Science.gov

Sample records for arabidopsis 70mer oligo

  1. The development of an Arabidopsis model system for genome-wide analysis of polyploidy effects

    PubMed Central

    JEFFREY CHEN, Z.; WANG, JIANLIN; TIAN, LU; LEE, HYEON-SE; WANG, JIYUAN J.; CHEN, MENG; LEE, JINSUK J.; JOSEFSSON, CAROLINE; MADLUNG, ANDREAS; WATSON, BRIAN; LIPPMAN, ZACH; VAUGHN, MATT; CHRIS PIRES, J.; COLOT, VINCENT; DOERGE, R. W.; MARTIENSSEN, ROBERT A.; COMAI, LUCA; OSBORN, THOMAS C.

    2007-01-01

    Arabidopsis is a model system not only for studying numerous aspects of plant biology, but also for understanding mechanisms of the rapid evolutionary process associated with genome duplication and polyploidization. Although in animals interspecific hybrids are often sterile and aneuploids are related to disease syndromes, both Arabidopsis autopolyploids and allopolyploids occur in nature and can be readily formed in the laboratory, providing an attractive system for comparing changes in gene expression and genome structure among relatively ‘young’ and ‘established’ or ‘ancient’ polyploids. Powerful reverse and forward genetics in Arabidopsis offer an exceptional means by which regulatory mechanisms of gene and genome duplication may be revealed. Moreover, the Arabidopsis genome is completely sequenced; both coding and non-coding sequences are available. We have developed spotted oligo-gene and chromosome microarrays using the complete Arabidopsis genome sequence. The oligo-gene microarray consists of ~26 000 70-mer oligonucleotides that are designed from all annotated genes in Arabidopsis, and the chromosome microarray contains 1 kb genomic tiling fragments amplified from a chromosomal region or the complete sequence of chromosome 4. We have demonstrated the utility of microarrays for genome-wide analysis of changes in gene expression, genome organization and chromatin structure in Arabidopsis polyploids and related species. PMID:18079994

  2. EvoOligo: oligonucleotide probe design with multiobjective evolutionary algorithms.

    PubMed

    Shin, Soo-Yong; Lee, In-Hee; Cho, Young-Min; Yang, Kyung-Ae; Zhang, Byoung-Tak

    2009-12-01

    Probe design is one of the most important tasks in successful deoxyribonucleic acid microarray experiments. We propose a multiobjective evolutionary optimization method for oligonucleotide probe design based on the multiobjective nature of the probe design problem. The proposed multiobjective evolutionary approach has several distinguished features, compared with previous methods. First, the evolutionary approach can find better probe sets than existing simple filtering methods with fixed threshold values. Second, the multiobjective approach can easily incorporate the user's custom criteria or change the existing criteria. Third, our approach tries to optimize the combination of probes for the given set of genes, in contrast to other tools that independently search each gene for qualifying probes. Lastly, the multiobjective optimization method provides various sets of probe combinations, among which the user can choose, depending on the target application. The proposed method is implemented as a platform called EvoOligo and is available for service on the web. We test the performance of EvoOligo by designing probe sets for 19 types of Human Papillomavirus and 52 genes in the Arabidopsis Calmodulin multigene family. The design results from EvoOligo are proven to be superior to those from well-known existing probe design tools, such as OligoArray and OligoWiz.

  3. BOND: Basic OligoNucleotide Design

    PubMed Central

    2013-01-01

    Background DNA microarrays have become ubiquitous in biological and medical research. The most difficult problem that needs to be solved is the design of DNA oligonucleotides that (i) are highly specific, that is, bind only to the intended target, (ii) cover the highest possible number of genes, that is, all genes that allow such unique regions, and (iii) are computed fast. None of the existing programs meet all these criteria. Results We introduce a new approach with our software program BOND (Basic OligoNucleotide Design). According to Kane’s criteria for oligo design, BOND computes highly specific DNA oligonucleotides, for all the genes that admit unique probes, while running orders of magnitude faster than the existing programs. The same approach enables us to introduce also an evaluation procedure that correctly measures the quality of the oligonucleotides. Extensive comparison is performed to prove our claims. BOND is flexible, easy to use, requires no additional software, and is freely available for non-commercial use from http://www.csd.uwo.ca/∼ilie/BOND/. Conclusions We provide an improved solution to the important problem of oligonucleotide design, including a thorough evaluation of oligo design programs. We hope BOND will become a useful tool for researchers in biological and medical sciences by making the microarray procedures faster and more accurate. PMID:23444904

  4. OligoCalc: an online oligonucleotide properties calculator

    PubMed Central

    Kibbe, Warren A.

