex is also a supercomplex. Our data provide direct evidence supporting that chloroplast preproteins are imported through TOC-TIC supercomplexes, and also provide the first size estimation of these supercomplexes. Furthermore, unlike in mitochondria where translocon supercomplexes are only transiently assembled during preprotein import, in chloroplasts at least some of the supercomplexes are preassembled stable structures. © 2017 The Authors The Plant Journal published by John Wiley & Sons Ltd and Society for Experimental Biology.

Chloroplast genome resources and molecular markers differentiate rubber dandelion species from weedy relatives.

Science.gov (United States)

Zhang, Yingxiao; Iaffaldano, Brian J; Zhuang, Xiaofeng; Cardina, John; Cornish, Katrina

2017-02-02

Rubber dandelion (Taraxacum kok-saghyz, TK) is being developed as a domestic source of natural rubber to meet increasing global demand. However, the domestication of TK is complicated by its colocation with two weedy dandelion species, Taraxacum brevicorniculatum (TB) and the common dandelion (Taraxacum officinale, TO). TB is often present as a seed contaminant within TK accessions, while TO is a pandemic weed, which may have the potential to hybridize with TK. To discriminate these species at the molecular level, and facilitate gene flow studies between the potential rubber crop, TK, and its weedy relatives, we generated genomic and marker resources for these three dandelion species. Complete chloroplast genome sequences of TK (151,338 bp), TO (151,299 bp), and TB (151,282 bp) were obtained using the Illumina GAII and MiSeq platforms. Chloroplast sequences were analyzed and annotated for all the three species. Phylogenetic analysis within Asteraceae showed that TK has a closer genetic distance to TB than to TO and Taraxacum species were most closely related to lettuce (Lactuca sativa). By sequencing multiple genotypes for each species and testing variants using gel-based methods, four chloroplast Single Nucleotide Polymorphism (SNP) variants were found to be fixed between TK and TO in large populations, and between TB and TO. Additionally, Expressed Sequence Tag (EST) resources developed for TO and TK permitted the identification of five nuclear species-specific SNP markers. The availability of chloroplast genomes of these three dandelion species, as well as chloroplast and nuclear molecular markers, will provide a powerful genetic resource for germplasm differentiation and purification, and the study of potential gene flow among Taraxacum species.

Reproducibility of up-flow column percolation tests for contaminated soils.

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Tetsuo Yasutaka

Full Text Available Up-flow column percolation tests are used at laboratory scale to assess the leaching behavior of hazardous substance from contaminated soils in a specific condition as a function of time. Monitoring the quality of these test results inter or within laboratory is crucial, especially if used for Environment-related legal policy or for routine testing purposes. We tested three different sandy loam type soils (Soils I, II and III to determine the reproducibility (variability inter laboratory of test results and to evaluate the difference in the test results within laboratory. Up-flow column percolation tests were performed following the procedure described in the ISO/TS 21268-3. This procedure consists of percolating solution (calcium chloride 1 mM from bottom to top at a flow rate of 12 mL/h through softly compacted soil contained in a column of 5 cm diameter and 30 ± 5 cm height. Eluate samples were collected at liquid-to-solid ratio of 0.1, 0.2, 0.5, 1, 2, 5 and 10 L/kg and analyzed for quantification of the target elements (Cu, As, Se, Cl, Ca, F, Mg, DOC and B in this research. For Soil I, 17 institutions in Japan joined this validation test. The up-flow column experiments were conducted in duplicate, after 48 h of equilibration time and at a flow rate of 12 mL/h. Column percolation test results from Soils II and III were used to evaluate the difference in test results from the experiments conducted in duplicate in a single laboratory, after 16 h of equilibration time and at a flow rate of 36 mL/h. Overall results showed good reproducibility (expressed in terms of the coefficient of variation, CV, calculated by dividing the standard deviation by the mean, as the CV was lower than 30% in more than 90% of the test results associated with Soil I. Moreover, low variability (expressed in terms of difference between the two test results divided by the mean was observed in the test results related to Soils II and III, with a variability lower than 30

Universality for first passage percolation on sparse random graphs

NARCIS (Netherlands)

Bhamidi, S.; Van Der Hofstad, R.W.; Hooghiemstra, G.

2017-01-01

We consider first passage percolation on the configuration model with n vertices, and general independent and identically distributed edge weights assumed to have a density. Assuming that the degree distribution satisfies a uniform X2 logX-condition, we analyze the asymptotic distribution for the

Universality for first passage percolation on sparse random graphs

NARCIS (Netherlands)

Bhamidi, S.; Hofstad, van der R.W.; Hooghiemstra, G.

2014-01-01

We consider first passage percolation on the conguration model with n vertices, and general independent and identically distributed edge weights assumed to have a density. Assuming that the degree distribution satisfies a uniform X2 logX-condition, we analyze the asymptotic distribution for the

Methods for Purifying Enzymes for Mycoremediation

Science.gov (United States)

Cullings, Kenneth W. (Inventor); DeSimone, Julia C. (Inventor); Paavola, Chad D. (Inventor)

2014-01-01

A process for purifying laccase from an ectomycorrhizal fruiting body is disclosed. The process includes steps of homogenization, sonication, centrifugation, filtration, affinity chromatography, ion exchange chromatography, and gel filtration. Purified laccase can also be separated into isomers.

Multifractal properties of resistor diode percolation.

Science.gov (United States)

Stenull, Olaf; Janssen, Hans-Karl

2002-03-01

Focusing on multifractal properties we investigate electric transport on random resistor diode networks at the phase transition between the nonpercolating and the directed percolating phase. Building on first principles such as symmetries and relevance we derive a field theoretic Hamiltonian. Based on this Hamiltonian we determine the multifractal moments of the current distribution that are governed by a family of critical exponents [psi(l)]. We calculate the family [psi(l)] to two-loop order in a diagrammatic perturbation calculation augmented by renormalization group methods.

Percolation Theory and Modern Hydraulic Fracturing

Science.gov (United States)

Norris, J. Q.; Turcotte, D. L.; Rundle, J. B.

2015-12-01

During the past few years, we have been developing a percolation model for fracking. This model provides a powerful tool for understanding the growth and properties of the complex fracture networks generated during a modern high volume hydraulic fracture stimulations of tight shale reservoirs. The model can also be used to understand the interaction between the growing fracture network and natural reservoir features such as joint sets and faults. Additionally, the model produces a power-law distribution of bursts which can easily be compared to observed microseismicity.

New scaling results in quantum percolation

International Nuclear Information System (INIS)

Srivastava, V.; Chaturvedi, M.

1983-06-01

Scaling arguments for distribution of cluster size and size of localized states have been developed to calculate average number of lattice sites falling under a localized wave function as a function of concentration for a model binary system with ''infinite disorder''. We find distinct features near classical and quantum percolation thresholds. Analytical results are compared with computer-experiment results and the predicted features are found to be confirmed. Possibility of appearance of extended states in two-dimensional binary systems even at infinite disorder is pointed out. (author)

Self Healing Percolation

Science.gov (United States)

Scala, Antonio

2015-03-01

We introduce the concept of self-healing in the field of complex networks modelling; in particular, self-healing capabilities are implemented through distributed communication protocols that exploit redundant links to recover the connectivity of the system. Self-healing is a crucial in implementing the next generation of smart grids allowing to ensure a high quality of service to the users. We then map our self-healing procedure in a percolation problem and analyse the interplay between redundancies and topology in improving the resilience of networked infrastructures to multiple failures. We find exact results both for planar lattices and for random lattices, hinting the role of duality in the design of resilient networks. Finally, we introduce a cavity method approach to study the recovery of connectivity after damage in self-healing networks. CNR-PNR National Project ``Crisis-Lab,'' EU HOME/2013/CIPS/AG/4000005013 project CI2C and EU FET project MULTIPLEX nr.317532.

Ozone-induced changes in the chloroplast structure of conifer needles, and their use in ozone diagnostics

International Nuclear Information System (INIS)

Kivimaeenpaeae, M.; Sellden, G.; Sutinen, S.

2005-01-01

Ozone induces characteristic symptoms in the chloroplasts of the needles of several coniferous species. Chloroplasts are (1) reduced in size and (2) the stroma is electron dense. Moreover (3) these chloroplast alterations are more pronounced in the outer mesophyll cell layers and in the upper side of the needle compared to the inner layers and lower side. The syndrome, including the three symptoms (1)-(3), is found in the green needles of Scots pine and Norway spruce not only in the experimental fumigations, but also in mature trees in the field, and has potential for diagnosis of ozone stress. For sound ozone diagnostics all three symptoms must be present in the samples studied. The symptoms in relation to needle anatomy and physiology is discussed, and recommendations for sampling and analysis are given. - Ozone-induced alterations in chloroplast structure of conifer needles are reviewed, and recommendations for field monitoring given

Complete chloroplast genome of Trachelium caeruleum: extensiverearrangements are associated with repeats and tRNAs

Energy Technology Data Exchange (ETDEWEB)

Haberle, Rosemarie C.; Fourcade, Matthew L.; Boore, Jeffrey L.; Jansen, Robert K.

2006-01-09

Chloroplast genome structure, gene order and content arehighly conserved in land plants. We sequenced the complete chloroplastgenome sequence of Trachelium caeruleum (Campanulaceae) a member of anangiosperm family known for highly rearranged chloroplast genomes. Thetotal genome size is 162,321 bp with an IR of 27,273 bp, LSC of 100,113bp and SSC of 7,661 bp. The genome encodes 115 unique genes, with 19duplicated in the IR, a tRNA (trnI-CAU) duplicated once in the LSC and aprotein coding gene (psbJ) duplicated twice, for a total of 137 genes.Four genes (ycf15, rpl23, infA and accD) are truncated and likelynonfunctional; three others (clpP, ycf1 and ycf2) are so highly divergedthat they may now be pseudogenes. The most conspicuous feature of theTrachelium genome is the presence of eighteen internally unrearrangedblocks of genes that have been inverted or relocated within the genome,relative to the typical gene order of most angiosperm chloroplastgenomes. Recombination between repeats or tRNAs has been suggested as twomeans of chloroplast genome rearrangements. We compared the relativenumber of repeats in Trachelium to eight other angiosperm chloroplastgenomes, and evaluated the location of repeats and tRNAs in relation torearrangements. Trachelium has the highest number and largest repeats,which are concentrated near inversion endpoints or other rearrangements.tRNAs occur at many but not all inversion endpoints. There is likely nosingle mechanism responsible for the remarkable number of alterations inthis genome, but both repeats and tRNAs are clearly associated with theserearrangements. Land plant chloroplast genomes are highly conserved instructure, gene order and content. The chloroplast genomes of ferns, thegymnosperm Ginkgo, and most angiosperms are nearly collinear, reflectingthe gene order in lineages that diverged from lycopsids and the ancestralchloroplast gene order over 350 million years ago (Raubeson and Jansen,1992). Although earlier mapping studies

Percolation Analysis as a Tool to Describe the Topology of the Large Scale Structure of the Universe

Science.gov (United States)

Yess, Capp D.

1997-09-01

Percolation analysis is the study of the properties of clusters. In cosmology, it is the statistics of the size and number of clusters. This thesis presents a refinement of percolation analysis and its application to astronomical data. An overview of the standard model of the universe and the development of large scale structure is presented in order to place the study in historical and scientific context. Then using percolation statistics we, for the first time, demonstrate the universal character of a network pattern in the real space, mass distributions resulting from nonlinear gravitational instability of initial Gaussian fluctuations. We also find that the maximum of the number of clusters statistic in the evolved, nonlinear distributions is determined by the effective slope of the power spectrum. Next, we present percolation analyses of Wiener Reconstructions of the IRAS 1.2 Jy Redshift Survey. There are ten reconstructions of galaxy density fields in real space spanning the range β = 0.1 to 1.0, where β=Ω0.6/b,/ Ω is the present dimensionless density and b is the linear bias factor. Our method uses the growth of the largest cluster statistic to characterize the topology of a density field, where Gaussian randomized versions of the reconstructions are used as standards for analysis. For the reconstruction volume of radius, R≈100h-1 Mpc, percolation analysis reveals a slight 'meatball' topology for the real space, galaxy distribution of the IRAS survey. Finally, we employ a percolation technique developed for pointwise distributions to analyze two-dimensional projections of the three northern and three southern slices in the Las Campanas Redshift Survey and then give consideration to further study of the methodology, errors and application of percolation. We track the growth of the largest cluster as a topological indicator to a depth of 400 h-1 Mpc, and report an unambiguous signal, with high signal-to-noise ratio, indicating a network topology which in

Whole-gene positive selection, elevated synonymous substitution rates, duplication, and indel evolution of the chloroplast clpP1 gene.

Directory of Open Access Journals (Sweden)

Per Erixon

Full Text Available BACKGROUND: Synonymous DNA substitution rates in the plant chloroplast genome are generally relatively slow and lineage dependent. Non-synonymous rates are usually even slower due to purifying selection acting on the genes. Positive selection is expected to speed up non-synonymous substitution rates, whereas synonymous rates are expected to be unaffected. Until recently, positive selection has seldom been observed in chloroplast genes, and large-scale structural rearrangements leading to gene duplications are hitherto supposed to be rare. METHODOLOGY/PRINCIPLE FINDINGS: We found high substitution rates in the exons of the plastid clpP1 gene in Oenothera (the Evening Primrose family and three separate lineages in the tribe Sileneae (Caryophyllaceae, the Carnation family. Introns have been lost in some of the lineages, but where present, the intron sequences have substitution rates similar to those found in other introns of their genomes. The elevated substitution rates of clpP1 are associated with statistically significant whole-gene positive selection in three branches of the phylogeny. In two of the lineages we found multiple copies of the gene. Neighboring genes present in the duplicated fragments do not show signs of elevated substitution rates or positive selection. Although non-synonymous substitutions account for most of the increase in substitution rates, synonymous rates are also markedly elevated in some lineages. Whereas plant clpP1 genes experiencing negative (purifying selection are characterized by having very conserved lengths, genes under positive selection often have large insertions of more or less repetitive amino acid sequence motifs. CONCLUSIONS/SIGNIFICANCE: We found positive selection of the clpP1 gene in various plant lineages to correlated with repeated duplication of the clpP1 gene and surrounding regions, repetitive amino acid sequences, and increase in synonymous substitution rates. The present study sheds light on the

GENETIC POLYMORPHISM IN GYMNODINIUM GALATHEANUM CHLOROPLAST DNA SEQUENCES AND DEVELOPMENT OF A MOLECULAR DETECTION ASSAY. (R827084)

Science.gov (United States)

Nuclear and chloroplast-encoded small subunit ribosomal DNA sequences were obtainedfrom several strains of the toxic dinoflagellate Gymnodinium galatheanum. Phylogenetic analyses andcomparison of sequences indicate that the chloroplast sequences show a higher degree of se...

Carbon and hydrogen metabolism of green algae in light and dark

Energy Technology Data Exchange (ETDEWEB)

1990-01-01

After adaptation to a hydrogen metabolism, Chlamydomonas reinhardtii can photoanaerobically metabolize acetate with the evolution of H{sub 2} and CO{sub 2}. An enzyme profile of the chloroplastic, cytoplasmic, and mitochondrial fractions were obtained with a cellular fractionation procedure that incorporated cell wall removal by autolysine, digestion of the plasmalemma with digitonin and fractionation by differential centrifugation on a Percoll step gradient. The sequence of events leading to the photo-evolution of H{sub 2} from acetate includes the conversion of acetate into succinate via the extraplastidic glyoxylate cycle, the oxidation of succinate to fumarate by chloroplastic succinic dehydrogenase and the oxidation of malate to oxaloacetate in the chloroplast by NAD dependent malate dehydrogenase. The level of potential activity of the enzymes was sufficient to accommodate the observed rate of gas evolution. The isolated darkened chloroplast evolves aerobically CO{sub 2} from glucose indicating a chloroplastic respiratory pathway. Evolution of CO{sub 2} is blocked by mitochondrial inhibitors.

