Electrostatic contribution to DNA condensation - application of 'energy minimization' in a simple model in strong Coulomb coupling regime

Bending of DNA from a straight rod to a circular form in presence of any of the mono-, di-, tri- or tetravalent counterions has been simulated in strong Coulomb coupling environment employing a previously developed energy minimization simulation technique. The inherent characteristics of the simulation technique allow monitoring the required electrostatic contribution to the bending. The curvature of the bending has been found to play crucial roles in facilitating electrostatic attractive potential energy. The total electrostatic potential energy has been found to decrease with bending which indicates that bending a straight DNA to a circular form or to a toroidal form in presence of neutralizing counterions is energetically favorable and practically is a spontaneous phenomenon

A compatible interaction of Alternaria brassicicola with Arabidopsis thaliana ecotype DiG: evidence for a specific transcriptional signature

<p>Abstract</p> <p>Background</p> <p>The interaction of <it>Arabidopsis </it>with <it>Alternaria brassicicola </it>provides a model for disease caused by necrotrophs, but a drawback has been the lack of a compatible pathosystem. Infection of most ecotypes, including the widely-studied line Col-0, with this pathogen generally leads to a lesion that does not expand beyond the inoculated area. This study examines an ecotype, Dijon G (DiG), which is considered sensitive to <it>A. brassicicola</it>.</p> <p>Results</p> <p>We show that the interaction has the characteristics of a compatible one, with expanding rather than limited lesions. To ask whether DiG is merely more sensitive to the pathogen or, rather, interacts in distinct manner, we identified genes whose regulation differs between Col-0 and DiG challenged with <it>A. brassicicola</it>. Suppression subtractive hybridization was used to identify differentially expressed genes, and their expression was verified using semi-quantitative PCR. We also tested a set of known defense-related genes for differential regulation in the two plant-pathogen interactions. Several known pathogenesis-related (<it>PR</it>) genes are up-regulated in both interactions. <it>PR1</it>, and a monooxygenase gene identified in this study, <it>MO1</it>, are preferentially up-regulated in the compatible interaction. In contrast, <it>GLIP1</it>, which encodes a secreted lipase, and <it>DIOX1</it>, a pathogen-response related dioxygenase, are preferentially up-regulated in the incompatible interaction.</p> <p>Conclusion</p> <p>The results show that DiG is not only more susceptible, but demonstrate that its interaction with <it>A. brassicicola </it>has a specific transcriptional signature.</p

Prijenos gena za proizvodnju opina (Agrobacterium pRi TL-DNA rolB i TR-DNA) u stanice zrnatog šćira Amaranthus spinosus L.

In vitro rhizogenesis occurred with a characteristic pattern typical of transformed roots following explant (internode/leaf) inoculation of Amaranthus spinosus L. with four different wild type Agrobacterium rhizogenes strains. The extent of rhizogenesis varied considerably with the explant type and source, and with the Agrobacterium strains employed; internodal segments performed better than leaves. Of the strains employed for cocultivation, A. rhizogenes LBA 9402 carrying pRi 1855 was the most virulent and infectious, causing hairy root induction in the maximum number of explants regardless of their type. Individual root clones (rhizoclones) were maintained on Murashige and Skoog\u27s basal medium without growth regulators. The physical presence of the rolB gene in the TL-DNA segment of the Ri plasmid of the infecting Agrobacterium in leaf tissues of plants regenerated from selected rhizoclones was confirmed by a positive PCR amplification. The ability of the genetically transformed plants to harbour and express TR-DNA specific opine synthase genes (man2 and ags) was substantiated by PCR and opine assay respectively, demonstrating the production of characteristic opines. Such findings are implicated in the context of pharmaceutical exploitation of transformed root cultures of A. spinosus and also towards protecting this nutraceutically important crop, amaranth, against biotic stress challenges via transgenic manipulations.Inokulacijom eksplantata (internodija ili listova) zrnatog šćira Amaranthus spinosus L. sa četiri divlja soja bakterije Agrobacterium rhizogenes dobiven je karakterističan uzorak transformiranog korijenja nakon in vitro rizogeneze. Stupanj rizogeneze uvelike je ovisio o upotrijebljenom tipu i porijeklu eksplantata te soju bakterije, pri čemu su bolji rezultati dobiveni inokulacijom internodija, nego pomoću listova šćira. Soj A. rhizogenes LBA 9042, koji posjeduje plazmid pRi 1855, bio je najvirulentniji i najinfektivniji, pa je uzrokovao pojavu čupavog (adventivnog) korijenja u maksimalnom broju eksplantata, neovisno o njihovom tipu. Pojedinačni klonovi transgenog korijenja uzgajani su na hranjivoj podlozi Murashige i Skoog, bez dodatka regulatora rasta. Prisutnost gena rolB u segmentu TL-DNA plazmida Ri iz bakterije Agrobacterium u lisnom tkivu biljaka regeneriranih iz odabranih klonova potvrđena je pozitivnim rezultatom PCR umnožavanja DNA. PCR umnožavanjem i analizom opina utvrđeno je da genetički transformirane biljke mogu primiti i eksprimirati TRDNA-specifične gene (man2 i ags) za sintezu karakterističnih opina. Rezultati upućuju na to da se transformirano korijenje šćira može upotrijebiti u farmaceutici, te da se transgenim uzgojem ova važna žitarica može zaštititi od biotičkog stresa