    2007-01-01

    We developed OligoCalc as a web-accessible, client-based computational engine for reporting DNA and RNA single-stranded and double-stranded properties, including molecular weight, solution concentration, melting temperature, estimated absorbance coefficients, inter-molecular self-complementarity estimation and intra-molecular hairpin loop formation. OligoCalc has a familiar ‘calculator’ look and feel, making it readily understandable and usable. OligoCalc incorporates three common methods for calculating oligonucleotide-melting temperatures, including a nearest-neighbor thermodynamic model for melting temperature. Since it first came online in 1997, there have been more than 900 000 accesses of OligoCalc from nearly 200 000 distinct hosts, excluding search engines. OligoCalc is available at http://basic.northwestern.edu/biotools/OligoCalc.html, with links to the full source code, usage patterns and statistics at that link as well. PMID:17452344

  5. OligoRAP – an Oligo Re-Annotation Pipeline to improve annotation and estimate target specificity

    PubMed Central

    Neerincx, Pieter BT; Rauwerda, Han; Nie, Haisheng; Groenen, Martien AM; Breit, Timo M; Leunissen, Jack AM

    2009-01-01

    Background High throughput gene expression studies using oligonucleotide microarrays depend on the specificity of each oligonucleotide (oligo or probe) for its target gene. However, target specific probes can only be designed when a reference genome of the species at hand were completely sequenced, when this genome were completely annotated and when the genetic variation of the sampled individuals were completely known. Unfortunately there is not a single species for which such a complete data set is available. Therefore, it is important that probe annotation can be updated frequently for optimal interpretation of microarray experiments. Results In this paper we present OligoRAP, a pipeline to automatically update the annotation of oligo libraries and estimate oligo target specificity. OligoRAP uses a reference genome assembly with Ensembl and Entrez Gene annotation supplemented with a set of unmapped transcripts derived from RefSeq and UniGene to handle assembly gaps. OligoRAP produces alignments of each oligo with the reference assembly as well as with unmapped transcripts. These alignments are re-mapped to the annotation sources, which results in a concise, as complete as possible and up-to-date annotation of the oligo library. The building blocks of this pipeline are BioMoby web services creating a highly modular and distributed system with a robust, remote programmatic interface. OligoRAP was used to update the annotation for a subset of 791 oligos from the ARK-Genomics 20 K chicken array, which were selected as starting material for the oligo annotation session of the EADGENE/SABRE Post-analysis workshop. Based on the updated annotation about one third of these oligos is problematic with regard to target specificity. In addition, the accession numbers or ids the oligos were originally designed for no longer exist in the updated annotation for almost half of the oligos. Conclusion As microarrays are designed on incomplete data, it is important to update probe

  6. T-oligo as an anticancer agent in colorectal cancer

    SciTech Connect

    Wojdyla, Luke; Stone, Amanda L.; Sethakorn, Nan; Uppada, Srijayaprakash B.; Devito, Joseph T.; Bissonnette, Marc; Puri, Neelu