Metastability Thresholds for Anisotropic Bootstrap Percolation in Three Dimensions

NARCIS (Netherlands)

Enter, Aernout C.D. van; Fey, Anne

In this paper we analyze several anisotropic bootstrap percolation models in three dimensions. We present the order of magnitude for the metastability thresholds for a fairly general class of models. In our proofs, we use an adaptation of the technique of dimensional reduction. We find that the

Abscisic acid represses the transcription of chloroplast genes

Czech Academy of Sciences Publication Activity Database

Yamburenko, M.V.; Zubo, Y.O.; Vaňková, Radomíra; Kusnetsov, V.; Kulaeva, O.N.; Borner, T.

2013-01-01

Roč. 64, č. 14 (2013), s. 4491-4502 ISSN 0022-0957 R&D Projects: GA ČR GA522/09/2058 Institutional research plan: CEZ:AV0Z50380511 Keywords : Abscisic acid (ABA) * chloroplast * cytokinin Subject RIV: ED - Physiology Impact factor: 5.794, year: 2013

Percolation effect in thick film superconductors

Energy Technology Data Exchange (ETDEWEB)

Sali, R.; Harsanyi, G. [Technical Univ. of Budapest (Hungary)

1994-12-31

A thick film superconductor paste has been developed to study the properties of granulated superconductor materials, to observe the percolation effect and to confirm the theory of the conducting mechanism in the superconducting thick films. This paste was also applied to make a superconducting planar transformer. Due to high T{sub c} and advantageous current density properties the base of the paste was chosen to be of Bi(Pb)SrCaCuO system. For contacts a conventional Ag/Pt paste was used. The critical temperature of the samples were between 110 K and 115 K depending on the printed layer thickness. The critical current density at the boiling temperature of the liquid He- was between 200-300 A/cm{sup 2}. The R(T) and V(I) functions were measured with different parameters. The results of the measurements have confirmed the theory of conducting mechanism in the material. The percolation structure model has been built and described. As an application, a superconducting planar thick film transformer was planned and produced. Ten windings of the transformer were printed on one side of the alumina substrate and one winding was printed on the other side. The coupling between the two sides was possible through the substrate. The samples did not need special drying and firing parameters. After the preparation, the properties of the transformer were measured. The efficiency and the losses were determined. Finally, some fundamental advantages and problems of the process were discussed.

Percolation effect in thick film superconductors

International Nuclear Information System (INIS)

Sali, R.; Harsanyi, G.

1994-01-01

A thick film superconductor paste has been developed to study the properties of granulated superconductor materials, to observe the percolation effect and to confirm the theory of the conducting mechanism in the superconducting thick films. This paste was also applied to make a superconducting planar transformer. Due to high T c and advantageous current density properties the base of the paste was chosen to be of Bi(Pb)SrCaCuO system. For contacts a conventional Ag/Pt paste was used. The critical temperature of the samples were between 110 K and 115 K depending on the printed layer thickness. The critical current density at the boiling temperature of the liquid He- was between 200-300 A/cm 2 . The R(T) and V(I) functions were measured with different parameters. The results of the measurements have confirmed the theory of conducting mechanism in the material. The percolation structure model has been built and described. As an application, a superconducting planar thick film transformer was planned and produced. Ten windings of the transformer were printed on one side of the alumina substrate and one winding was printed on the other side. The coupling between the two sides was possible through the substrate. The samples did not need special drying and firing parameters. After the preparation, the properties of the transformer were measured. The efficiency and the losses were determined. Finally, some fundamental advantages and problems of the process were discussed

The complete chloroplast genome sequence of Helwingia himalaica (Helwingiaceae, Aquifoliales and a chloroplast phylogenomic analysis of the Campanulidae

Directory of Open Access Journals (Sweden)

Xin Yao

2016-11-01

Full Text Available Complete chloroplast genome sequences have been very useful for understanding phylogenetic relationships in angiosperms at the family level and above, but there are currently large gaps in coverage. We report the chloroplast genome for Helwingia himalaica, the first in the distinctive family Helwingiaceae and only the second genus to be sequenced in the order Aquifoliales. We then combine this with 36 published sequences in the large (c. 35,000 species subclass Campanulidae in order to investigate relationships at the order and family levels. The Helwingia genome consists of 158,362 bp containing a pair of inverted repeat (IR regions of 25,996 bp separated by a large single-copy (LSC region and a small single-copy (SSC region which are 87,810 and 18,560 bp, respectively. There are 142 known genes, including 94 protein-coding genes, eight ribosomal RNA genes, and 40 tRNA genes. The topology of the phylogenetic relationships between Apiales, Asterales, and Dipsacales differed between analyses based on complete genome sequences and on 36 shared protein-coding genes, showing that further studies of campanulid phylogeny are needed.

Arabidopsis EMB1990 Encoding a Plastid-Targeted YlmG Protein Is Required for Chloroplast Biogenesis and Embryo Development

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Hongyu Chen

2018-02-01

Full Text Available In higher plants, embryo development originated from fertilized egg cell is the first step of the life cycle. The chloroplast participates in many essential metabolic pathways, and its function is highly associated with embryo development. However, the mechanisms and relevant genetic components by which the chloroplast functions in embryogenesis are largely uncharacterized. In this paper, we describe the Arabidopsis EMB1990 gene, encoding a plastid-targeted YlmG protein which is required for chloroplast biogenesis and embryo development. Loss of the EMB1990/YLMG1-1 resulted in albino seeds containing abortive embryos, and the morphological development of homozygous emb1990 embryos was disrupted after the globular stage. Our results showed that EMB1990/YLMG1-1 was expressed in the primordia and adaxial region of cotyledon during embryogenesis, and the encoded protein was targeted to the chloroplast. TEM observation of cellular ultrastructure showed that chloroplast biogenesis was impaired in emb1990 embryo cells. Expression of certain plastid genes was also affected in the loss-of-function mutants, including genes encoding core protein complex subunits located in the thylakoid membrane. Moreover, the tissue-specific genes of embryo development were misexpressed in emb1990 mutant, including genes known to delineate cell fate decisions in the SAM (shoot apical meristem, cotyledon and hypophysis. Taken together, we propose that the nuclear-encoded YLMG1-1 is targeted to the chloroplast and required for normal plastid gene expression. Hence, YLMG1-1 plays a critical role in Arabidopsis embryogenesis through participating in chloroplast biogenesis.

Transcriptional regulation and DNA methylation in plastids during transitional conversion of chloroplasts to chromoplasts.

OpenAIRE

Kobayashi, H; Ngernprasirtsiri, J; Akazawa, T

1990-01-01

During transitional conversion of chloroplasts to chromoplasts in ripening tomato (Lycopersicon esculentum) fruits, transcripts for several plastid genes for photosynthesis decreased to undetectable levels. Run-on transcription of plastids indicated that transcriptional regulation operated as a predominant factor. We found that most of the genes in chloroplasts were actively transcribed in vitro by Escherichia coli and soluble plastid RNA polymerases, but some genes in chromoplasts seemed to ...

Modified Invasion Percolation Models for Multiphase Processes

Energy Technology Data Exchange (ETDEWEB)

Karpyn, Zuleima [Pennsylvania State Univ., State College, PA (United States)

2015-01-31

This project extends current understanding and modeling capabilities of pore-scale multiphase flow physics in porous media. High-resolution X-ray computed tomography imaging experiments are used to investigate structural and surface properties of the medium that influence immiscible displacement. Using experimental and computational tools, we investigate the impact of wetting characteristics, as well as radial and axial loading conditions, on the development of percolation pathways, residual phase trapping and fluid-fluid interfacial areas.

A tiling microarray for global analysis of chloroplast genome expression in cucumber and other plants

Directory of Open Access Journals (Sweden)

Pląder Wojciech

2011-09-01

Full Text Available Abstract Plastids are small organelles equipped with their own genomes (plastomes. Although these organelles are involved in numerous plant metabolic pathways, current knowledge about the transcriptional activity of plastomes is limited. To solve this problem, we constructed a plastid tiling microarray (PlasTi-microarray consisting of 1629 oligonucleotide probes. The oligonucleotides were designed based on the cucumber chloroplast genomic sequence and targeted both strands of the plastome in a non-contiguous arrangement. Up to 4 specific probes were designed for each gene/exon, and the intergenic regions were covered regularly, with 70-nt intervals. We also developed a protocol for direct chemical labeling and hybridization of as little as 2 micrograms of chloroplast RNA. We used this protocol for profiling the expression of the cucumber chloroplast plastome on the PlasTi-microarray. Owing to the high sequence similarity of plant plastomes, the newly constructed microarray can be used to study plants other than cucumber. Comparative hybridization of chloroplast transcriptomes from cucumber, Arabidopsis, tomato and spinach showed that the PlasTi-microarray is highly versatile.

Combined effects of simulated acid rain and lanthanum chloride on chloroplast structure and functional elements in rice.

Science.gov (United States)

Hu, Huiqing; Wang, Lihong; Zhou, Qing; Huang, Xiaohua

2016-05-01

Acid rain and rare earth element (REE) pollution exist simultaneously in many agricultural regions. However, how REE pollution and acid rain affect plant growth in combination remains largely unknown. In this study, the combined effects of simulated acid rain and lanthanum chloride (LaCl3) on chloroplast morphology, chloroplast ultrastructure, functional element contents, chlorophyll content, and the net photosynthetic rate (P n) in rice (Oryza sativa) were investigated by simulating acid rain and rare earth pollution. Under the combined treatment of simulated acid rain at pH 4.5 and 0.08 mM LaCl3, the chloroplast membrane was smooth, proteins on this membrane were uniform, chloroplast structure was integrated, and the thylakoids were orderly arranged, and simulated acid rain and LaCl3 exhibited a mild antagonistic effect; the Mg, Ca, Mn contents, the chlorophyll content, and the P n increased under this combined treatment, with a synergistic effect of simulated acid rain and LaCl3. Under other combined treatments of simulated acid rain and LaCl3, the chloroplast membrane surface was uneven, a clear "hole" was observed on the surface of chloroplasts, and the thylakoids were dissolved and loose; and the P n and contents of functional elements (P, Mg, K, Ca, Mn, Fe, Ni, Cu, Zn and Mo) and chlorophyll decreased. Under these combined treatments, simulated acid rain and LaCl3 exhibited a synergistic effect. Based on the above results, a model of the combined effects of simulated acid rain and LaCl3 on plant photosynthesis was established in order to reveal the combined effects on plant photosynthesis, especially on the photosynthetic organelle-chloroplast. Our results would provide some references for further understanding the mechanism of the combined effects of simulated acid rain and LaCl3 on plant photosynthesis.

Cluster concentrations in correlated and non-correlated continuum percolation problems

International Nuclear Information System (INIS)

Borstnik, B.; Jesudason, C.G.; Lukman, D.

1996-01-01

The methodologies are developed how to evaluate properties of clusters of correlated and non-correlated particles. As an example of correlated particles, the two dimensional hard core disks with attractive square well potential are taken. Narrow and deep square well potential is used in order to mimic the adhesive potential, suitable for modeling of colloidal systems. Permeable disks in two dimensions are taken as an example of non-correlated systems. In both cases the dependence of cluster concentrations upon the density of particles is studied. Percolation threshold densities and critical exponents which govern the zeroth, first and second moments of cluster distributions are evaluated. It is found that the calculation of density dependence of cluster concentrations gives enough information to evaluate the percolation threshold density, some critical exponents, as well as to reproduce the Rushbrooke scaling law

Damage percolation during stretch flange forming of aluminum alloy sheet

Science.gov (United States)

Chen, Zengtao; Worswick, Michael J.; Keith Pilkey, A.; Lloyd, David J.

2005-12-01

A multi-scale finite element (FE)-damage percolation model was employed to simulate stretch flange forming of aluminum alloys AA5182 and AA5754. Material softening and strain gradients were captured using a Gurson-based FE model. FE results were then fed into the so-called damage percolation code, from which the damage development was modelled within measured microstructures. The formability of the stretch flange samples was predicted based upon the onset of catastrophic failure triggered by profuse void coalescence within the measured second-phase particle field. Damage development is quantified in terms of crack and void areal fractions, and compared to metallographic results obtained from interrupted stretch flange specimens. Parametric study is conducted on the effect of void nucleation strain in the prediction of formability of stretch flanges to "calibrate" proper nucleation strains for both alloys.

Percolative Theory of Organic Magnetoresistance and Fringe-Field Magnetoresistance

Science.gov (United States)

Flatté, Michael E.

2013-03-01

A recently-introduced percolation theory for spin transport and magnetoresistance in organic semiconductors describes the effects of spin dynamics on hopping transport by considering changes in the effective density of hopping sites, a key quantity determining the properties of percolative transport. Increases in the spin-flip rate open up ``spin-blocked'' pathways to become viable conduction channels and hence, as the spin-flip rate changes with magnetic field, produce magnetoresistance. Features of this percolative magnetoresistance can be found analytically in several regimes, and agree with measurements of the shape and saturation of measured magnetoresistance curves. We find that the threshold hopping distance is analogous to the branching parameter of a phenomenological two-site model, and that the distinction between slow and fast hopping is contingent on the threshold hopping distance. Regimes of slow and fast hopping magnetoresistance are uniquely characterized by their line shapes. Studies of magnetoresistance in known systems with controllable positional disorder would provide an additional stringent test of this theory. Extensions to this theory also describe fringe-field magnetoresistance, which is the influence of fringe magnetic fields from a nearby unsaturated magnetic electrode on the conductance of an organic film. This theory agrees with several key features of the experimental fringe-field magnetoresistance, including the applied fields where the magnetoresistance reaches extrema, the applied field range of large magnetoresistance effects from the fringe fields, and the sign of the effect. All work done in collaboration with N. J. Harmon, and fringe-field magnetoresistance work in collaboration also with F. Macià, F. Wang, M. Wohlgenannt and A. D. Kent. This work was supported by an ARO MURI.

Study of the interaction of cytochrome c and ferredoxine with the double membrane of chloroplast

International Nuclear Information System (INIS)

Neuburger, M.; Joyard, J.; Douce, R.

1975-01-01

The adsorption of two 59 Fe-labelled proteins on the chloroplast envelope was studied. The former molecule used was ferredoxine extracted from spinach leaves, the latter was cytochrome c, extracted from yeast (Saccharomyces cerevisiae D 261). The chloroplast envelope is thought to be involved in the transport of some proteins such as ferredoxine synthetized in the cytoplasm [fr

The complete chloroplast genome sequence of the medicinal plant Andrographis paniculata.

Science.gov (United States)

Ding, Ping; Shao, Yanhua; Li, Qian; Gao, Junli; Zhang, Runjing; Lai, Xiaoping; Wang, Deqin; Zhang, Huiye

2016-07-01

The complete chloroplast genome of Andrographis paniculata, an important medicinal plant with great economic value, has been studied in this article. The genome size is 150,249 bp in length, with 38.3% GC content. A pair of inverted repeats (IRs, 25,300 bp) are separated by a large single copy region (LSC, 82,459 bp) and a small single-copy region (SSC, 17,190 bp). The chloroplast genome contains 114 unique genes, 80 protein-coding genes, 30 tRNA genes and 4 rRNA genes. In these genes, 15 genes contained 1 intron and 3 genes comprised of 2 introns.

