RNA interference has revolutionized our ability to study the effects of altering the expression of single genes in mammalian (and other) cells through targeted knockdown of gene expression. In this ...report we describe a web-based computational tool, siRNA Information Resource (sIR), which consists of a new open source database that contains validation information about published siRNA sequences and also provides a user-friendly interface to design and analyze siRNA sequences against a chosen target sequence.
The siRNA design tool described in this paper employs empirically determined rules derived from a meta-analysis of the published data; it uses a weighted scoring system that determines the optimal sequence within a target mRNA and thus aids in the rational selection of siRNA sequences. This scoring system shows a non-linear correlation with the knockdown efficiency of siRNAs. sIR provides a fast, customized BLAST output for all selected siRNA sequences against a variety of databases so that the user can verify the uniqueness of the design. We have pre-designed siRNAs for all the known human genes (24,502) in the Refseq database. These siRNAs were pre-BLASTed against the human Unigene database to estimate the target specificity and all results are available online.
Although most of the rules for this scoring system were influenced by previously published rules, the weighted scoring system provides better flexibility in designing an appropriate siRNA when compared to the un-weighted scoring system. sIR is not only a comprehensive tool used to design siRNA sequences and lookup pre-designed siRNAs, but it is also a platform where researchers can share information on siRNA design and use.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Although oxylipins can be synthesized from free fatty acids, recent evidence suggests that oxylipins are components of plastid-localized polar complex lipids in Arabidopsis (Arabidopsis thaliana). ...Using a combination of electrospray ionization (ESI) collisionally induced dissociation time-of-flight mass spectrometry (MS) to identify acyl chains, ESI triple-quadrupole (Q) MS in the precursor mode to identify the nominal masses of complex polar lipids containing each acyl chain, and ESI Q-time-of-flight MS to confirm the identifications of the complex polar lipid species, 17 species of oxylipin-containing phosphatidylglycerols, monogalactosyldiacylglycerols (MGDG), and digalactosyldiacylglycerols (DGDG) were identified. The oxylipins of these polar complex lipid species include oxophytodienoic acid (OPDA), dinor-OPDA (dnOPDA), 18-carbon ketol acids, and 16-carbon ketol acids. Using ESI triple-Q MS in the precursor mode, the accumulation of five OPDA- and/or dnOPDA-containing MGDG and two OPDA-containing DGDG species were monitored as a function of time in mechanically wounded leaves. In unwounded leaves, the levels of these oxylipin-containing complex lipid species were low, between 0.001 and 0.023 nmol/mg dry weight. However, within the first 15 min after wounding, the levels of OPDA-dnOPDA MGDG, OPDA-OPDA MGDG, and OPDA-OPDA DGDG, each containing two oxylipin chains, increased 200- to 1,000-fold. In contrast, levels of OPDA-hexadecatrienoic acid MGDG, linolenic acid (18:3)-dnOPDA MGDG, OPDA-18:3 MGDG, and OPDA-18:3 DGDG, each containing a single oxylipin chain, rose 2- to 9-fold. The rapid accumulation of high levels of galactolipid species containing OPDA-OPDA and OPDA-dnOPDA in wounded leaves is consistent with these lipids being the primary products of plastidic oxylipin biosynthesis.
Cotton is an economically important crop worldwide that suffers severe losses due to a wide range of fungal/bacterial pathogens and nematodes. Given its susceptibility to various pathogens, it is ...important to obtain a broad-spectrum resistance in cotton. Resistance to several fungal and bacterial diseases has been obtained by overexpressing the Non-expressor of Pathogenesis-Related genes-1 (NPR1) in various plant species with apparently minimal or no pleiotropic effects. We examined the efficacy of this approach in cotton by constitutive expression of the Arabidopsis (Arabidopsis thaliana) NPR1 gene. The results show that NPR1-expressing lines exhibited significant resistance to Verticillium dahliae isolate TS2, Fusarium oxysporum f. sp. vasinfectum, Rhizoctonia solani, and Alternaria alternata. Interestingly, the transformants also showed significant resistance to reniform nematodes. Analysis of defense-related, biochemical and molecular responses suggest that when challenged with pathogens or certain systemic acquired resistance-inducing chemicals, the transgenic lines respond to a greater degree compared to the wild-type plants. Importantly, the basal activities of the defense-related genes and enzymes in uninduced transformants were no different than those in their non-transgenic counterparts. The results provide additional evidence supporting the role of NPR1 as an important part of the plant defense system and suggest a means to achieve broad-spectrum resistance to pathogens via genetic engineering.
A core-shell structured PANI/Li0.5Fe2.5−xGdxO4 (0.0⩽x⩽0.2) nanocomposite material has been prepared by in situ emulsion polymerization method as is evidenced by X-ray diffraction and Scanning ...electron microscopy. Transmission electron microscopy confirms the formation of core (ferrite)-shell (PANI matrix) structured nanocomposite material. These materials have been investigated for electromagnetic interference (EMI) shielding in the X-band (8–12GHz) frequency range. Higher shielding effectiveness (SET) of around 42dB has been obtained in this study than many other systems reported recently. The main contributing factor has been ascribed to the absorption (SEA=34–36dB) instead of reflection (SER=4.0–6.3dB), owing to the enhancement in the electromagnetic attributes. Effect of increasing Gd3+ ion content in PANI/Li0.5Fe2.5−xGdxO4 nano-composite has been analyzed for the electromagnetic attenuation. It depicts a decreasing trend of SE with Gd3+ doping except for x=0.2 sample. This has been attributed to the increasing particle size of ferrites, resulting into the decrease in dielectric (ε′=59–56 at 9.5GHz) attributes owing to increased grain to grain contact. Higher value of SE for x=0.2 sample can be due to the secondary phase formation in ferrite, which increases the number of grain boundaries and thereby increases ε′. However, increasing magnetization with Gd3+ doping is less likely a factor affecting shielding as compared to dielectric attributes. Such a material with high SE demonstrates the potential of these materials for making future microwave shields.