    2014-04-04

    Highlights: • T-oligo induces cell cycle arrest, senescence, apoptosis, and differentiation in CRC. • Treatment with T-oligo downregulates telomere-associated proteins. • T-oligo combined with an EGFR-TKI additively inhibits cellular proliferation. • T-oligo has potential as an effective therapeutic agent for CRC. - Abstract: In the United States, there will be an estimated 96,830 new cases of colorectal cancer (CRC) and 50,310 deaths in 2014. CRC is often detected at late stages of the disease, at which point there is no effective chemotherapy. Thus, there is an urgent need for effective novel therapies that have minimal effects on normal cells. T-oligo, an oligonucleotide homologous to the 3′-telomere overhang, induces potent DNA damage responses in multiple malignant cell types, however, its efficacy in CRC has not been studied. This is the first investigation demonstrating T-oligo-induced anticancer effects in two CRC cell lines, HT-29 and LoVo, which are highly resistant to conventional chemotherapies. In this investigation, we show that T-oligo may mediate its DNA damage responses through the p53/p73 pathway, thereby inhibiting cellular proliferation and inducing apoptosis or senescence. Additionally, upregulation of downstream DNA damage response proteins, including E2F1, p53 or p73, was observed. In LoVo cells, T-oligo induced senescence, decreased clonogenicity, and increased expression of senescence associated proteins p21, p27, and p53. In addition, downregulation of POT1 and TRF2, two components of the shelterin protein complex which protects telomeric ends, was observed. Moreover, we studied the antiproliferative effects of T-oligo in combination with an EGFR tyrosine kinase inhibitor, Gefitinib, which resulted in an additive inhibitory effect on cellular proliferation. Collectively, these data provide evidence that T-oligo alone, or in combination with other molecularly targeted therapies, has potential as an anti-cancer agent in CRC.

  7. Yeast Oligo-mediated Genome Engineering (YOGE)

    PubMed Central

    DiCarlo, JE; Conley, AJ; Penttilä, M; Jäntti, J; Wang, HH; Church, GM

    2014-01-01

    High-frequency oligonucleotide-directed recombination engineering (recombineering) has enabled rapid modification of several prokaryotic genomes to date. Here, we present a method for oligonucleotide-mediated recombineering in the model eukaryote and industrial production host S. cerevisiae, which we call Yeast Oligo-mediated Genome Engineering (YOGE). Through a combination of overexpression and knockouts of relevant genes and optimization of transformation and oligonucleotide designs, we achieve high gene modification frequencies at levels that only require screening of dozens of cells. We demonstrate the robustness of our approach in three divergent yeast strains, including those involved in industrial production of bio-based chemicals. Furthermore, YOGE can be iteratively executed via cycling to generate genomic libraries up to 105 individuals at each round for diversity generation. YOGE cycling alone, or in combination with phenotypic selections or endonuclease-based negative genotypic selections, can be used to easily generate modified alleles in yeast populations with high frequencies. PMID:24160921

  8. "Fibonacci's route" to regioregular oligo(3-hexylthiophene)s.

    PubMed

    Koch, Felix P V; Smith, Paul; Heeney, Martin

    2013-09-18

    We describe a new synthetic approach to regioregular monodisperse oligo(3-alkylthiophene)s allowing for simple separation of regioregular material in gram quantities. The number of repeat units follows the Fibonacci numbers up to a length of 21. In a small adaption of this approach, introduction of a protecting group was used to synthesize an oligo(3-hexylthiophene) with 36 repeating units, the longest regioregular 3-hexylthiophene oligomer synthesized to date.

  9. Mango: multiple alignment with N gapped oligos.

    PubMed

    Zhang, Zefeng; Lin, Hao; Li, Ming

    2008-06-01

    Multiple sequence alignment is a classical and challenging task. The problem is NP-hard. The full dynamic programming takes too much time. The progressive alignment heuristics adopted by most state-of-the-art works suffer from the "once a gap, always a gap" phenomenon. Is there a radically new way to do multiple sequence alignment? In this paper, we introduce a novel and orthogonal multiple sequence alignment method, using both multiple optimized spaced seeds and new algorithms to handle these seeds efficiently. Our new algorithm processes information of all sequences as a whole and tries to build the alignment vertically, avoiding problems caused by the popular progressive approaches. Because the optimized spaced seeds have proved significantly more sensitive than the consecutive k-mers, the new approach promises to be more accurate and reliable. To validate our new approach, we have implemented MANGO: Multiple Alignment with N Gapped Oligos. Experiments were carried out on large 16S RNA benchmarks, showing that MANGO compares favorably, in both accuracy and speed, against state-of-the-art multiple sequence alignment methods, including ClustalW 1.83, MUSCLE 3.6, MAFFT 5.861, ProbConsRNA 1.11, Dialign 2.2.1, DIALIGN-T 0.2.1, T-Coffee 4.85, POA 2.0, and Kalign 2.0. We have further demonstrated the scalability of MANGO on very large datasets of repeat elements. MANGO can be downloaded at http://www.bioinfo.org.cn/mango/ and is free for academic usage.