Hydrogen purifier module with membrane support

Science.gov (United States)

A hydrogen purifier utilizing a hydrogen-permeable membrane to purify hydrogen from mixed gases containing hydrogen is disclosed. Improved mechanical support for the permeable membrane is described, enabling forward or reverse differential pressurization of the membrane, which further stabilizes the membrane from wrinkling upon hydrogen uptake.

2012-07-24

A hydrogen purifier utilizing a hydrogen-permeable membrane to purify hydrogen from mixed gases containing hydrogen is disclosed. Improved mechanical support for the permeable membrane is described, enabling forward or reverse differential pressurization of the membrane, which further stabilizes the membrane from wrinkling upon hydrogen uptake.

Photosynthesis by isolated chloroplasts. IV. General concept and comparison of three photochemical reactions

Energy Technology Data Exchange (ETDEWEB)

Arnon, D I; Allen, M B; Whatley, F R

1956-01-01

Procedures are described for the preparation of chloroplasts capable of carrying out three photochemical reactions, each representing an increasingly complex phase of photosynthesis: photolysis of water (Hill reaction), esterification of inorganic phosphate into adenosine triphosphate (photosynthetic phosphorylation) and the reduction of carbon dioxide to the level of carbohydrates with a simultaneous evolution of oxygen. The three photochemical reactions were separable by variations in the technique for preparation of chloroplasts and by differential inhibition by several reagents. Inhibition of a more complex phase of photosynthesis does not affect the simpler one which precedes it and, conversely, the inhibition of a simpler phase of photosynthesis is paralleled by an inhibition of the more complex phase which follows. Reversible inhibition of CO/sub 2/ fixation and photosynthetic phosphorylation, but not of photolysis, by sulfhydryl group inhibitors suggests that sulfhydryl compounds (enzymes, cofactors, or both) are involved in phosphorylation and CO/sub 2/ fixation, but not in the primary conversion of light into chemical energy as measured by the Hill reaction. Evidence is presented in support of the conclusion that the synthesis of ATP by green cells occurs at two distinct sites: anaerobically in chloroplasts by photosynthetic phosphorylation, and acrobically in smaller cytoplasmic particles, presumably mitochondria, by oxidative phosphorylation independent of light. A general scheme of photosynthesis by chloroplasts, consistent with these findings, is presented. 44 references, 8 figures, 4 tables.

Critical two-point functions and the lace expansion for spread-out high-dimensional percolation and related models

NARCIS (Netherlands)

Hara, T.; Hofstad, van der R.W.; Slade, G.

2003-01-01

We consider spread-out models of self-avoiding walk, bond percolation, lattice trees and bond lattice animals on ${\\mathbb{Z}^d}$, having long finite-range connections, above their upper critical dimensions $d=4$ (self-avoiding walk), $d=6$ (percolation) and $d=8$ (trees and animals). The two-point

Overland flow connectivity on planar patchy hillslopes - modified percolation theory approaches and combinatorial model of urns

Science.gov (United States)

Nezlobin, David; Pariente, Sarah; Lavee, Hanoch; Sachs, Eyal

2017-04-01

Source-sink systems are very common in hydrology; in particular, some land cover types often generate runoff (e.g. embedded rocks, bare soil) , while other obstruct it (e.g. vegetation, cracked soil). Surface runoff coefficients of patchy slopes/plots covered by runoff generating and obstructing covers (e.g., bare soil and vegetation) depend critically on the percentage cover (i.e. sources/sinks abundance) and decrease strongly with observation scale. The classic mathematical percolation theory provides a powerful apparatus for describing the runoff connectivity on patchy hillslopes, but it ignores strong effect of the overland flow directionality. To overcome this and other difficulties, modified percolation theory approaches can be considered, such as straight percolation (for the planar slopes), quasi-straight percolation and models with limited obstruction. These approaches may explain both the observed critical dependence of runoff coefficients on percentage cover and their scale decrease in systems with strong flow directionality (e.g. planar slopes). The contributing area increases sharply when the runoff generating percentage cover approaches the straight percolation threshold. This explains the strong increase of the surface runoff and erosion for relatively low values (normally less than 35%) of the obstructing cover (e.g., vegetation). Combinatorial models of urns with restricted occupancy can be applied for the analytic evaluation of meaningful straight percolation quantities, such as NOGA's (Non-Obstructed Generating Area) expected value and straight percolation probability. It is shown that the nature of the cover-related runoff scale decrease is combinatorial - the probability for the generated runoff to avoid obstruction in unit area decreases with scale for the non-trivial percentage cover values. The magnitude of the scale effect is found to be a skewed non-monotonous function of the percentage cover. It is shown that the cover-related scale

Percolative ionic conduction in the LiAlSiO4 glass-ceramic system

International Nuclear Information System (INIS)

Biefeld, R.M.; Pike, G.E.; Johnson, R.T. Jr.

1977-01-01

The effect f crystallinity on the lithium ion conductivity in LiAlSiO 4 glass and glass-ceramic solid electrolytes has been determined. The ionic conductivity is thermally activated with an activation energy and pre-exponential factor that change in a marked and nonsimple manner as the volume fraction of crystallinity changes. These results are explained by using a continuum percolation model (effective-medium approximation) which assumes that ionic conduction in the glass-ceramic is almost entirely within the glass phase until the crystalline volume fraction rises above approx. 55%. The LiAlSiO 4 system would seem to be nearly ideal for application of percolation theory since the crystalline phase, β eucryptite, has nearly the same composition as the glass phase. Hence, as the crystallite volume fraction increases in the glass ceramic, the residual glass composition and conductivity remain the same. This is the first application of percolation theory to ionic transport in glass-ceramics and excellent agreement is obtained between theory and experiment for the LiAlSiO 4 system

A nuclear-encoded chloroplast protein harboring a single CRM domain plays an important role in the Arabidopsis growth and stress response.

Science.gov (United States)

Lee, Kwanuk; Lee, Hwa Jung; Kim, Dong Hyun; Jeon, Young; Pai, Hyun-Sook; Kang, Hunseung

2014-04-16

Although several chloroplast RNA splicing and ribosome maturation (CRM) domain-containing proteins have been characterized for intron splicing and rRNA processing during chloroplast gene expression, the functional role of a majority of CRM domain proteins in plant growth and development as well as chloroplast RNA metabolism remains largely unknown. Here, we characterized the developmental and stress response roles of a nuclear-encoded chloroplast protein harboring a single CRM domain (At4g39040), designated CFM4, in Arabidopsis thaliana. Analysis of CFM4-GFP fusion proteins revealed that CFM4 is localized to chloroplasts. The loss-of-function T-DNA insertion mutants for CFM4 (cfm4) displayed retarded growth and delayed senescence, suggesting that CFM4 plays a role in growth and development of plants under normal growth conditions. In addition, cfm4 mutants showed retarded seed germination and seedling growth under stress conditions. No alteration in the splicing patterns of intron-containing chloroplast genes was observed in the mutant plants, but the processing of 16S and 4.5S rRNAs was abnormal in the mutant plants. Importantly, CFM4 was determined to possess RNA chaperone activity. These results suggest that the chloroplast-targeted CFM4, one of two Arabidopsis genes encoding a single CRM domain-containing protein, harbors RNA chaperone activity and plays a role in the Arabidopsis growth and stress response by affecting rRNA processing in chloroplasts.

Photosynthesis in a different light: Spectro-microscopy for in vivo characterisation of chloroplasts

Directory of Open Access Journals (Sweden)

Sébastien ePeter

2014-06-01

Full Text Available During photosynthesis, energy conversion at the two photosystems is controlled by highly complex and dynamic adaptation processes triggered by external factors such as light quality, intensity, and duration, or internal cues such as carbon availability. These dynamics have remained largely concealed so far, because current analytical techniques are based on the investigation of isolated chloroplasts lacking full adaptation ability and are performed at non-physiologically low temperatures. Here, we use non-invasive in planta spectro-microscopic approaches to investigate living chloroplasts in their native environment at ambient temperatures. This is a valuable approach to study the complex function of these systems, because an intrinsic property – the fluorescence emission – is exploited and no additional external perturbations are introduced. Our analysis demonstrates a dynamic adjustment of not only the photosystemI/photosystemII (PSI/PSII intensity ratio in the chloroplasts but also of the capacity of the LHCs for energy transfer in response to environmental and internal cues.

Differential Subplastidial Localization and Turnover of Enzymes Involved in Isoprenoid Biosynthesis in Chloroplasts.

Directory of Open Access Journals (Sweden)

Catalina Perello

Full Text Available Plastidial isoprenoids are a diverse group of metabolites with roles in photosynthesis, growth regulation, and interaction with the environment. The methylerythritol 4-phosphate (MEP pathway produces the metabolic precursors of all types of plastidial isoprenoids. Proteomics studies in Arabidopsis thaliana have shown that all the enzymes of the MEP pathway are localized in the plastid stroma. However, immunoblot analysis of chloroplast subfractions showed that the first two enzymes of the pathway, deoxyxylulose 5-phosphate synthase (DXS and reductoisomerase (DXR, can also be found in non-stromal fractions. Both transient and stable expression of GFP-tagged DXS and DXR proteins confirmed the presence of the fusion proteins in distinct subplastidial compartments. In particular, DXR-GFP was found to accumulate in relatively large vesicles that could eventually be released from chloroplasts, presumably to be degraded by an autophagy-independent process. Together, we propose that protein-specific mechanisms control the localization and turnover of the first two enzymes of the MEP pathway in Arabidopsis chloroplasts.

Thioredoxin Selectivity for Thiol-based Redox Regulation of Target Proteins in Chloroplasts*

Science.gov (United States)

Yoshida, Keisuke; Hara, Satoshi; Hisabori, Toru

2015-01-01

Redox regulation based on the thioredoxin (Trx) system is believed to ensure light-responsive control of various functions in chloroplasts. Five Trx subtypes have been reported to reside in chloroplasts, but their functional diversity in the redox regulation of Trx target proteins remains poorly clarified. To directly address this issue, we studied the Trx-dependent redox shifts of several chloroplast thiol-modulated enzymes in vitro and in vivo. In vitro assays using a series of Arabidopsis recombinant proteins provided new insights into Trx selectivity for the redox regulation as well as the underpinning for previous suggestions. Most notably, by combining the discrimination of thiol status with mass spectrometry and activity measurement, we identified an uncharacterized aspect of the reductive activation of NADP-malate dehydrogenase; two redox-active Cys pairs harbored in this enzyme were reduced via distinct utilization of Trxs even within a single polypeptide. In our in vitro assays, Trx-f was effective in reducing all thiol-modulated enzymes analyzed here. We then investigated the in vivo physiological relevance of these in vitro findings, using Arabidopsis wild-type and Trx-f-deficient plants. Photoreduction of fructose-1,6-bisphosphatase was partially impaired in Trx-f-deficient plants, but the global impact of Trx-f deficiency on the redox behaviors of thiol-modulated enzymes was not as striking as expected from the in vitro data. Our results provide support for the in vivo functionality of the Trx system and also highlight the complexity and plasticity of the chloroplast redox network. PMID:25878252

Proton gradients and proton-dependent transport processes in the chloroplast

Directory of Open Access Journals (Sweden)

Ricarda eHöhner

2016-02-01

Full Text Available Proton gradients are fundamental to chloroplast function. Across thylakoid membranes, the light induced proton gradient is essential for ATP synthesis. As a result of proton pumping into the thylakoid lumen, an alkaline stromal pH develops, which is required for full activation of pH-dependent Calvin Benson cycle enzymes. This implies that a pH gradient between the cytosol (pH 7 and the stroma (pH 8 is established upon illumination. To maintain this pH gradient chloroplasts actively extrude protons. More than 30 years ago it was already established that these proton fluxes are electrically counterbalanced by Mg2+, K+ or Cl- fluxes, but only recently the first transport systems that regulate the pH gradient were identified. Notably several (Na+,K+/H+ antiporter systems where identified, that play a role in pH gradient regulation, ion homeostasis, osmoregulation, or coupling of secondary active transport. The established pH gradients are important to drive uptake of essential ions and solutes, but not many transporters involved have been identified to date. In this mini review we summarize the current status in the field and the open questions that need to be addressed in order to understand how pH gradients are maintained, how this is interconnected with other transport processes and what this means for chloroplast function.

Ultrathin percolated WO{sub 3} cluster film and its resistive response to H{sub 2}

Energy Technology Data Exchange (ETDEWEB)

Zhao, Meng [Research Center for Solid State Physics and Materials, School of Mathematics and Physics, Suzhou University of Science and Technology, Suzhou 215009 (China); Department of Applied Physics and Materials Research Center, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong (China); Wong, Man Hon; Huang, Jian Xing [Department of Applied Physics and Materials Research Center, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong (China); Ong, Chung Wo, E-mail: c.w.ong@polyu.edu.hk [Department of Applied Physics and Materials Research Center, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong (China)

2014-11-05

Highlights: • Ultrathin percolated network of WO{sub 3} clusters was fabricated. • The WO{sub 3} clusters are modeled by spherical caps connected by ultrafine linkages. • The ultrathin percolated network of WO{sub 3} clusters shows fast response rate to H{sub 2}. • The fast response is attributed to the rapid electrical switching of the linkages. • Improved H{sub 2} sensing properties may be achieved if narrower linkages are used. - Abstract: Thin films composed of tungsten oxide (WO{sub 3}) nanoclusters were fabricated by oxidizing supersonic cluster beam deposited tungsten films at various temperatures. Oxidation at 700 °C resulted in aggregation of the deposits, forming a percolated network of WO{sub 3} spherical caps connected by fine links. The resistance response of the palladium-(Pd-) coated film sample to hydrogen (H{sub 2}) was investigated. The response rate was faster than those of other samples oxidized at lower temperatures. This is the result of the rapid electrical switching of the intercluster links between the highly resistive depleted state and conducting hydrogenated state. The possibility of improving the H{sub 2} sensing response rate with the use of the percolated WO{sub 3} film structure is illustrated.

Chloroplast Movement May Impact Plant Phenotyping and Photochemistry Results

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Malas, J.; Pleban, J. R.; Wang, D. R.; Riley, C.; Mackay, D. S.

2017-12-01

Investigating phenotypic responses of crop species across environmental conditions is vital to improving agricultural productivity. Crop production is closely linked with photosynthetic activity, which can be evaluated using parameters such as relative chlorophyll, SPAD, and variable chlorophyll fluorescence. Recently, a handheld device known as the MultispeQ emerged on the market as an open-source instrument that aims to provide high-output, high-quality field data at a low cost to the plant research community. MultispeQ takes measurements of both environmental conditions (light intensity, temperature, humidity, etc.) and photosynthetic parameters (relative chlorophyll, SPAD, photosystem II quantum efficiency (FII), and non-photochemical quenching (NPQ)). Data are automatically backed up and shared on the PhotosynQ network, which serves as a collaborative platform for researchers and professionals. Here, we used the instrument to quantify photosynthetic time-courses of two Brassica rapa genotypes in response to two contrasting nutrient management strategies (Control; High Nitrogen). Previous research found that chloroplast movement is one strategy plants use to optimize photosynthesis across varying light conditions. We were able to detect chloroplast movement throughout the day using the MultispeQ device. Our results support the idea that chloroplast movement serves both as an intrinsic feature of the circadian clock and as a light avoidance strategy. Under low light conditions (PAR 0-300) more light at the near-infrared and red regions was absorbed than under higher light conditions (PAR 500-800). In one genotype by treatment combination, absorbance at 730nm was around 60% at low light, versus only 30% at high light conditions. In light of our results that relative chlorophyll may change throughout a day, we suggest that it is important to take note of these effects when collecting photosynthesis efficiency data in order to avoid bias in measurements. We also

Characterization of polymorphic SSRs among Prunus chloroplast genomes

Science.gov (United States)

An in silico mining process yielded 80, 75, and 78 microsatellites in the chloroplast genome of Prunus persica, P. kansuensis, and P. mume. A and T repeats were predominant in the three genomes, accounting for 67.8% on average and most of them were successful in primer design. For the 80 P. persica ...