Assessment of genetic diversity among 16 promising cultivars of ginger using cytological and molecular markers

Ginger (Zingiber officinale Roscoe) is an economically important plant, valued all over the world. The existing variation among 16 promising cultivars as observed through differential rhizome yield (181.9 to 477.3 g) was proved to have a genetic basis using different genetic markers such as karyotype, 4C nuclear DNA content and random amplified polymorphic DNA (RAPD). The karyotypic analysis revealed a differential distribution of A, B, C, D and E type of chromosomes among different cultivars as represented by different karyotype formulas. A significant variation of 4C DNA content was recorded in ginger at an intraspecific level with values ranging from 17.1 to 24.3 pg. RAPD analysis revealed a differential polymorphism of DNA showing a number of polymorphic bands ranging from 26 to 70 among 16 cultivars. The RAPD primers OPC02, OPA02, OPD20 and OPN06 showing strong resolving power were able to distinguish all 16 cultivars. The extent of genetic diversity among these cultivars was computed through parameters of gene diversity, sum of allele numbers per locus and Shannon&apos;s information indices. Cluster analysis, Nei&apos;s genetic similarity and genetic distances, distribution of cultivars into special distance classes and principal coordinate analysis and the analysis of molecular variance suggested a conspicuous genetic diversity among different cultivars studied. The genetic variation thus detected among promising cultivars of ginger has significance for ginger improvement programs. Key words: Ginger, Karyotype, RAPD Introduction Zingiber officinale is rich in secondary metabolites such as oleoresin. It possesses an unique combination of properties like anti-inflammatory, aphrodisiac, antioxidant and antibacterial activity S. Nayak et al. · Genetic Diversity among Ginger Cultivars In the past decade, DNA polymorphism has become the marker of choice for the identification and characterization of plants. It is a relatively reliable, generally applicable method to obtain large samples of markers from any species of plant. However, each marker system samples a different fraction of the genomes and therefore has a different resolving power, range of applicability and probability of homology. The random amplified polymorphic DNA (RAPD) technique has been widely used in cultivar identification programs The objectives of this study were to (1) fingerprint ginger cultivars for identification and (2) detect the genetic diversity and relatedness of 16 cultivars sampled from different geographical regions using karyotypic analysis, 4C DNA content and RAPD analysis. In this study, many analytical procedures such as a n-j method, bootstrapping, spatial genetic structure analysis (SGS), and analysis of molecular variance (AMOVA) have been widely used to derive genetic distances among cultivars and to assess the structure of genetic data in a reduced dimensional space. Materials and Methods Plant materials Sixteen promising cultivars of ginger (Zingiber officinale) were included in the present study which were collected from the turmeric germplasm collection of the Orissa University of Agriculture and Techology (OUAT), Bhubaneswar, Orissa, India. These cultivars were initially collected from different parts of India Karyotype analysis Young and healthy root-tips of different cultivars of ginger were pre-treated in a (0.02 m) hydroxyquinoline mixture (1:1) for 3.5 h at 14 ∞C followed by overnight fixation in propionic ethanol. Chromosome staining was made in 2% lacto propionic orcin after cold hydrolysis in 5 n HCl for 7 min. Root-tips were squashed in 45% propionic acid. Ten well scattered metaphase plates were selected for karyotype analysis of each species. The chromosome morphology was determined following the method of 4C DNA content For Feulgen cytophotometric estimation of 4C DNA, ten fixed root-tips from each cultivar (2n = 22 chromosomes) were hydrolysed in 1 n HCl for 12 min at 60 ∞C, washed in distilled water and stained in Schiff&apos;s reagent for 2 h at 14 ∞C; each root-tip squash was prepared in 75% acetic acid. Ten scorings were made from each slide and the 4C DNA content was estimated from metaphase chromosomes using a NIKON Optiphot microscope with a microspectrophotometer following the method of Sharma and Sharma (1980) with monochromatic light at 550 nm. In situ DNA values were obtained on the basis of optical density measurements which were converted to picograms (pg) using Vant Hoff&apos;s 4C nuclear DNA value (67.1 pg) for Allium cepa as standard Isolation of DNA Total plant DNA was isolated from fresh and young leaves. The leaves were harvested freshly and washed thoroughly with cold autoclaved distilled water and then blotted to dry. About 2 g leaf was excised from the upper tip portion of the buds. DNA extraction was done on the day of collection. The genomic DNA was isolated following the protocol of Doyle and Doyle (1990) with a little modification. Insoluble poly(vinylpyrrolidone) was added to the leaf tissue prior to grinding. The crude DNA was purified with RNase A (@ 60 µg ml Ð1 of DNA solution) followed by washing with S. Nayak et al. · Genetic Diversity among Ginger Cultivars 487 purified chloroform/isoamylalcohol (24:1). To test the quality and quantity of the purified DNA, the samples were electrophoresed in a 0.8% agarose gel along with a known amount of uncut lambda DNA (Bangalore Genei Pvt. Ltd, Bangalore, India) as standard. The sample DNA was diluted as 25 ng µl Ð1 for RAPD-PCR analysis. RAPD amplification Twenty random decamer primers (Operon Tech., USA) from A, C, D and N series (OPA02, 03, 04, 08, 16; OPAF14; OPC02, 05; OPD03, 07, 08, 18, 20; and OPN02, 03, 04, 06, 07, 10, 12) were used for RAPD analysis. RAPD assays were performed in a final volume of 25 µl containing 10 mm Tris-HCl [tris(hydroxymethyl)aminomethane], pH 9.0, 1.5 mm MgCl 2 , 50 mm KCl and 0.01% gelatin, 200 µm of each dNTPs, 0.4 µm primer, 25 ng template DNA and 0.5 unit of Taq DNA polymerase (Bangalore Genei, Bangalore, India). The RAPD analysis was performed as per the methodology described by The amplification products were electrophoresed in 1.5% agarose gel containing ethidium bromide (@ 0.5 µg ml Ð1 ) in TAE buffer (40 mm Tris base, 20 mm sodium acetate, 20 mm EDTA, glacial acetic acid to pH 7.2) for 3 h at 60 V. A total of 2.5 µl loading buffer (1.0 X TAE, 50% glycerol, 0.25% bromophenol blue and 0.25% xylene cyanol) was added to each reaction before electrophoresis. After electrophoresis, the gels were observed under an UV-transilluminator, documented in Gel-Doc 2000 (Bio-Rad) and photographed. Resolving power According to Prevost and Wilkinson (1999) the resolving power (Rp) of a primer is: Rp = Σ IB, where IB (band informativeness) takes the value of: 1-[2 ¥ (0.5 Ð p)], p being the proportion of the 16 genotypes (ginger cultivars analyzed) containing the band. Data collection and analysi