  10. Detection, isolation, and characterization of oligo/poly(sialic acid) and oligo/poly(deaminoneuraminic acid) units in glycoconjugates.

    PubMed

    Kitazume, S; Kitajima, K; Inoue, S; Inoue, Y

    1992-04-01

    We have evaluated methods for separation, preparation, and characterization of alpha-2----8-linked oligomers of sialic acids (Neu5Ac and Neu5Gc) and deaminated neuraminic acid (KDN; 2-keto-3-deoxy-D-glycero-D-galacto-nononic acid) recently found as a naturally occurring novel type of sialic acid analogue. (A) We examined preparative anion-exchange chromatography for fractionation and preparation of oligo(Neu5Ac), oligo(Neu5Gc), and oligo(KDN). (B) We also examined the TLC method for separation and differentiation of the partial acid hydrolysates of colominic acid, as well as polysialoglycoproteins (PSGP) and poly(KDN)-glycoproteins (KDN-gp) isolated from rainbow trout eggs, and for discrimination of lower oligomers of Neu5Ac, Neu5Gc, and KDN. (C) We developed the high-performance adsorption-partition chromatographic method for (a) separation of monomers and oligomers of three nonulosonates according to the difference in substituents at C-5 and the presence or absence of 9-O-acetyl groups in oligo(KDN) and (b) separation of three homologous series of lower oligomers according to the degree of polymerization. (D) We examined and compared high-performance anion-exchange chromatographic separation of 3H-labeled oligo(Neu5Ac), oligo(Neu5Gc), and oligo(KDN) alditols by using Mono-Q HR 5/5 resin. (E) We examined a method of selective and quantitative microprecipitation for separation and purification of oligomers and polymers of Neu5Ac by treating them with cetylpyridinium chloride. We also used PSGP and KDN-gp to test both the sensitivity and the selectivity of this method.

  11. Preparation of graphite intercalation compounds containing oligo and polyethers

    NASA Astrophysics Data System (ADS)

    Zhang, Hanyang; Lerner, Michael M.

    2016-02-01

    Layered host-polymer nanocomposites comprising polymeric guests between inorganic sheets have been prepared with many inorganic hosts, but there is limited evidence for the incorporation of polymeric guests into graphite. Here we report for the first time the preparation, and structural and compositional characterization of graphite intercalation compounds (GICs) containing polyether bilayers. The new GICs are obtained by either (1) reductive intercalation of graphite with an alkali metal in the presence of an oligo or polyether and an electrocatalyst, or (2) co-intercalate exchange of an amine for an oligo or polyether in a donor-type GIC. Structural characterization of products using powder X-ray diffraction, Raman spectroscopy, and thermal analyses supports the formation of well-ordered, first-stage GICs containing alkali metal cations and oligo or polyether bilayers between reduced graphene sheets.Layered host-polymer nanocomposites comprising polymeric guests between inorganic sheets have been prepared with many inorganic hosts, but there is limited evidence for the incorporation of polymeric guests into graphite. Here we report for the first time the preparation, and structural and compositional characterization of graphite intercalation compounds (GICs) containing polyether bilayers. The new GICs are obtained by either (1) reductive intercalation of graphite with an alkali metal in the presence of an oligo or polyether and an electrocatalyst, or (2) co-intercalate exchange of an amine for an oligo or polyether in a donor-type GIC. Structural characterization of products using powder X-ray diffraction, Raman spectroscopy, and thermal analyses supports the formation of well-ordered, first-stage GICs containing alkali metal cations and oligo or polyether bilayers between reduced graphene sheets. Electronic supplementary information (ESI) available: Domain size, additional Raman spectra info, compositional calculation, and packing fractions. See DOI: 10.1039/c5