Temporal percolation of the susceptible network in an epidemic spreading.

Science.gov (United States)

Valdez, Lucas Daniel; Macri, Pablo Alejandro; Braunstein, Lidia Adriana

2012-01-01

In this work, we study the evolution of the susceptible individuals during the spread of an epidemic modeled by the susceptible-infected-recovered (SIR) process spreading on the top of complex networks. Using an edge-based compartmental approach and percolation tools, we find that a time-dependent quantity ΦS(t), namely, the probability that a given neighbor of a node is susceptible at time t, is the control parameter of a node void percolation process involving those nodes on the network not-reached by the disease. We show that there exists a critical time t(c) above which the giant susceptible component is destroyed. As a consequence, in order to preserve a macroscopic connected fraction of the network composed by healthy individuals which guarantee its functionality, any mitigation strategy should be implemented before this critical time t(c). Our theoretical results are confirmed by extensive simulations of the SIR process.

Effect of Radiation Dosage on Efficiency of Chloroplast Transfer by Protoplast Fusion in Nicotiana

OpenAIRE

Menczel, László; Galiba, Gábor; Nagy, Ferenc; Maliga, Pál

1982-01-01

Chloroplasts of Nicotiana tabacum SR1 were transferred into Nicotiana plumbaginifolia by protoplast fusion. The protoplasts of the organelle donor were irradiated with different lethal doses using a 60Co source, to facilitate the elimination of their nuclei from the fusion products. After fusion induction, clones derived from fusion products and containing streptomycin-resistant N. tabacum SR1 chloroplasts were selected by their ability to green on a selective medium. When N. tabacum protopla...

21 CFR 880.6710 - Medical ultraviolet water purifier.

Science.gov (United States)

2010-04-01

... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Medical ultraviolet water purifier. 880.6710... Miscellaneous Devices § 880.6710 Medical ultraviolet water purifier. (a) Identification. A medical ultraviolet water purifier is a device intended for medical purposes that is used to destroy bacteria in water by...

Percolation pond as a method of managed aquifer recharge in a ...

Indian Academy of Sciences (India)

Raicy Mani Christy

2017-07-17

Jul 17, 2017 ... Percolation ponds have become very popular methods of managed aquifer recharge due to their low ... effect of recharge structures by some researchers .... qualitative comparison of observed responses of .... Two types of.

Estimating filtration coefficients for straining from percolation and random walk theories

DEFF Research Database (Denmark)

Yuan, Hao; Shapiro, Alexander; You, Zhenjiang

2012-01-01

In this paper, laboratory challenge tests are carried out under unfavorable attachment conditions, so that size exclusion or straining is the only particle capture mechanism. The experimental results show that far above the percolation threshold the filtration coefficients are not proportional...... size exclusion theory or the model of parallel tubes with mixing chambers, where the filtration coefficients are proportional to the flux through smaller pores, and the predicted penetration depths are much lower. A special capture mechanism is proposed, which makes it possible to explain...... the experimentally observed power law dependencies of filtration coefficients and large penetration depths of particles. Such a capture mechanism is realized in a 2D pore network model with periodical boundaries with the random walk of particles on the percolation lattice. Geometries of infinite and finite clusters...

Measurement of cation exchange capacity (CEC) on natural zeolite by percolation method

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Wiyantoko, Bayu; Rahmah, Nafisa

2017-12-01

The cation exchange capacity (CEC)measurement has been carried out in natural zeolite by percolation method. The natural zeolite samples used for cation exchange capacity measurement were activated beforehand with physical activation and chemical activation. The physically activated zeolite was done by calcination process at 600 °C for 4 hours. The natural zeolite was activated chemically by using sodium hydroxide by refluxing process at 60-80 °C for 3 hours. In summary, cation exchange capacity (CEC) determination was performed by percolation, distillation and titration processes. Based on the measurement that has been done, the exchange rate results from physical activated and chemical activated of natural zeolite were 181.90cmol (+)/kg and 901.49cmol (+)/kg respectively.

DISRUPTION OF ARABIDOPSIS RETICULON GENE RTNLB16 RESULTS IN CHLOROPLAST DYSFUNCTION AND OXIDATIVE STRESS

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Tarasenko V.I.

2012-08-01

Full Text Available Reticulons (RTNs are endoplasmic reticulum (ER-localized proteins that have recently attracted much attention. RTNs are ubiquitous proteins present in all eukaryotic organisms examined so far. In animal and yeast, in which knowledge of this protein family is more advanced, RTNs are involved in numerous cellular processes such as apoptosis, cell division and intracellular trafficking. Up to now, a little attention has been paid to their plant counterparts, RTNLBs. Meanwhile, gene search across sequenced genomes revealed that the RTN gene family is more diverse and numerous in plants than in animals and yeasts, which possibly suggests existence of functions specific for plant RTNs. Recently, the localization in different ER regions was shown for two members of plant reticulon family. The location in close proximity to chloroplast membrane was revealed for one of RTNLBs, which is argument in favor of its role in interorganellar interactions. In spite of growing interest towards to plant RTNs, there are no investigations devoted to insertion mutagenesis of genes encoding these proteins. We have genotyped an Arabidopsis line containing T-DNA insertion in RTNLB16 gene encoding uncharacterized member of RTNLB family. The obtained homozygous plants have marked phenotype expressed in a decreased growth rate and a pale-green leaf color. The leaf total chlorophyll content as well as the chlorophyll a/b ratio was significantly lower in mutant plants. It is interesting to note that the extent of phenotypic expression depended on a light intensity. The growth rate of wild-type and mutant plants was the same in low light conditions. The growth rate was significantly decreased and chlorophyll content was 3-5-fold lower in mutant plants growing under moderate light conditions. The growing of plants under high light conditions led to halted growth and death of mutants on the seedling stage. The demonstrated phenotype probably points out to a chloroplast

The Complete Chloroplast Genome of Ye-Xing-Ba (Scrophularia dentata; Scrophulariaceae), an Alpine Tibetan Herb.

Science.gov (United States)

Ni, Lianghong; Zhao, Zhili; Dorje, Gaawe; Ma, Mi

2016-01-01

Scrophularia dentata is an important Tibetan medicinal plant and traditionally used for the treatment of exanthema and fever in Traditional Tibetan Medicine (TTM). However, there is little sequence and genomic information available for S. dentata. In this paper, we report the complete chloroplast genome sequence of S. dentata and it is the first sequenced member of the Sect. Tomiophyllum within Scrophularia (Scrophulariaceae). The gene order and organization of the chloroplast genome of S. dentata are similar to other Lamiales chloroplast genomes. The plastome is 152,553 bp in length and includes a pair of inverted repeats (IRs) of 25,523 bp that separate a large single copy (LSC) region of 84,058 bp and a small single copy (SSC) region of 17,449 bp. It has 38.0% GC content and includes 114 unique genes, of which 80 are protein-coding, 30 are transfer RNA, and 4 are ribosomal RNA. Also, it contains 21 forward repeats, 19 palindrome repeats and 41 simple sequence repeats (SSRs). The repeats and SSRs within S. dentata were compared with those of S. takesimensis and present certain discrepancies. The chloroplast genome of S. dentata was compared with other five publicly available Lamiales genomes from different families. All the coding regions and non-coding regions (introns and intergenic spacers) within the six chloroplast genomes have been extracted and analysed. Furthermore, the genome divergent hotspot regions were identified. Our studies could provide basic data for the alpine medicinal species conservation and molecular phylogenetic researches of Scrophulariaceae and Lamiales.

The Complete Chloroplast Genome of Ye-Xing-Ba (Scrophularia dentata; Scrophulariaceae, an Alpine Tibetan Herb.

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Lianghong Ni

Full Text Available Scrophularia dentata is an important Tibetan medicinal plant and traditionally used for the treatment of exanthema and fever in Traditional Tibetan Medicine (TTM. However, there is little sequence and genomic information available for S. dentata. In this paper, we report the complete chloroplast genome sequence of S. dentata and it is the first sequenced member of the Sect. Tomiophyllum within Scrophularia (Scrophulariaceae. The gene order and organization of the chloroplast genome of S. dentata are similar to other Lamiales chloroplast genomes. The plastome is 152,553 bp in length and includes a pair of inverted repeats (IRs of 25,523 bp that separate a large single copy (LSC region of 84,058 bp and a small single copy (SSC region of 17,449 bp. It has 38.0% GC content and includes 114 unique genes, of which 80 are protein-coding, 30 are transfer RNA, and 4 are ribosomal RNA. Also, it contains 21 forward repeats, 19 palindrome repeats and 41 simple sequence repeats (SSRs. The repeats and SSRs within S. dentata were compared with those of S. takesimensis and present certain discrepancies. The chloroplast genome of S. dentata was compared with other five publicly available Lamiales genomes from different families. All the coding regions and non-coding regions (introns and intergenic spacers within the six chloroplast genomes have been extracted and analysed. Furthermore, the genome divergent hotspot regions were identified. Our studies could provide basic data for the alpine medicinal species conservation and molecular phylogenetic researches of Scrophulariaceae and Lamiales.

Rubber elasticity for percolation network consisting of Gaussian chains

Energy Technology Data Exchange (ETDEWEB)

Nishi, Kengo, E-mail: kengo.nishi@phys.uni-goettingen.de, E-mail: sakai@tetrapod.t.u-tokyo.ac.jp, E-mail: sibayama@issp.u-tokyo.ac.jp; Noguchi, Hiroshi; Shibayama, Mitsuhiro, E-mail: kengo.nishi@phys.uni-goettingen.de, E-mail: sakai@tetrapod.t.u-tokyo.ac.jp, E-mail: sibayama@issp.u-tokyo.ac.jp [Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581 (Japan); Sakai, Takamasa, E-mail: kengo.nishi@phys.uni-goettingen.de, E-mail: sakai@tetrapod.t.u-tokyo.ac.jp, E-mail: sibayama@issp.u-tokyo.ac.jp [Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656 (Japan)

2015-11-14

A theory describing the elastic modulus for percolation networks of Gaussian chains on general lattices such as square and cubic lattices is proposed and its validity is examined with simulation and mechanical experiments on well-defined polymer networks. The theory was developed by generalizing the effective medium approximation (EMA) for Hookian spring network to Gaussian chain networks. From EMA theory, we found that the ratio of the elastic modulus at p, G to that at p = 1, G{sub 0}, must be equal to G/G{sub 0} = (p − 2/f)/(1 − 2/f) if the position of sites can be determined so as to meet the force balance, where p is the degree of cross-linking reaction. However, the EMA prediction cannot be applicable near its percolation threshold because EMA is a mean field theory. Thus, we combine real-space renormalization and EMA and propose a theory called real-space renormalized EMA, i.e., REMA. The elastic modulus predicted by REMA is in excellent agreement with the results of simulations and experiments of near-ideal diamond lattice gels.

Rubber elasticity for percolation network consisting of Gaussian chains

International Nuclear Information System (INIS)

Nishi, Kengo; Noguchi, Hiroshi; Shibayama, Mitsuhiro; Sakai, Takamasa

2015-01-01

A theory describing the elastic modulus for percolation networks of Gaussian chains on general lattices such as square and cubic lattices is proposed and its validity is examined with simulation and mechanical experiments on well-defined polymer networks. The theory was developed by generalizing the effective medium approximation (EMA) for Hookian spring network to Gaussian chain networks. From EMA theory, we found that the ratio of the elastic modulus at p, G to that at p = 1, G 0 , must be equal to G/G 0 = (p − 2/f)/(1 − 2/f) if the position of sites can be determined so as to meet the force balance, where p is the degree of cross-linking reaction. However, the EMA prediction cannot be applicable near its percolation threshold because EMA is a mean field theory. Thus, we combine real-space renormalization and EMA and propose a theory called real-space renormalized EMA, i.e., REMA. The elastic modulus predicted by REMA is in excellent agreement with the results of simulations and experiments of near-ideal diamond lattice gels

Transport of Ions Across the Inner Envelope Membrane of Chloroplasts

International Nuclear Information System (INIS)

McCarty, R. E.

2004-01-01

The technical report outlines the results of nine years of research on how ions cross the inner envelope membrane of chloroplasts. The ions include protons, nitrite, calcium and ferrous iron. Bicarbonate transport was also studied

Chloroplast DNA codon use: evidence for selection at the psb A locus based on tRNA availability.

Science.gov (United States)

Morton, B R

1993-09-01

Codon use in the three sequenced chloroplast genomes (Marchantia, Oryza, and Nicotiana) is examined. The chloroplast has a bias in that codons NNA and NNT are favored over synonymous NNC and NNG codons. This appears to be a consequence of an overall high A + T content of the genome. This pattern of codon use is not followed by the psb A gene of all three genomes and other psb A sequences examined. In this gene, the codon use favors NNC over NNT for twofold degenerate amino acids. In each case the only tRNA coded by the genome is complementary to the NNC codon. This codon use is similar to the codon use by chloroplast genes examined from Chlamydomonas reinhardtii. Since psb A is the major translation product of the chloroplast, this suggests that selection is acting on the codon use of this gene to adapt codons to tRNA availability, as previously suggested for unicellular organisms.

Complete chloroplast DNA sequence from a Korean endemic genus, Megaleranthis saniculifolia, and its evolutionary implications.

Science.gov (United States)

Kim, Young-Kyu; Park, Chong-wook; Kim, Ki-Joong

2009-03-31

The chloroplast DNA sequences of Megaleranthis saniculifolia, an endemic and monotypic endangered plant species, were completed in this study (GenBank FJ597983). The genome is 159,924 bp in length. It harbors a pair of IR regions consisting of 26,608 bp each. The lengths of the LSC and SSC regions are 88,326 bp and 18,382 bp, respectively. The structural organizations, gene and intron contents, gene orders, AT contents, codon usages, and transcription units of the Megaleranthis chloroplast genome are similar to those of typical land plant cp DNAs. However, the detailed features of Megaleranthis chloroplast genomes are substantially different from that of Ranunculus, which belongs to the same family, the Ranunculaceae. First, the Megaleranthis cp DNA was 4,797 bp longer than that of Ranunculus due to an expanded IR region into the SSC region and duplicated sequence elements in several spacer regions of the Megaleranthis cp genome. Second, the chloroplast genomes of Megaleranthis and Ranunculus evidence 5.6% sequence divergence in the coding regions, 8.9% sequence divergence in the intron regions, and 18.7% sequence divergence in the intergenic spacer regions, respectively. In both the coding and noncoding regions, average nucleotide substitution rates differed markedly, depending on the genome position. Our data strongly implicate the positional effects of the evolutionary modes of chloroplast genes. The genes evidencing higher levels of base substitutions also have higher incidences of indel mutations and low Ka/Ks ratios. A total of 54 simple sequence repeat loci were identified from the Megaleranthis cp genome. The existence of rich cp SSR loci in the Megaleranthis cp genome provides a rare opportunity to study the population genetic structures of this endangered species. Our phylogenetic trees based on the two independent markers, the nuclear ITS and chloroplast matK sequences, strongly support the inclusion of the Megaleranthis to the Trollius. Therefore, our

A Comparison of the First Two Sequenced Chloroplast Genomes in Asteraceae: Lettuce and Sunflower

Energy Technology Data Exchange (ETDEWEB)

Timme, Ruth E.; Kuehl, Jennifer V.; Boore, Jeffrey L.; Jansen, Robert K.