Salicylic acid is an important signal molecule in plant defense. In the past two years, significant progress has been made in understanding the mechanism of salicylic-acid biosynthesis and signaling ...in plants. A pathway similar to that found in some bacteria synthesizes salicylic acid from chorismate via isochorismate. Salicylic-acid signaling is mediated by at least two mechanisms, one requiring the
NON-EXPRESSOR OF PR1 (
NPR1) gene and a second that is independent of
NPR1. Feedback loops involving salicylic acid modulate upstream signals. These feedback loops may provide a point for integrating developmental, environmental and other defense-associated signals, and thus fine-tune the defense responses of plants.
Water is crucial for life. Being the world’s third-largest industry, the textile industry pollutes 93 billion cubic meters of water each year. Only 28% of textile wastewater is treated by lower- to ...middle-income countries due to the costly treatment methods. The present work demonstrates the utilization of surface oxygen defects and nanopores in Mg0.8Li0.2Fe2O4 (Li-MgF) to treat textile effluents by a highly economical, scalable, and eco-friendly process. Nanoporous, oxygen-deficient Li-MgF splits water by a nonphotocatalytic process at room temperature to produce green electricity as hydroelectric cell. The adsorbent Li-MgF can be easily regenerated by heat treatment. A 70–90% reduction in the UV absorption intensity of adsorbent-treated textile effluents was observed by UV–visible spectroscopy. The oxygen defects on Li-MgF surface and nanopores were confirmed by X-ray photoelectron spectroscopy and Brunauer–Emmett–Teller (BET) measurements, respectively. To analyze the adsorption mechanism, three known organic water-soluble dyes, brilliant green, crystal violet, and congo red, were treated with nanoporous Li-MgF. The dye decolorization efficiency of Li-MgF was recorded to be 99.84, 99.27, and 99.31% at 250 μM concentrations of brilliant green, congo red, and crystal violet, respectively. The results of Fourier transform infrared (FTIR) spectroscopy confirmed the presence of dyes on the material surface attached through hydroxyl groups generated by water splitting on the surface of the material. Total organic carbon analysis confirmed the removal of organic carbon from the dye solutions by 82.8, 77.0, and 46.5% for brilliant green, Congo red, and crystal violet, respectively. Based on the kinetic and isotherm models, the presence of a large number of surface hydroxyl groups on the surface of the material and OH– ions in solutions generated by water splitting was found to be responsible for the complete decolorization of all of the dyes. Adsorption of chemically diverse dyes by the nanoporous, eco-friendly, ferromagnetic, economic, and reusable Li-MgF provides a sustainable and easy way to treat textile industry effluents in large amounts.
Hemipterans encompass a large group of insect pests of plants that utilize mouthparts which are modified for piercing and consuming fluids from plants. In addition, hemipterans vector viral and ...bacterial diseases of plants. This book brings together a set of reviews and research papers that showcase the the range of activities being undertaken to advance our understanding of the multi-organismal interaction between plant, hemipterans and microbes.
Salicylic acid (SA) plays an important role in activating various plant defense responses, including expression of the pathogenesis-related (PR) genes and systemic acquired resistance. A critical ...positive regulator of the SA signaling pathway in Arabidopsis is encoded by the NPR1 gene. However, there is growing evidence that NPR1-independent pathways can also activate PR expression and disease resistance. To elucidate the components associated with NPR1-independent defense signaling, we isolated a suppressor of the npr1-5 allele, designated ssi2. The recessive ssi2 mutation confers constitutive PR gene expression, spontaneous lesion formation, and enhanced resistance to Peronospora parasitica. In contrast, a subset of defense responses regulated by the jasmonic acid (JA) signaling pathway, including expression of the defensin gene PDF1.2 and resistance to Botrytis cinerea, is impaired in ssi2 plants. With the use of a map-based approach, the SSI2 gene was cloned and shown to encode a stearoyl-ACP desaturase (S-ACP DES). S-ACP DES is an archetypical member of a family of soluble fatty acid (FA) desaturases; these enzymes play an important role in regulating the overall level of desaturated FAs in the cell. The activity of mutant S-ACP DES enzyme was reduced 10-fold, resulting in elevation of the 18:0 FA content in ssi2 plants. Because reduced S-ACP DES activity leads to the induction of certain defense responses and the inhibition of others, we propose that a FA-derived signal modulates crosstalk between different defense signaling pathways.
Plants provide the bulk of the nearly 12,000 diterpenoid natural products, which include diterpene resin acids that have important medicinal and industrial applications. However, the biological ...function of these terpenoids in plants is poorly understood. Here, we highlight recent work that implicates a signaling function in angiosperms for some of these diterpenoids. In particular, this review will focus on the involvement of an abietane diterpenoid, dehydroabietinal, in the activation of systemic acquired resistance, and draw attention to new evidence that supports a role for dehydroabietinal in the transition from the vegetative phase of growth to reproductive development in the crucifer plant
Arabidopsis thaliana.
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