  12. In Situ Super-Resolution Imaging of Genomic DNA with OligoSTORM and OligoDNA-PAINT.

    PubMed

    Beliveau, Brian J; Boettiger, Alistair N; Nir, Guy; Bintu, Bogdan; Yin, Peng; Zhuang, Xiaowei; Wu, C-Ting

    2017-01-01

    OligoSTORM and OligoDNA-PAINT meld the Oligopaint technology for fluorescent in situ hybridization (FISH) with, respectively, Stochastic Optical Reconstruction Microscopy (STORM) and DNA-based Point Accumulation for Imaging in Nanoscale Topography (DNA-PAINT) to enable in situ single-molecule super-resolution imaging of nucleic acids. Both strategies enable ≤20 nm resolution and are appropriate for imaging nanoscale features of the genomes of a wide range of species, including human, mouse, and fruit fly (Drosophila).

  13. Amorphous phase-segregated copoly(ether)esterurethane thermoset networks with oligo(propylene glycol) and oligo[(rac-lactide)-co-glycolide] segments: synthesis and characterization.

    PubMed

    Zotzmann, Jörg; Alteheld, Armin; Behl, Marc; Lendlein, Andreas

    2009-09-01

    Completely amorphous copoly(ether)ester networks based on oligo(propylene glycol) and oligo[(rac-dilactide)-co-glycolide] segments were synthesized by crosslinking star-shaped hydroxyl-telechelic cooligomers using an aliphatic low-molecular weight diisocyanate. Two different network architectures were applied exhibiting differences in the phase-separation behavior. For networks from oligo(propylene glycol)-block-oligo[(rac-lactide)-co-glycolide] triols (G(3)OPG-bl-OLG) only one glass transition was obtained. However, networks from a mixture of oligo(propylene glycol) triols (G(3)OPG) and oligo[(rac-lactide)-co-glycolide] tetrols (P(4)OLG) with a ratio of components in a certain range show two glass transition temperatures (T (g)) being attributed to two segregated amorphous phases. In this way a wide spectrum of mechanical properties can be realized and adjusted to the requirements of a specific application.

  14. Oligo/polynucleotide-based gene modification: strategies and therapeutic potential.

    PubMed

    Sargent, R Geoffrey; Kim, Soya; Gruenert, Dieter C

    2011-01-01

    Oligonucleotide- and polynucleotide-based gene modification strategies were developed as an alternative to transgene-based and classical gene targeting-based gene therapy approaches for treatment of genetic disorders. Unlike the transgene-based strategies, oligo/polynucleotide gene targeting approaches maintain gene integrity and the relationship between the protein coding and gene-specific regulatory sequences. Oligo/polynucleotide-based gene modification also has several advantages over classical vector-based homologous recombination approaches. These include essentially complete homology to the target sequence and the potential to rapidly engineer patient-specific oligo/polynucleotide gene modification reagents. Several oligo/polynucleotide-based approaches have been shown to successfully mediate sequence-specific modification of genomic DNA in mammalian cells. The strategies involve the use of polynucleotide small DNA fragments, triplex-forming oligonucleotides, and single-stranded oligodeoxynucleotides to mediate homologous exchange. The primary focus of this review will be on the mechanistic aspects of the small fragment homologous replacement, triplex-forming oligonucleotide-mediated, and single-stranded oligodeoxynucleotide-mediated gene modification strategies as it relates to their therapeutic potential.