2006-01-20

Asteraceae is the second largest family of plants, with over 20,000 species. For the past few decades, numerous phylogenetic studies have contributed to our understanding of the evolutionary relationships within this family, including comparisons of the fast evolving chloroplast gene, ndhF, rbcL, as well as non-coding DNA from the trnL intron plus the trnLtrnF intergenic spacer, matK, and, with lesser resolution, psbA-trnH. This culminated in a study by Panero and Funk in 2002 that used over 13,000 bp per taxon for the largest taxonomic revision of Asteraceae in over a hundred years. Still, some uncertainties remain, and it would be very useful to have more information on the relative rates of sequence evolution among various genes and on genome structure as a potential set of phylogenetic characters to help guide future phylogenetic structures. By way of contributing to this, we report the first two complete chloroplast genome sequences from members of the Asteraceae, those of Helianthus annuus and Lactuca sativa. These plants belong to two distantly related subfamilies, Asteroideae and Cichorioideae, respectively. In addition to these, there is only one other published chloroplast genome sequence for any plant within the larger group called Eusterids II, that of Panax ginseng (Araliaceae, 156,318 bps, AY582139). Early chloroplast genome mapping studies demonstrated that H. annuus and L. sativa share a 22 kb inversion relative to members of the subfamily Barnadesioideae. By comparison to outgroups, this inversion was shown to be derived, indicating that the Asteroideae and Cichorioideae are more closely related than either is to the Barnadesioideae. Later sequencing study found that taxa that share this 22 kb inversion also contain within this region a second, smaller, 3.3 kb inversion. These sequences also enable an analysis of patterns of shared repeats in the genomes at fine level and of RNA editing by comparison to available EST sequences. In addition, since

Expression of Trichoderma reesei β-mannanase in tobacco chloroplasts and its utilization in lignocellulosic woody biomass hydrolysis.

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Pankaj Agrawal

Full Text Available Lignocellulosic ethanol offers a promising alternative to conventional fossil fuels. One among the major limitations in the lignocellulosic biomass hydrolysis is unavailability of efficient and environmentally biomass degrading technologies. Plant-based production of these enzymes on large scale offers a cost-effective solution. Cellulases, hemicellulases including mannanases and other accessory enzymes are required for conversion of lignocellulosic biomass into fermentable sugars. β-mannanase catalyzes endo-hydrolysis of the mannan backbone, a major constituent of woody biomass. In this study, the man1 gene encoding β-mannanase was isolated from Trichoderma reesei and expressed via the chloroplast genome. PCR and Southern hybridization analysis confirmed site-specific transgene integration into the tobacco chloroplast genomes and homoplasmy. Transplastomic plants were fertile and set viable seeds. Germination of seeds in the selection medium showed inheritance of transgenes into the progeny without any Mendelian segregation. Expression of endo-β-mannanase for the first time in plants facilitated its characterization for use in enhanced lignocellulosic biomass hydrolysis. Gel diffusion assay for endo-β-mannanase showed the zone of clearance confirming functionality of chloroplast-derived mannanase. Endo-β-mannanase expression levels reached up to 25 units per gram of leaf (fresh weight. Chloroplast-derived mannanase had higher temperature stability (40 °C to 70 °C and wider pH optima (pH 3.0 to 7.0 than E.coli enzyme extracts. Plant crude extracts showed 6-7 fold higher enzyme activity than E.coli extracts due to the formation of disulfide bonds in chloroplasts, thereby facilitating their direct utilization in enzyme cocktails without any purification. Chloroplast-derived mannanase when added to the enzyme cocktail containing a combination of different plant-derived enzymes yielded 20% more glucose equivalents from pinewood than the

Origins of the amphiploid species Brassica napus L. investigated by chloroplast and nuclear molecular markers

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Allender Charlotte J

2010-03-01

Full Text Available Abstract Background The amphiploid species Brassica napus (oilseed rape, Canola is a globally important oil crop yielding food, biofuels and industrial compounds such as lubricants and surfactants. Identification of the likely ancestors of each of the two genomes (designated A and C found in B. napus would facilitate incorporation of novel alleles from the wider Brassica genepool in oilseed rape crop genetic improvement programmes. Knowledge of the closest extant relatives of the genotypes involved in the initial formation of B. napus would also allow further investigation of the genetic factors required for the formation of a stable amphiploid and permit the more efficient creation of fully fertile re-synthesised B. napus. We have used a combination of chloroplast and nuclear genetic markers to investigate the closest extant relatives of the original maternal progenitors of B. napus. This was based on a comprehensive sampling of the relevant genepools, including 83 accessions of A genome B. rapa L. (both wild and cultivated types, 94 accessions of B. napus and 181 accessions of C genome wild and cultivated B. oleracea L. and related species. Results Three chloroplast haplotypes occurred in B. napus. The most prevalent haplotype (found in 79% of accessions was not present within the C genome accessions but was found at low frequencies in B. rapa. Chloroplast haplotypes characteristic of B. napus were found in a small number of wild and weedy B. rapa populations, and also in two accessions of cultivated B. rapa 'brocoletto'. Whilst introgression of the B. napus chloroplast type in the wild and weedy B. rapa populations has been proposed by other studies, the presence of this haplotype within the two brocoletto accessions is unexplained. Conclusions The distribution of chloroplast haplotypes eliminate any of the C genome species as being the maternal ancestor of the majority of the B. napus accessions. The presence of multiple chloroplast

β-Carotene as a factor in the reconstitution of cyclic phospho rylation in damaged chloroplast membranes

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Anna Tukendorf

2014-01-01

Full Text Available Phenazine methosulphate mediated cyclic phosphorylation suppressed by heptane extraction or galactolipase treatment of spinach chloroplasts is restored by β -carotene, in 100% and 50%, respectively. Xanthophylls are not able to reconstitute this reaction. β-Carotene replaces galactolipids in reactivation of galactolipase treated chloroplasts, indicating a nonspecific effect of lipids in photosystem I dependent reactions.

Photosynthesis by isolated chloroplasts. VIII. Photosynthetic phosphorylation and the generation of assimilatory power

Energy Technology Data Exchange (ETDEWEB)

Arnon, D I; Whatley, F R; Allen, M B

1959-01-01

Photochemical ATP formation by isolated chloroplasts was coupled with a reduction of ferricyanide or TPN. Esterification of two moles of orthophosphate was coupled with the formation of two moles of TPNH/sub 2/ and the evolution of one mole of oxygen. The addition of catalytic amounts of FMN, vitamin K or phenazine methosulfate to the TPN phosphorylating system suppressed TPNH/sub 2/ accumulation as well as oxygen evolution and greatly increased the light-dependent ATP formation. A revised general scheme is presented for photosynthesis by isolated chloroplasts. 35 references, 9 figures, 4 tables.

Brassinosteroid-induced CO2 assimilation is associated with increased stability of redox-sensitive photosynthetic enzymes in the chloroplasts in cucumber plants

International Nuclear Information System (INIS)

Jiang, Yu Ping; Cheng, Fei; Zhou, Yan Hong; Xia, Xiao Jian; Mao, Wei Hua; Shi, Kai; Chen, Zhi Xiang; Yu, Jing Quan

2012-01-01

Highlights: ► Activity of certain Calvin cycle enzymes and CO 2 assimilation are induced by BRs. ► BRs upregulate the activity of the ascorbate–glutathione cycle in the chloroplasts. ► BRs increase the chloroplast thiol reduction state. ► A BR-induced reducing environment increases the stability of photosynthetic enzymes. -- Abstract: Brassinosteroids (BRs) play important roles in plant growth, development, photosynthesis and stress tolerance; however, the mechanism underlying BR-enhanced photosynthesis is currently unclear. Here, we provide evidence that an increase in the BR level increased the quantum yield of PSII, activities of Rubisco activase (RCA) and fructose-1,6-bisphosphatase (FBPase), and CO 2 assimilation. BRs upregulated the transcript levels of genes and activity of enzymes involved in the ascorbate–glutathione cycle in the chloroplasts, leading to an increased ratio of reduced (GSH) to oxidized (GSSG) glutathione in the chloroplasts. An increased GSH/GSSG ratio protected RCA from proteolytic digestion and increased the stability of redox-sensitive enzymes in the chloroplasts. These results strongly suggest that BRs are capable of regulating the glutathione redox state in the chloroplasts through the activation of the ascorbate–glutathione cycle. The resulting increase in the chloroplast thiol reduction state promotes CO 2 assimilation, at least in part, by enhancing the stability and activity of redox-sensitive photosynthetic enzymes through post-translational modifications.

Electrical Properties of Zinc-Kaolin Composites below its Percolation ...

African Journals Online (AJOL)

In this paper, we present some electrical properties of the zinc-kaolin cermet resistors with zinc metal fillers below the percolation threshold. Rectangular cermet rods of dimensions 65 mm by 6.5 mm by 3.2 mm were produced in a mould with semi-dry the zinc/kaolin powder mixture which is compressed with a force of about ...

Probing the energy barriers and magnetization reversal processes of nanoperforated membrane based percolated media

International Nuclear Information System (INIS)

Neu, V; Schultz, L; Schulze, C; Makarov, D; Albrecht, M; Faustini, M; Grosso, D; Lee, J; Kim, S-K; Suess, D

2013-01-01

Magnetization reversal processes in Co/Pt multilayers prepared on nanoperforated templates are probed by magnetization relaxation measurements. The signature of pinning controlled domain wall movement as expected for percolated media is identified. This contrasts with the nucleation-type reversal mechanism of a Co/Pt reference film prepared on a smooth substrate. A zero field energy barrier of 93k B T is determined by fluctuation field measurements and is elucidated by micromagnetic calculations using the nudged elastic band method. This value is sufficiently large to qualify the material as a promising percolated medium. (paper)

Various types of chromoproteins extracted from tobacco chloroplasts

International Nuclear Information System (INIS)

Sirchis, Jean; Duranton, Jacques

1959-01-01

From tobacco chloroplasts a chroma-proteic complex is isolated; this can be fractionally divided into two different species by the difference in their chemical compositions and their speeds of sedimentation. Reprint of a paper published in 'Comptes Rendus des Seances de l'Academie des Sciences', tome 248, p. 2528-2530, sitting of 27 April 1959 [fr

Rethinking Rice Preparation for Highly Efficient Removal of Inorganic Arsenic Using Percolating Cooking Water.

Science.gov (United States)

Carey, Manus; Jiujin, Xiao; Gomes Farias, Júlia; Meharg, Andrew A

2015-01-01

A novel way of cooking rice to maximize the removal of the carcinogen inorganic arsenic (Asi) is presented here. In conventional rice cooking water and grain are in continuous contact, and it is known that the larger the water:rice cooking ratio, the more Asi removed by cooking, suggesting that the Asi in the grain is mobile in water. Experiments were designed where rice is cooked in a continual stream of percolating near boiling water, either low in Asi, or Asi free. This has the advantage of not only exposing grain to large volumes of cooking water, but also physically removes any Asi leached from the grain into the water receiving vessel. The relationship between cooking water volume and Asi removal in conventional rice cooking was demonstrated for the rice types under study. At a water-to-rice cooking ratio of 12:1, 57±5% of Asi could be removed, average of 6 wholegrain and 6 polished rice samples. Two types of percolating technology were tested, one where the cooking water was recycled through condensing boiling water steam and passing the freshly distilled hot water through the grain in a laboratory setting, and one where tap water was used to cook the rice held in an off-the-shelf coffee percolator in a domestic setting. Both approaches proved highly effective in removing Asi from the cooking rice, with up to 85% of Asi removed from individual rice types. For the recycled water experiment 59±8% and 69±10% of Asi was removed, on average, compared to uncooked rice for polished (n=27) and wholegrain (n=13) rice, respectively. For coffee percolation there was no difference between wholegrain and polished rice, and the effectiveness of Asi removal was 49±7% across 6 wholegrain and 6 polished rice samples. The manuscript explores the potential applications and further optimization of this percolating cooking water, high Asi removal, discovery.

The first complete chloroplast genome sequence of a lycophyte,Huperzia lucidula (Lycopodiaceae)

Energy Technology Data Exchange (ETDEWEB)

Wolf, Paul G.; Karol, Kenneth G.; Mandoli, Dina F.; Kuehl,Jennifer V.; Arumuganathan, K.; Ellis, Mark W.; Mishler, Brent D.; Kelch,Dean G.; Olmstead, Richard G.; Boore, Jeffrey L.

2005-02-01

We used a unique combination of techniques to sequence the first complete chloroplast genome of a lycophyte, Huperzia lucidula. This plant belongs to a significant clade hypothesized to represent the sister group to all other vascular plants. We used fluorescence-activated cell sorting (FACS) to isolate the organelles, rolling circle amplification (RCA) to amplify the genome, and shotgun sequencing to 8x depth coverage to obtain the complete chloroplast genome sequence. The genome is 154,373bp, containing inverted repeats of 15,314 bp each, a large single-copy region of 104,088 bp, and a small single-copy region of 19,671 bp. Gene order is more similar to those of mosses, liverworts, and hornworts than to gene order for other vascular plants. For example, the Huperziachloroplast genome possesses the bryophyte gene order for a previously characterized 30 kb inversion, thus supporting the hypothesis that lycophytes are sister to all other extant vascular plants. The lycophytechloroplast genome data also enable a better reconstruction of the basaltracheophyte genome, which is useful for inferring relationships among bryophyte lineages. Several unique characters are observed in Huperzia, such as movement of the gene ndhF from the small single copy region into the inverted repeat. We present several analyses of evolutionary relationships among land plants by using nucleotide data, amino acid sequences, and by comparing gene arrangements from chloroplast genomes. The results, while still tentative pending the large number of chloroplast genomes from other key lineages that are soon to be sequenced, are intriguing in themselves, and contribute to a growing comparative database of genomic and morphological data across the green plants.

Restriction endonuclease analysis of chloroplast DNA in interspecies somatic Hybrids of Petunia.

Science.gov (United States)

Kumar, A; Cocking, E C; Bovenberg, W A; Kool, A J

1982-12-01

Restriction endonuclease cleavage pattern analysis of chloroplast DNA (cpDNA) of three different interspecific somatic hybrid plants revealed that the cytoplasms of the hybrids contained only cpDNA of P. parodii. The somatic hybrid plants analysed were those between P. parodii (wild type) + P. hybrida (wild type); P. parodii (wild type)+P. inflata (cytoplasmic albino mutant); P. parodii (wild type) + P. parviflora (nuclear albino mutant). The presence of only P. parodii chloroplasts in the somatic hybrid of P. parodii + P. inflata is possibly due to the stringent selection used for somatic hybrid production. However, in the case of the two other somatic hybrids P. parodii + P. hybrida and P. parodii + P. parviflora it was not possible to determine whether the presence of only P. parodii chloroplasts in these somatic hybrid plants was due to the nature of the selection schemes used or simply occurred by chance. The relevance of such somatic hybrid material for the study of genomic-cytoplasmic interaction is discussed, as well as the use of restriction endonuclease fragment patterns for the analysis of taxonomic and evolutionary inter-relationships in the genus Petunia.