Interface-engineered templates for molecular spin memory devices

The use of molecular spin state as a quantum of information for storage, sensing and computing has generated considerable interest in the context of next-generation data storage and communication devices(1, 2), opening avenues for developing multifunctional molecular spintronics(3). Such ideas have been researched extensively, using single-molecule magnets(4, 5) and molecules with a metal ion(6) or nitrogen vacancy(7) as localized spin-carrying centres for storage and for realizing logic operations(8). However, the electronic coupling between the spin centres of these molecules is rather weak, which makes construction of quantum memory registers a challenging task(9). In this regard, delocalized carbon-based radical species with unpaired spin, such as phenalenyl(10), have shown promise. These phenalenyl moieties, which can be regarded as graphene fragments, are formed by the fusion of three benzene rings and belong to the class of open-shell systems. The spin structure of these molecules responds to external stimuli(11, 12) (such as light, and electric and magnetic fields), which provides novel schemes for performing spin memory and logic operations. Here we construct a molecular device using such molecules as templates to engineer interfacial spin transfer resulting from hybridization and magnetic exchange interaction with the surface of a ferromagnet ; the device shows an unexpected interfacial magnetoresistance of more than 20 per cent near room temperature. Moreover, we successfully demonstrate the formation of a nanoscale magnetic molecule with a well-defined magnetic hysteresis on ferromagnetic surfaces. Owing to strong magnetic coupling with the ferromagnet, such independent switching of an adsorbed magnetic molecule has been unsuccessful with single-molecule magnets(13). Our findings suggest the use of chemically amenable phenalenyl-based molecules as a viable and scalable platform for building molecular-scale quantum spin memory and processors for technological development