  15. Oligo/Polynucleotide-Based Gene Modification: Strategies and Therapeutic Potential

    PubMed Central

    Sargent, R. Geoffrey; Kim, Soya

    2011-01-01

    Oligonucleotide- and polynucleotide-based gene modification strategies were developed as an alternative to transgene-based and classical gene targeting-based gene therapy approaches for treatment of genetic disorders. Unlike the transgene-based strategies, oligo/polynucleotide gene targeting approaches maintain gene integrity and the relationship between the protein coding and gene-specific regulatory sequences. Oligo/polynucleotide-based gene modification also has several advantages over classical vector-based homologous recombination approaches. These include essentially complete homology to the target sequence and the potential to rapidly engineer patient-specific oligo/polynucleotide gene modification reagents. Several oligo/polynucleotide-based approaches have been shown to successfully mediate sequence-specific modification of genomic DNA in mammalian cells. The strategies involve the use of polynucleotide small DNA fragments, triplex-forming oligonucleotides, and single-stranded oligodeoxynucleotides to mediate homologous exchange. The primary focus of this review will be on the mechanistic aspects of the small fragment homologous replacement, triplex-forming oligonucleotide-mediated, and single-stranded oligodeoxynucleotide-mediated gene modification strategies as it relates to their therapeutic potential. PMID:21417933

  16. Designing oligo libraries taking alternative splicing into account

    NASA Astrophysics Data System (ADS)

    Shoshan, Avi; Grebinskiy, Vladimir; Magen, Avner; Scolnicov, Ariel; Fink, Eyal; Lehavi, David; Wasserman, Alon

    2001-06-01

    We have designed sequences for DNA microarrays and oligo libraries, taking alternative splicing into account. Alternative splicing is a common phenomenon, occurring in more than 25% of the human genes. In many cases, different splice variants have different functions, are expressed in different tissues or may indicate different stages of disease. When designing sequences for DNA microarrays or oligo libraries, it is very important to take into account the sequence information of all the mRNA transcripts. Therefore, when a gene has more than one transcript (as a result of alternative splicing, alternative promoter sites or alternative poly-adenylation sites), it is very important to take all of them into account in the design. We have used the LEADS transcriptome prediction system to cluster and assemble the human sequences in GenBank and design optimal oligonucleotides for all the human genes with a known mRNA sequence based on the LEADS predictions.

  17. Biosynthesis and Degradation of Mono-, Oligo-, and Polysaccharides: Introduction

    NASA Astrophysics Data System (ADS)

    Wilson, Iain B. H.

    Glycomolecules, whether they be mono-, oligo-, or polysaccharides or simple glycosides, are—as any biological molecules—the products of biosynthetic processes; on the other hand, at the end of their lifespan, they are also subject to degradation. The beginning point, biochemically, is the fixation of carbon by photosynthesis; subsequent metabolism in plants and other organisms results in the generation of the various monosaccharides. These must be activated—typically as nucleotide sugars or lipid-phosphosugars—before transfer by glycosyltransferases can take place in order to produce the wide variety of oligo- and polysaccharides seen in Nature; complicated remodelling processes may take place—depending on the pathway—which result in partial trimming of a precursor by glycosidases prior to the addition of further monosaccharide units. Upon completion of the 'life' of a glycoconjugate, glycosidases will degrade the macromolecule finally into monosaccharide units which can be metabolized or salvaged for incorporation into new glycan chains. In modern glycoscience, a wide variety of methods—genetic, biochemical, analytical—are being employed in order to understand these various pathways and to place them within their biological and medical context. In this chapter, these processes and relevant concepts and methods are introduced, prior to elaboration in the subsequent more specialized chapters on biosynthesis and degradation of mono-, oligo-, and polysaccharides.

  18. Oligo(trimethylene carbonate)-poly(ethylene glycol)-oligo(trimethylene carbonate) triblock-based hydrogels for cartilage tissue engineering.

    PubMed

    Zhang, Chao; Sangaj, Nivedita; Hwang, Yongsung; Phadke, Ameya; Chang, Chien-Wen; Varghese, Shyni