Percolation blockage: A process that enables melt pond formation on first year Arctic sea ice

Science.gov (United States)

Polashenski, Chris; Golden, Kenneth M.; Perovich, Donald K.; Skyllingstad, Eric; Arnsten, Alexandra; Stwertka, Carolyn; Wright, Nicholas

2017-01-01

Melt pond formation atop Arctic sea ice is a primary control of shortwave energy balance in the Arctic Ocean. During late spring and summer, the ponds determine sea ice albedo and how much solar radiation is transmitted into the upper ocean through the sea ice. The initial formation of ponds requires that melt water be retained above sea level on the ice surface. Both theory and observations, however, show that first year sea ice is so highly porous prior to the formation of melt ponds that multiday retention of water above hydraulic equilibrium should not be possible. Here we present results of percolation experiments that identify and directly demonstrate a mechanism allowing melt pond formation. The infiltration of fresh water into the pore structure of sea ice is responsible for blocking percolation pathways with ice, sealing the ice against water percolation, and allowing water to pool above sea level. We demonstrate that this mechanism is dependent on fresh water availability, known to be predominantly from snowmelt, and ice temperature at melt onset. We argue that the blockage process has the potential to exert significant control over interannual variability in ice albedo. Finally, we suggest that incorporating the mechanism into models would enhance their physical realism. Full treatment would be complex. We provide a simple temperature threshold-based scheme that may be used to incorporate percolation blockage behavior into existing model frameworks.

Percolation simulation of laser-guided electrical discharges.

Science.gov (United States)

Sasaki, Akira; Kishimoto, Yasuaki; Takahashi, Eiichi; Kato, Susumu; Fujii, Takashi; Kanazawa, Seiji

2010-08-13

A three-dimensional simulation of laser-guided discharges based on percolation is presented. The model includes both local growth of a streamer due to the enhanced electric field at the streamer's tip and propagation of a leader by remote ionization such as that caused by runaway electrons. The stochastic behavior of the discharge through a preformed plasma channel is reproduced by the calculation, which shows complex path with detouring and bifurcation. The probability of guiding is investigated with respect to the ionized, conductive fraction along the channel.

Note: Optimization of the numerical data analysis for conductivity percolation studies of drying moist porous systems

Energy Technology Data Exchange (ETDEWEB)

Moscicki, J. K.; Sokolowska, D.; Dziob, D.; Nowak, J. [Smoluchowski Institute of Physics, Jagiellonian University, Reymonta 4, 30-059 Krakow (Poland); Kwiatkowski, L. [Department of Econometrics and Operations Research, Cracow University of Economics, Rakowicka 27, 31-510 Krakow (Poland)

2014-02-15

A simplified data analysis protocol, for dielectric spectroscopy use to study conductivity percolation in dehydrating granular media is discussed. To enhance visibility of the protonic conductivity contribution to the dielectric loss spectrum, detrimental effects of either low-frequency dielectric relaxation or electrode polarization are removed. Use of the directly measurable monofrequency dielectric loss factor rather than estimated DC conductivity to parameterize the percolation transition substantially reduces the analysis work and time.

When interflow also percolates: downslope travel distances and hillslope process zones.

Energy Technology Data Exchange (ETDEWEB)

Jackson, C. Rhett [Warnell School of Forestry and Natural Resources, University of Georgia, GA 30602 Athens USA; Bitew, Menberu [Warnell School of Forestry and Natural Resources, University of Georgia, GA 30602 Athens USA; Du, Enhao [Climate Science Department, Lawrence Berkeley National Laboratory, CA 94720 Berkeley USA

2014-02-17

In hillslopes with soils characterized by deep regoliths, such as Ultisols,Oxisols, and Alfisols, interflow occurs episodically over impeding layers near and parallel to the soil surface such as low-conductivity B horizons (e.g.Newman et al., 1998; Buttle andMcDonald, 2002; Du et al., In Review), till layers (McGlynn et al., 1999; Bishop et al., 2004), hardpans (McDaniel et al., 2008), C horizons (Detty and McGuire, 2010), and permeable bedrock (Tromp van Meerveld et al., 2007). As perched saturation develops within and above these impeding but permeable horizons, flow moves laterally downslope, but the perched water also continues to percolate through the impeding horizon to the unsaturated soils and saprolite below. Perched water and solutes will eventually traverse the zone of perched saturation above the impeding horizon and then enter and percolate through the impeding horizon. In such flow situations, only lower hillslope segments with sufficient downslope travel distance will deliver water to the riparian zone within the time scale of a storm.farther up the slope, lateral flow within the zone of perched saturation. will act mainly to shift the point of percolation (location where a water packet leaves the downslope flow zone in the upper soil layer and enters the impeding layer) down the hillslope from the point of infiltration. In flatter parts of the hillslope or in areas with little contrast between the conductivities of the upper and impeding soil layers, lateral flow distances will be negligible.

The role of autophagy in chloroplast degradation and chlorophagy in immune defenses during Pst DC3000 (AvrRps4 infection.

Directory of Open Access Journals (Sweden)

Junjian Dong

Full Text Available BACKGROUND: Chlorosis of leaf tissue normally observed during pathogen infection may result from the degradation of chloroplasts. There is a growing evidence to suggest that the chloroplast plays a significant role during pathogen infection. Although most degradation of the organelles and cellular structures in plants is mediated by autophagy, its role in chloroplast catabolism during pathogen infection is largely unknown. RESULTS: In this study, we investigated the function of autophagy in chloroplast degradation during avirulent Pst DC3000 (AvrRps4 infection. We examined the expression of defensive marker genes and suppression of bacterial growth using the electrolyte leakage assay in normal light (N and low light (L growing environments of wild-type and atg5-1 plants during pathogen treatment. Stroma-targeted GFP proteins (CT-GFP were observed with LysoTracker Red (LTR staining of autophagosome-like structures in the vacuole. The results showed that Arabidopsis expressed a significant number of small GFP-labeled bodies when infected with avirulent Pst DC3000 (AvrRps4. While barely detectable, there were small GFP-labeled bodies in plants with the CT-GFP expressing atg5-1 mutation. The results showed that chloroplast degradation depends on autophagy and this may play an important role in inhibiting pathogen growth. CONCLUSION: Autophagy plays a role in chloroplast degradation in Arabidopsis during avirulent Pst DC3000 (AvrRps4 infection. Autophagy dependent chloroplast degradation may be the primary source of reactive oxygen species (ROS as well as the pathogen-response signaling molecules that induce the defense response.

Diversity of chloroplast genome among local clones of cocoa (Theobroma cacao, L.) from Central Sulawesi

Science.gov (United States)

Suwastika, I. Nengah; Pakawaru, Nurul Aisyah; Rifka, Rahmansyah, Muslimin, Ishizaki, Yoko; Cruz, André Freire; Basri, Zainuddin; Shiina, Takashi

2017-02-01

Chloroplast genomes typically range in size from 120 to 170 kilo base pairs (kb), which relatively conserved among plant species. Recent evaluation on several species, certain unique regions showed high variability which can be utilized in the phylogenetic analysis. Many fragments of coding regions, introns, and intergenic spacers, such as atpB-rbcL, ndhF, rbcL, rpl16, trnH-psbA, trnL-F, trnS-G, etc., have been used for phylogenetic reconstructions at various taxonomic levels. Based on that status, we would like to analysis the diversity of chloroplast genome within species of local cacao (Theobroma cacao L.) from Central Sulawesi. Our recent data showed, there were more than 20 clones from local farming in Central Sulawesi, and it can be detected based on phenotypic and nuclear-genome-based characterization (RAPD- Random Amplified Polymorphic DNA and SSR- Simple Sequences Repeat) markers. In developing DNA marker for this local cacao, here we also included analysis based on the variation of chloroplast genome. At least several regions such as rpl32-TurnL, it can be considered as chloroplast markers on our local clone of cocoa. Furthermore, we could develop phylogenetic analysis in between clones of cocoa.

Predicting deep percolation with eddy covariance under mulch drip irrigation

Science.gov (United States)

Ming, Guanghui; Tian, Fuqiang; Hu, Hongchang

2016-04-01

Water is essential for the agricultural development and ecological sustainability of the arid and semi-arid oasis with rare precipitation input and high evaporation demand. Deep percolation (DP) defined as excess irrigation water percolating below the plant root zone will reduce irrigation water use efficiency (WUE). But the DP was often ignored in mulch drip irrigation (MDI) which has reached the area of 1.6 million hectares in Xinjiang, the northwest of China. In this study DP experiments were conducted at an agricultural experiment station located within an irrigation district in the Tarim River Basin for four cotton growing periods. First it was detected the irrigation water infiltrated into the soil layers below 100cm and the groundwater level responded to the irrigation events well. Then DP below 100cm soil layers was calculated using the soil water balance method with the aid of eddy covariance (with the energy balance closure of 0.72). The negative DP (groundwater contribution to the crop-water use through capillary rising) at the seedling and harvesting stages can reach 77mm and has a good negative correlation with the groundwater level and positive correlation with potential evaporation. During the drip irrigation stage approximately 45% of the irrigation became DP and resulted in the low irrigation WUE of 0.6. The DP can be 164mm to 270mm per year which was positive linearly correlated to irrigation depth and negative linear correlated to irrigation interval. It is better to establish the irrigation schedule with small irrigation depth and given frequently to reduce deep percolation and meet crop needs.

Respirators: Air Purifying, Self-Study, Course 40723

Energy Technology Data Exchange (ETDEWEB)

Chochoms, Michael [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

2017-12-21

Respirators: Air Purifying Self-Study (COURSE 40723) is designed for Los Alamos National Laboratory (LANL) workers, support services subcontractors, and other LANL subcontractors who work under the LANL Respiratory Protection Program (RPP). This course also meets the air-purifying respirators (APRs) retraining requirement.

Chloroplast and mitochondrial microsatellites for Millettia pinnata (Fabaceae) and cross-amplification in related species 1

OpenAIRE

Wang, Yanling; Xie, Hongxian; Yang, Yi; Huang, Yelin; Wang, Jianwu; Tan, Fengxiao

2017-01-01

Premise of the study: Chloroplast and mitochondrial microsatellites were identified to study the population genetics of Millettia pinnata (Fabaceae). Methods and Results: Based on publicly available plastid genome sequence data of M. pinnata, 42 primer pairs were developed, of which 17 displayed polymorphisms across 89 individuals from four populations. For chloroplast loci, two to six alleles were recovered and the unbiased haploid diversity per locus ranged from 0.391 to 0.857. For mitochon...

Assembly of the Complete Sitka Spruce Chloroplast Genome Using 10X Genomics' GemCode Sequencing Data.

Directory of Open Access Journals (Sweden)

Lauren Coombe

Full Text Available The linked read sequencing library preparation platform by 10X Genomics produces barcoded sequencing libraries, which are subsequently sequenced using the Illumina short read sequencing technology. In this new approach, long fragments of DNA are partitioned into separate micro-reactions, where the same index sequence is incorporated into each of the sequencing fragment inserts derived from a given long fragment. In this study, we exploited this property by using reads from index sequences associated with a large number of reads, to assemble the chloroplast genome of the Sitka spruce tree (Picea sitchensis. Here we report on the first Sitka spruce chloroplast genome assembled exclusively from P. sitchensis genomic libraries prepared using the 10X Genomics protocol. We show that the resulting 124,049 base pair long genome shares high sequence similarity with the related white spruce and Norway spruce chloroplast genomes, but diverges substantially from a previously published P. sitchensis- P. thunbergii chimeric genome. The use of reads from high-frequency indices enabled separation of the nuclear genome reads from that of the chloroplast, which resulted in the simplification of the de Bruijn graphs used at the various stages of assembly.

A Numerical Study on Electrical Percolation of Polymer-Matrix Composites with Hybrid Fillers of Carbon Nanotubes and Carbon Black

Directory of Open Access Journals (Sweden)

Yuli Chen

2014-01-01

Full Text Available The electrical percolation of polymer-matrix composites (PMCs containing hybrid fillers of carbon nanotubes (CNTs and carbon black (CB is estimated by studying the connection possibility of the fillers using Monte Carlo simulation. The 3D simulation model of CB-CNT hybrid filler is established, in which CNTs are modeled by slender capped cylinders and CB groups are modeled by hypothetical spheres with interspaces because CB particles are always agglomerated. The observation on the effects of CB and CNT volume fractions and dimensions on the electrical percolation threshold of hybrid filled composites is then carried out. It is found that the composite electrical percolation threshold can be reduced by increasing CNT aspect ratio, as well as increasing the diameter ratio of CB groups to CNTs. And adding CB into CNT composites can decrease the CNT volume needed to convert the composite conductivity, especially when the CNT volume fraction is close to the threshold of PMCs with only CNT filler. Different from previous linear assumption, the nonlinear relation between CB and CNT volume fractions at composite percolation threshold is revealed, which is consistent with the synergistic effect observed in experiments. Based on the nonlinear relation, the estimating equation for the electrical percolation threshold of the PMCs containing CB-CNT hybrid fillers is established.

Large Diversity of Nonstandard Genes and Dynamic Evolution of Chloroplast Genomes in Siphonous Green Algae (Bryopsidales, Chlorophyta).

Science.gov (United States)

Cremen, Ma Chiela M; Leliaert, Frederik; Marcelino, Vanessa R; Verbruggen, Heroen

2018-04-01

Chloroplast genomes have undergone tremendous alterations through the evolutionary history of the green algae (Chloroplastida). This study focuses on the evolution of chloroplast genomes in the siphonous green algae (order Bryopsidales). We present five new chloroplast genomes, which along with existing sequences, yield a data set representing all but one families of the order. Using comparative phylogenetic methods, we investigated the evolutionary dynamics of genomic features in the order. Our results show extensive variation in chloroplast genome architecture and intron content. Variation in genome size is accounted for by the amount of intergenic space and freestanding open reading frames that do not show significant homology to standard plastid genes. We show the diversity of these nonstandard genes based on their conserved protein domains, which are often associated with mobile functions (reverse transcriptase/intron maturase, integrases, phage- or plasmid-DNA primases, transposases, integrases, ligases). Investigation of the introns showed proliferation of group II introns in the early evolution of the order and their subsequent loss in the core Halimedineae, possibly through RT-mediated intron loss.

Vaccination via Chloroplast Genetics: Affordable Protein Drugs for the Prevention and Treatment of Inherited or Infectious Human Diseases.

Science.gov (United States)

Daniell, Henry; Chan, Hui-Ting; Pasoreck, Elise K

2016-11-23

Plastid-made biopharmaceuticals treat major metabolic or genetic disorders, including Alzheimer's, diabetes, hypertension, hemophilia, and retinopathy. Booster vaccines made in chloroplasts prevent global infectious diseases, such as tuberculosis, malaria, cholera, and polio, and biological threats, such as anthrax and plague. Recent advances in this field include commercial-scale production of human therapeutic proteins in FDA-approved cGMP facilities, development of tags to deliver protein drugs to targeted human cells or tissues, methods to deliver precise doses, and long-term stability of protein drugs at ambient temperature, maintaining their efficacy. Codon optimization utilizing valuable information from sequenced chloroplast genomes enhanced expression of eukaryotic human or viral genes in chloroplasts and offered unique insights into translation in chloroplasts. Support from major biopharmaceutical companies, development of hydroponic production systems, and evaluation by regulatory agencies, including the CDC, FDA, and USDA, augur well for advancing this novel concept to the clinic and revolutionizing affordable healthcare.

Developmental changes in aspartate-family amino acid biosynthesis in pea chloroplasts

International Nuclear Information System (INIS)

Mills, W.R.; Cato, L.W.; Stephens, B.W.; Reeves, M.

1990-01-01

Isolated chloroplasts are known to synthesize the asp-derived amino acids (ile, hse, lys and thr) from [ 14 C]asp (Mills et al, 1980, Plant Physiol. 65, 1166). Now, we have studied the influence of tissue age on essential amino acid biosynthesis in pea (Pisum sativum) plastids. Chloroplasts from the younger (third and fourth) leaves of 12 day old plants, were 2-3 times more active in synthesizing lys and thr from [ 14 C]asp than those from older (first or second) leaves. We also examined two key pathway enzymes (aspartate kinase and homoserine dehydrogenase); with each enzyme,a activity in younger leaves was about 2 times that in plastids from older tissue. Both lys- and thr-sensitive forms of aspartate kinase are known in plants; in agreement with earlier work, we found that lys-sensitive activity was about 4 times higher in the younger tissues, while the thr-sensitive activity changed little during development (Davies and Miflin, 1977, Plant Sci. Lett. 9, 323). Recently the role of aspartate kinase and homoserine dehydrogenase in controlling asp-family amino acid synthesis has been questioned (Giovanelli et al, 1989, Plant Physiol. 90, 1584); we hope that measurements of amino acid levels in chloroplasts as well as further enzyme studies will help us to better understand the regulation of asp-family amino acid synthesis

Photosynthetic Characteristics and Chloroplast Ultrastructure of Summer Maize Response to Different Nitrogen Supplies.

Science.gov (United States)

Liu, Zheng; Gao, Jia; Gao, Fei; Liu, Peng; Zhao, Bin; Zhang, Jiwang

2018-01-01

Maize ( Zea mays L.) is the important crop over the world. Nitrogen (N) as necessary element affects photosynthetic characteristics and grain yield of summer maize. In this study, N0 (0 kg N ha -1 ), N1 (129 kg N ha -1 ), N2 (185 kg N ha -1 ), and N3 (300 kg N ha -1 ) was conducted using hybrid 'ZhengDan958' at Dawenkou research field (36°11'N, 117°06'E, 178 m altitude) in the North China Plain to explore the effects of N rate on photosynthetic characteristics and chloroplast ultrastructure. Gas exchange parameters, chlorophyll fluorescence parameters, leaf area index (LAI), chlorophyll SPAD value, chloroplast ultrastructure, dry matter weight and grain yield were measured. At physiological maturity stage, dry matter weight and grain yield of N2 increased by 33-52% ( P ≤ 0.05) and 6-32% ( P ≤ 0.05), respectively, compared with other treatments. During the growing from silking (R1) to milk (R3) stage, LAI of N0 and N1 were 35-38% ( P ≤ 0.05) and 9-23% ( P ≤ 0.05) less than that of N2, respectively. Chlorophyll SPAD value of N0 and N1 were 13-22% ( P ≤ 0.05) and 5-11% ( P ≤ 0.05) lower than that of N2. There was no significant difference in LAI and chlorophyll SPAD value between N2 and N3 during the period from R1 to R3 ( P > 0.05). The net photosynthetic rate ( P n ), maximal quantum efficiency of PSII ( F v / F m ) and quantum efficiency of PSII (Φ PSII ) were higher with the increase of N rate up to N2 ( P ≤ 0.05), and those of N3 were significantly less than N2 ( P ≤ 0.05). In compared with N2, the chloroplast configuration of N0 and N1 became elliptical, almost circular or irregular. The membrane of chloroplast and thylakoid resolved with growing stage, and the number of chloroplast per cell and lamellae per grana decreased under N0 and N1 treatment ( P ≤ 0.05). Under N0 and N1 treatments, summer maize had more negative photosynthetic characteristics. The more number of osmium granule and vesicle and the larger gap between lamellae were

Photosynthetic Characteristics and Chloroplast Ultrastructure of Summer Maize Response to Different Nitrogen Supplies

Directory of Open Access Journals (Sweden)

Zheng Liu

2018-05-01

Full Text Available Maize (Zea mays L. is the important crop over the world. Nitrogen (N as necessary element affects photosynthetic characteristics and grain yield of summer maize. In this study, N0 (0 kg N ha-1, N1 (129 kg N ha-1, N2 (185 kg N ha-1, and N3 (300 kg N ha-1 was conducted using hybrid ‘ZhengDan958’ at Dawenkou research field (36°11′N, 117°06′E, 178 m altitude in the North China Plain to explore the effects of N rate on photosynthetic characteristics and chloroplast ultrastructure. Gas exchange parameters, chlorophyll fluorescence parameters, leaf area index (LAI, chlorophyll SPAD value, chloroplast ultrastructure, dry matter weight and grain yield were measured. At physiological maturity stage, dry matter weight and grain yield of N2 increased by 33–52% (P ≤ 0.05 and 6–32% (P ≤ 0.05, respectively, compared with other treatments. During the growing from silking (R1 to milk (R3 stage, LAI of N0 and N1 were 35–38% (P ≤ 0.05 and 9–23% (P ≤ 0.05 less than that of N2, respectively. Chlorophyll SPAD value of N0 and N1 were 13–22% (P ≤ 0.05 and 5–11% (P ≤ 0.05 lower than that of N2. There was no significant difference in LAI and chlorophyll SPAD value between N2 and N3 during the period from R1 to R3 (P > 0.05. The net photosynthetic rate (Pn, maximal quantum efficiency of PSII (Fv/Fm and quantum efficiency of PSII (ΦPSII were higher with the increase of N rate up to N2 (P ≤ 0.05, and those of N3 were significantly less than N2 (P ≤ 0.05. In compared with N2, the chloroplast configuration of N0 and N1 became elliptical, almost circular or irregular. The membrane of chloroplast and thylakoid resolved with growing stage, and the number of chloroplast per cell and lamellae per grana decreased under N0 and N1 treatment (P ≤ 0.05. Under N0 and N1 treatments, summer maize had more negative photosynthetic characteristics. The more number of osmium granule and vesicle and the larger gap between lamellae were shown in N3

Spatial and temporal dynamics of deep percolation, lag time and recharge in an irrigated semi-arid region

Science.gov (United States)

Nazarieh, F.; Ansari, H.; Ziaei, A. N.; Izady, A.; Davari, K.; Brunner, P.

2018-05-01

The time required for deep percolating water to reach the water table can be considerable in areas with a thick vadose zone. Sustainable groundwater management, therefore, has to consider the spatial and temporal dynamics of groundwater recharge. The key parameters that control the lag time have been widely examined in soil physics using small-scale lysimeters and modeling studies. However, only a small number of studies have analyzed how deep-percolation rates affect groundwater recharge dynamics over large spatial scales. This study examined how the parameters influencing lag time affect groundwater recharge in a semi-arid catchment under irrigation (in northeastern Iran) using a numerical modeling approach. Flow simulations were performed by the MODFLOW-NWT code with the Vadose-Zone Flow (UZF) Package. Calibration of the groundwater model was based on data from 48 observation wells. Flow simulations showed that lag times vary from 1 to more than 100 months. A sensitivity analysis demonstrated that during drought conditions, the lag time was highly sensitive to the rate of deep percolation. The study illustrated two critical points: (1) the importance of providing estimates of the lag time as a basis for sustainable groundwater management, and (2) lag time not only depends on factors such as soil hydraulic conductivity or vadose zone depth but also depends on the deep-percolation rates and the antecedent soil-moisture condition. Therefore, estimates of the lag time have to be associated with specific percolation rates, in addition to depth to groundwater and soil properties.

The role of heterologous chloroplast sequence elements in transgene integration and expression.

Science.gov (United States)

Ruhlman, Tracey; Verma, Dheeraj; Samson, Nalapalli; Daniell, Henry

2010-04-01

Heterologous regulatory elements and flanking sequences have been used in chloroplast transformation of several crop species, but their roles and mechanisms have not yet been investigated. Nucleotide sequence identity in the photosystem II protein D1 (psbA) upstream region is 59% across all taxa; similar variation was consistent across all genes and taxa examined. Secondary structure and predicted Gibbs free energy values of the psbA 5' untranslated region (UTR) among different families reflected this variation. Therefore, chloroplast transformation vectors were made for tobacco (Nicotiana tabacum) and lettuce (Lactuca sativa), with endogenous (Nt-Nt, Ls-Ls) or heterologous (Nt-Ls, Ls-Nt) psbA promoter, 5' UTR and 3' UTR, regulating expression of the anthrax protective antigen (PA) or human proinsulin (Pins) fused with the cholera toxin B-subunit (CTB). Unique lettuce flanking sequences were completely eliminated during homologous recombination in the transplastomic tobacco genomes but not unique tobacco sequences. Nt-Ls or Ls-Nt transplastomic lines showed reduction of 80% PA and 97% CTB-Pins expression when compared with endogenous psbA regulatory elements, which accumulated up to 29.6% total soluble protein PA and 72.0% total leaf protein CTB-Pins, 2-fold higher than Rubisco. Transgene transcripts were reduced by 84% in Ls-Nt-CTB-Pins and by 72% in Nt-Ls-PA lines. Transcripts containing endogenous 5' UTR were stabilized in nonpolysomal fractions. Stromal RNA-binding proteins were preferentially associated with endogenous psbA 5' UTR. A rapid and reproducible regeneration system was developed for lettuce commercial cultivars by optimizing plant growth regulators. These findings underscore the need for sequencing complete crop chloroplast genomes, utilization of endogenous regulatory elements and flanking sequences, as well as optimization of plant growth regulators for efficient chloroplast transformation.

Electron percolation in realistic models of carbon nanotube networks

International Nuclear Information System (INIS)

Simoneau, Louis-Philippe; Villeneuve, Jérémie; Rochefort, Alain

2015-01-01

The influence of penetrable and curved carbon nanotubes (CNT) on the charge percolation in three-dimensional disordered CNT networks have been studied with Monte-Carlo simulations. By considering carbon nanotubes as solid objects but where the overlap between their electron cloud can be controlled, we observed that the structural characteristics of networks containing lower aspect ratio CNT are highly sensitive to the degree of penetration between crossed nanotubes. Following our efficient strategy to displace CNT to different positions to create more realistic statistical models, we conclude that the connectivity between objects increases with the hard-core/soft-shell radii ratio. In contrast, the presence of curved CNT in the random networks leads to an increasing percolation threshold and to a decreasing electrical conductivity at saturation. The waviness of CNT decreases the effective distance between the nanotube extremities, hence reducing their connectivity and degrading their electrical properties. We present the results of our simulation in terms of thickness of the CNT network from which simple structural parameters such as the volume fraction or the carbon nanotube density can be accurately evaluated with our more realistic models

Electron percolation in realistic models of carbon nanotube networks

Science.gov (United States)

Simoneau, Louis-Philippe; Villeneuve, Jérémie; Rochefort, Alain

2015-09-01

The influence of penetrable and curved carbon nanotubes (CNT) on the charge percolation in three-dimensional disordered CNT networks have been studied with Monte-Carlo simulations. By considering carbon nanotubes as solid objects but where the overlap between their electron cloud can be controlled, we observed that the structural characteristics of networks containing lower aspect ratio CNT are highly sensitive to the degree of penetration between crossed nanotubes. Following our efficient strategy to displace CNT to different positions to create more realistic statistical models, we conclude that the connectivity between objects increases with the hard-core/soft-shell radii ratio. In contrast, the presence of curved CNT in the random networks leads to an increasing percolation threshold and to a decreasing electrical conductivity at saturation. The waviness of CNT decreases the effective distance between the nanotube extremities, hence reducing their connectivity and degrading their electrical properties. We present the results of our simulation in terms of thickness of the CNT network from which simple structural parameters such as the volume fraction or the carbon nanotube density can be accurately evaluated with our more realistic models.

Ising percolation in a three-state majority vote model

Science.gov (United States)

Balankin, Alexander S.; Martínez-Cruz, M. A.; Gayosso Martínez, Felipe; Mena, Baltasar; Tobon, Atalo; Patiño-Ortiz, Julián; Patiño-Ortiz, Miguel; Samayoa, Didier

2017-02-01

In this Letter, we introduce a three-state majority vote model in which each voter adopts a state of a majority of its active neighbors, if exist, but the voter becomes uncommitted if its active neighbors are in a tie, or all neighbors are the uncommitted. Numerical simulations were performed on square lattices of different linear size with periodic boundary conditions. Starting from a random distribution of active voters, the model leads to a stable non-consensus state in which three opinions coexist. We found that the "magnetization" of the non-consensus state and the concentration of uncommitted voters in it are governed by an initial composition of system and are independent of the lattice size. Furthermore, we found that a configuration of the stable non-consensus state undergoes a second order percolation transition at a critical concentration of voters holding the same opinion. Numerical simulations suggest that this transition belongs to the same universality class as the Ising percolation. These findings highlight the effect of an updating rule for a tie between voter neighbors on the critical behavior of models obeying the majority vote rule whenever a strict majority exists.

Nonlinear Analysis on Cross-Correlation of Financial Time Series by Continuum Percolation System

Science.gov (United States)

Niu, Hongli; Wang, Jun

We establish a financial price process by continuum percolation system, in which we attribute price fluctuations to the investors’ attitudes towards the financial market, and consider the clusters in continuum percolation as the investors share the same investment opinion. We investigate the cross-correlations in two return time series, and analyze the multifractal behaviors in this relationship. Further, we study the corresponding behaviors for the real stock indexes of SSE and HSI as well as the liquid stocks pair of SPD and PAB by comparison. To quantify the multifractality in cross-correlation relationship, we employ multifractal detrended cross-correlation analysis method to perform an empirical research for the simulation data and the real markets data.

Double site-bond percolation model for biomaterial implants

OpenAIRE

Mely, H.; Mathiot, J. -F.

2011-01-01

9 figures - 10 pages; We present a double site-bond percolation model to account, on the one hand, for the vascularization and/or resorption of biomaterial implant in bones, and on the other hand, for its mechanical continuity. The transformation of the implant into osseous material, and the dynamical formation/destruction of this osseous material is accounted for by creation and destruction of links and sites in two, entangled, networks. We identify the relevant parameters to describe the im...

Ultralow percolation threshold of single walled carbon nanotube-epoxy composites synthesized via an ionic liquid dispersant/initiator

Science.gov (United States)

Watters, Arianna L.; Palmese, Giuseppe R.

2014-09-01

Uniform dispersion of single walled carbon nanotubes (SWNTs) in an epoxy was achieved by a streamlined mechano-chemical processing method. SWNT-epoxy composites were synthesized using a room temperature ionic liquid (IL) with an imidazolium cation and dicyanamide anion. The novel approach of using ionic liquid that behaves as a dispersant for SWNTs and initiator for epoxy polymerization greatly simplifies nanocomposite synthesis. The material was processed using simple and scalable three roll milling. The SWNT dispersion of the resultant composite was evaluated by electron microscopy and electrical conductivity measurements in conjunction with percolation theory. Processing conditions were optimized to achieve the lowest possible percolation threshold, 4.29 × 10-5 volume fraction SWNTs. This percolation threshold is among the best reported in literature yet it was obtained using a streamlined method that greatly simplifies processing.

The influence of percolation rate on the weathering rates of silicates in an E horizon of an Umbric Albaqualf

NARCIS (Netherlands)

Salm, van der C.; Verstraten, J.M.; Tiktak, A.

1996-01-01

Weathering rates from laboratory experiments are generally one or two orders of magnitude larger than field weathering rates. To obtain more information on this gap a large undisturbed soil column was percolated with a hydrochloric/sulphuric acid solution at rates of 0.15-0.89 cm/d. The percolate

A new percolation model for composite solid electrolytes and dispersed ionic conductors

Science.gov (United States)

Risyad Hasyim, Muhammad; Lanagan, Michael T.

2018-02-01

Composite solid electrolytes (CSEs) including conductor/insulator composites known as dispersed ionic conductors (DICs) have motivated the development of novel percolation models that describe their conductivity. Despite the long history, existing models lack in one or more key areas: (1) rigorous foundation for their physical theory, (2) explanation for non-universal conductor-insulator transition, (3) classification of DICs, and (4) extension to frequency-domain. This work describes a frequency-domain effective medium approximation (EMA) of a bond percolation model for CSEs. The EMA is derived entirely from Maxwell’s equations and contains basic microstructure parameters. The model was applied successfully to several composite systems from literature. Simulations and fitting of literature data address these key areas and illustrate the interplay between space charge layer properties and bulk microstructure.

Nonlinear random resistor diode networks and fractal dimensions of directed percolation clusters.

Science.gov (United States)

Stenull, O; Janssen, H K

2001-07-01

We study nonlinear random resistor diode networks at the transition from the nonpercolating to the directed percolating phase. The resistor-like bonds and the diode-like bonds under forward bias voltage obey a generalized Ohm's law V approximately I(r). Based on general grounds such as symmetries and relevance we develop a field theoretic model. We focus on the average two-port resistance, which is governed at the transition by the resistance exponent straight phi(r). By employing renormalization group methods we calculate straight phi(r) for arbitrary r to one-loop order. Then we address the fractal dimensions characterizing directed percolation clusters. Via considering distinct values of the nonlinearity r, we determine the dimension of the red bonds, the chemical path, and the backbone to two-loop order.

High Efficiency, Transparent, Reusable, and Active PM2.5 Filters by Hierarchical Ag Nanowire Percolation Network.

Science.gov (United States)

Jeong, Seongmin; Cho, Hyunmin; Han, Seonggeun; Won, Phillip; Lee, Habeom; Hong, Sukjoon; Yeo, Junyeob; Kwon, Jinhyeong; Ko, Seung Hwan

2017-07-12

Air quality has become a major public health issue in Asia including China, Korea, and India. Particulate matters are the major concern in air quality. We present the first environmental application demonstration of Ag nanowire percolation network for a novel, electrical type transparent, reusable, and active PM2.5 air filter although the Ag nanowire percolation network has been studied as a very promising transparent conductor in optoelectronics. Compared with previous particulate matter air filter study using relatively weaker short-range intermolecular force in polar polymeric nanofiber, Ag nanowire percolation network filters use stronger long-range electrostatic force to capture PM2.5, and they are highly efficient (>99.99%), transparent, working on an active mode, low power consumption, antibacterial, and reusable after simple washing. The proposed new particulate matter filter can be applied for a highly efficient, reusable, active and energy efficient filter for wearable electronics application.

Characterization of chloroplast phosphoproteins controlling manganese use efficiency using quantitative proteomics

DEFF Research Database (Denmark)

Petersen, Jørgen; Sprenger, Richard Remko; Rogowska-Wrzesinska, Adelina

Manganese is important for molecular functions in plants, i.e. as a co-factor in enzymes and in the oxygen evolving complex of photosystem II, located like most of the photosynthetic machinery, in the thylakoid membranes of chloroplasts. Soils that lack plant available micronutrients such as mang......Manganese is important for molecular functions in plants, i.e. as a co-factor in enzymes and in the oxygen evolving complex of photosystem II, located like most of the photosynthetic machinery, in the thylakoid membranes of chloroplasts. Soils that lack plant available micronutrients...... involved in manganese use efficiency, focusing on the phosphoproteome from thylakoid preparations from two barley genotypes, manganese efficient (Vanessa) and inefficient (Antonia) genotype. Experimental: By monitoring the photosynthetic efficiency (Fv/Fm) a decline in activity is observed as a consequence...

Downregulation of chloroplast-targeted beta-amylase leads to a starch-excess phenotype in leaves

DEFF Research Database (Denmark)

Scheidig, A.; Fröhlich, A.; Schulze, S.

2002-01-01

showed that the protein product was a functional beta-amylase that could degrade both starch granules and solubilized amylopectin, while import experiments demonstrated that the beta-amylase was imported and processed into pea chloroplasts. To study the function of the protein in transitory starch......A functional screen in Escherichia coli was established to identify potato genes coding for proteins involved in transitory starch degradation. One clone isolated had a sequence very similar to a recently described chloroplast-targeted 5-amylase of Arabidopsis. Expression of the gene in E. coli...

Complete Chloroplast Genome Sequence of Coptis chinensis Franch. and Its Evolutionary History

Science.gov (United States)

He, Yang; Deng, Cao; Fan, Gang; Qin, Shishang

2017-01-01

The Coptis chinensis Franch. is an important medicinal plant from the Ranunculales. We used next generation sequencing technology to determine the complete chloroplast genome of C. chinensis. This genome is 155,484 bp long with 38.17% GC content. Two 26,758 bp long inverted repeats separated the genome into a typical quadripartite structure. The C. chinensis chloroplast genome consists of 128 gene loci, including eight rRNA gene loci, 28 tRNA gene loci, and 92 protein-coding gene loci. Most of the SSRs in C. chinensis are poly-A/T. The numbers of mononucleotide SSRs in C. chinensis and other Ranunculaceae species are fewer than those in Berberidaceae species, while the number of dinucleotide SSRs is greater than that in the Berberidaceae. C. chinensis diverged from other Ranunculaceae species an estimated 81 million years ago (Mya). The divergence between Ranunculaceae and Berberidaceae was ~111 Mya, while the Ranunculales and Magnoliaceae shared a common ancestor during the Jurassic, ~153 Mya. Position 104 of the C. chinensis ndhG protein was identified as a positively selected site, indicating possible selection for the photosystem-chlororespiration system in C. chinensis. In summary, the complete sequencing and annotation of the C. chinensis chloroplast genome will facilitate future studies on this important medicinal species. PMID:28698879

Complete Chloroplast Genome Sequence of Coptis chinensis Franch. and Its Evolutionary History

Directory of Open Access Journals (Sweden)

Yang He

2017-01-01

Full Text Available The Coptis chinensis Franch. is an important medicinal plant from the Ranunculales. We used next generation sequencing technology to determine the complete chloroplast genome of C. chinensis. This genome is 155,484 bp long with 38.17% GC content. Two 26,758 bp long inverted repeats separated the genome into a typical quadripartite structure. The C. chinensis chloroplast genome consists of 128 gene loci, including eight rRNA gene loci, 28 tRNA gene loci, and 92 protein-coding gene loci. Most of the SSRs in C. chinensis are poly-A/T. The numbers of mononucleotide SSRs in C. chinensis and other Ranunculaceae species are fewer than those in Berberidaceae species, while the number of dinucleotide SSRs is greater than that in the Berberidaceae. C. chinensis diverged from other Ranunculaceae species an estimated 81 million years ago (Mya. The divergence between Ranunculaceae and Berberidaceae was ~111 Mya, while the Ranunculales and Magnoliaceae shared a common ancestor during the Jurassic, ~153 Mya. Position 104 of the C. chinensis ndhG protein was identified as a positively selected site, indicating possible selection for the photosystem-chlororespiration system in C. chinensis. In summary, the complete sequencing and annotation of the C. chinensis chloroplast genome will facilitate future studies on this important medicinal species.

Chloroplast osmotic adjustment allows for acclimation of photosynthesis to low water potentials

International Nuclear Information System (INIS)

Gupta, A.S.; Berkowitz, G.

1987-01-01

Previously in this laboratory, studies indicated that photosynthesis (PS) of chloroplasts isolated from spinach plants which underwent osmotic adjustment during in situ water deficits was inhibited less at low osmotic potentials (Psi/sub s/) in vitro than PS of plastids isolated from well watered plants. In this study, an attempt was made to determine if chloroplast acclimation to low Psi/sub s/ was associated with in situ stromal solute accumulation. During a 14d stress cycle, in situ stromal volume was estimated by measuring (using the 3 H 2 O, 14 C-sorbitol silicon oil centrifugation technique) the stromal space of plastids in solutions which had the Psi/sub s/ adjusted to the leaf Psi/sub s/. During the first lid of the cycle, stromal volume did not decline, despite a decrease of over 20% in the leaf RWC. After this time, stromal volume dropped rapidly. In situ stromal Psi/sub s/ was also estimated during a stress cycle. These studies indicated that stromal Psi/sub s/ was lowered by net solute accumulation. The data presented in this report suggest that chloroplast acclimation to low Psi/sub s/ may involve stromal solute accumulation and volume maintenance during cell water loss

Nuclear fragmentation with secondary decay in the context of conventional percolation model

International Nuclear Information System (INIS)

Santiago, A.J.

1989-09-01

Mass and energy spectra arising from proton-nucleus collisions at energies between 80 and 350 GeV were studied, using the conventional percolation model coupled with secondary decay of the clusters. (L.C.J.A.)

Importance of the green color, absorption gradient, and spectral absorption of chloroplasts for the radiative energy balance of leaves.

Science.gov (United States)

Kume, Atsushi

2017-05-01

Terrestrial green plants absorb photosynthetically active radiation (PAR; 400-700 nm) but do not absorb photons evenly across the PAR waveband. The spectral absorbance of photosystems and chloroplasts is lowest for green light, which occurs within the highest irradiance waveband of direct solar radiation. We demonstrate a close relationship between this phenomenon and the safe and efficient utilization of direct solar radiation in simple biophysiological models. The effects of spectral absorptance on the photon and irradiance absorption processes are evaluated using the spectra of direct and diffuse solar radiation. The radiation absorption of a leaf arises as a consequence of the absorption of chloroplasts. The photon absorption of chloroplasts is strongly dependent on the distribution of pigment concentrations and their absorbance spectra. While chloroplast movements in response to light are important mechanisms controlling PAR absorption, they are not effective for green light because chloroplasts have the lowest spectral absorptance in the waveband. With the development of palisade tissue, the incident photons per total palisade cell surface area and the absorbed photons per chloroplast decrease. The spectral absorbance of carotenoids is effective in eliminating shortwave PAR (solar radiation. However, most of the near infrared radiation is unabsorbed and heat stress is greatly reduced. The incident solar radiation is too strong to be utilized for photosynthesis under the current CO 2 concentration in the terrestrial environment. Therefore, the photon absorption of a whole leaf is efficiently regulated by photosynthetic pigments with low spectral absorptance in the highest irradiance waveband and through a combination of pigment density distribution and leaf anatomical structures.

A set of primers for analyzing chloroplast DNA diversity in Citrus and related genera.

Science.gov (United States)

Cheng, Yunjiang; de Vicente, M Carmen; Meng, Haijun; Guo, Wenwu; Tao, Nengguo; Deng, Xiuxin

2005-06-01

Chloroplast simple sequence repeat (cpSSR) markers in Citrus were developed and used to analyze chloroplast diversity of Citrus and closely related genera. Fourteen cpSSR primer pairs from the chloroplast genomes of tobacco (Nicotiana tabacum L.) and Arabidopsis were found useful for analyzing the Citrus chloroplast genome (cpDNA) and recoded with the prefix SPCC (SSR Primers for Citrus Chloroplast). Eleven of the 14 primer pairs revealed some degree of polymorphism among 34 genotypes of Citrus, Fortunella, Poncirus and some of their hybrids, with polymorphism information content (PIC) values ranging from 0.057 to 0.732, and 18 haplotypes were identified. The cpSSR data were analyzed with NTSYS-pc software, and the genetic relationships suggested by the unweighted pair group method based on arithmetic means (UPGMA) dendrogram were congruent with previous taxonomic investigations: the results showed that all samples fell into seven major clusters, i.e., Citrus medica L., Poncirus, Fortunella, C. ichangensis Blanco, C. reticulata Swingle, C. aurantifolia (Christm.) Swingle and C. grandis (L.) Osbeck. The results of previous studies combined with our cpSSR analyses revealed that: (1) Calamondin (C. madurensis Swingle) is the result of hybridization between kumquat (Fortunella) and mandarin (C. reticulata), where kumquat acted as the female parent; (2) Ichang papeda (C. ichangensis) has a unique taxonomic status; and (3) although Bendiguangju mandarin (C. reticulata) and Satsuma mandarin (C. reticulata) are similar in fruit shape and leaf morphology, they have different maternal parents. Bendiguangju mandarin has the same cytoplasm as sweet orange (C. sinensis), whereas Satsuma mandarin has the cytoplasm of C. reticulata. Seventeen PCR products from SPCC1 and 21 from SPCC11 were cloned and sequenced. The results revealed that mononucleotide repeats as well as insertions and deletions of small segments of DNA were associated with SPCC1 polymorphism, whereas polymorphism

Expression of recombinant interferon α-2a in tobacco chloroplasts ...

African Journals Online (AJOL)

Chloroplast transformation was accomplished upon bombardment of fully expanded 4 to 6 weeks-old tobacco leaves using helium gun. Green shoots regenerated from single antibiotic resistant cells were subjected to further rounds of selection and regeneration to develop homoplasmic clones. The molecular analysis of ...

Brassinosteroid-induced CO{sub 2} assimilation is associated with increased stability of redox-sensitive photosynthetic enzymes in the chloroplasts in cucumber plants

Energy Technology Data Exchange (ETDEWEB)

Jiang, Yu Ping; Cheng, Fei; Zhou, Yan Hong; Xia, Xiao Jian; Mao, Wei Hua; Shi, Kai [Department of Horticulture, Zijingang Campus, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058 (China); Chen, Zhi Xiang [Department of Horticulture, Zijingang Campus, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058 (China); Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907-2054 (United States); Yu, Jing Quan, E-mail: jqyu@zju.edu.cn [Department of Horticulture, Zijingang Campus, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058 (China); Key Laboratory of Horticultural Plants Growth, Development and Quality Improvement, Ministry of Agriculture of China, Yuhangtang Road 866, Hangzhou 310058 (China)

2012-09-28

Highlights: Black-Right-Pointing-Pointer Activity of certain Calvin cycle enzymes and CO{sub 2} assimilation are induced by BRs. Black-Right-Pointing-Pointer BRs upregulate the activity of the ascorbate-glutathione cycle in the chloroplasts. Black-Right-Pointing-Pointer BRs increase the chloroplast thiol reduction state. Black-Right-Pointing-Pointer A BR-induced reducing environment increases the stability of photosynthetic enzymes. -- Abstract: Brassinosteroids (BRs) play important roles in plant growth, development, photosynthesis and stress tolerance; however, the mechanism underlying BR-enhanced photosynthesis is currently unclear. Here, we provide evidence that an increase in the BR level increased the quantum yield of PSII, activities of Rubisco activase (RCA) and fructose-1,6-bisphosphatase (FBPase), and CO{sub 2} assimilation. BRs upregulated the transcript levels of genes and activity of enzymes involved in the ascorbate-glutathione cycle in the chloroplasts, leading to an increased ratio of reduced (GSH) to oxidized (GSSG) glutathione in the chloroplasts. An increased GSH/GSSG ratio protected RCA from proteolytic digestion and increased the stability of redox-sensitive enzymes in the chloroplasts. These results strongly suggest that BRs are capable of regulating the glutathione redox state in the chloroplasts through the activation of the ascorbate-glutathione cycle. The resulting increase in the chloroplast thiol reduction state promotes CO{sub 2} assimilation, at least in part, by enhancing the stability and activity of redox-sensitive photosynthetic enzymes through post-translational modifications.