    2011-09-01

    A triblock co-polymer of oligo(trimethylene carbonate)-block-poly(ethylene glycol) 20000-block-oligo(trimethylene carbonate) diacrylate (TMC20) was used as a photo-polymerizable precursor for the encapsulation of primary articular chondrocytes. The efficacy of TMC20 as a biodegradable scaffold for cartilage tissue engineering was compared with non-degradable poly(ethylene glycol) 20000 diacrylate (PEG20) hydrogel. Chondrocytes encapsulated in PEG hydrogels containing oligo(trimethylene carbonate) (OTMC) moieties underwent spontaneous aggregation during in vitro culture, which was not observed in the PEG hydrogel counterparts. The aggregation of cells was found to be dependent on the initial cell density, as well as the mesh size of the hydrogels. Similarly, cell aggregation was also found in biodegradable PEG hydrogels containing caprolactone moieties. The aggregation of cells in TMC20 hydrogels resulted in enhanced cartilage matrix production compared with their PEG20 counterparts over 3 weeks of culture. Taken together, these results indicate that PEG hydrogels containing degradable OTMC moieties promote the aggregation and biosynthetic activity of encapsulated chondrocytes, indicating their potential as scaffolds for the repair of cartilage tissue. Copyright © 2011 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

  19. Oligo-guanosine nucleotide induces neuropilin-1 internalization in endothelial cells and inhibits angiogenesis

    PubMed Central

    Narazaki, Masashi; Segarra, Marta; Hou, Xu; Tanaka, Toshio; Li, Xuri

    2010-01-01

    Ligand interaction with cognate cell-surface receptor often promotes receptor internalization, protecting cells from prolonged or excessive signaling from extracellular ligands. Compounds that induce internalization of surface receptors prevent ligand binding to cognate cell-surface receptors serving as inhibitors. Here, we show that synthetic polyriboguanosine (poly G) and oligo-deoxyriboguanosine (oligo G) reduce endothelial levels of surface neuropilin-1 (NRP1), a receptor shared by semaphorin 3A and vascular endothelial growth factor (VEGF), which plays critical roles in angiogenesis. Oligo G also reduces levels of cell-surface scavenger receptor expressed by endothelial cells I (SREC-I), but not levels of NRP2, gp130, CD31, VEGFR-1, or VEGFR-2. Poly or oligo A, T, and C do not promote NRP1 or SREC-I internalization. We find that oligo G binds to NRP1 with high affinity (Kd:1.3 ± 0.16nM), bridges the extracellular domain of NRP1 to that of SREC-I, and induces coordinate internalization of NRP1 and SREC-I. In vitro, oligo G blocks the binding and function of VEGF165 in endothelial cells. In vivo, intravitreal administration of oligo G reduces choroidal neovascularization in mice. These results demonstrate that synthetic oligo G is an inhibitor of pathologic angiogenenesis that reduces cell-surface levels and function of NRP1 acting as an internalization inducer. PMID:20606164

  20. Novel Insights of Oligometastases and Oligo-Recurrence and Review of the Literature

    PubMed Central

    Niibe, Yuzuru; Chang, Joe Y.

    2012-01-01

    Oligometastases and oligo-recurrence are among the most important notions of metastatic and recurrent cancer. The concept of oligometastases is related to the notion that cancer patients with 1–5 metastatic or recurrent lesions that could be treated by local therapy achieve long-term survival or cure, while the concept of oligo-recurrence is related to the notion that cancer patients with 1–5 metastatic or recurrent lesions that could be treated by local therapy have controlled primary lesions. Achievement of long-term survival or cure in patients with oligometastases and oligo-recurrence is cancer and organ specific. These facts rely on the seed and soil theory and multiple steps of cancer progression. Oligo-recurrence is considered to have a better prognosis than oligometastases. In patients with oligometastases and oligo-recurrence, the oligometastases and oligo-recurrence are sometimes cured with only local therapy, which is an example of the abscopal effect, previously described in relation to cure of lesions outside of the field of radiation therapy without systemic therapy. Oligometastases and oligo-recurrence can now be cured by less invasive local treatment methods combined with systemic therapy. The mechanisms of oligometastases and oligo-recurrence, as well as novel insights into these important concepts, are presented in this paper. PMID:22966429

  1. Probing cellular processes with oligo-mediated recombination; using knowledge gained to optimize recombineering

    PubMed Central

    Sawitzke, James A.; Costantino, Nina; Li, Xin-tian; Thomason, Lynn C.; Bubunenko, Mikhail; Court, Carolyn; Court, Donald L.

    2011-01-01

    Recombination with single-strand DNA oligonucleotides (oligos) in E. coli is an efficient and rapid way to modify replicons in vivo. The generation of a nucleotide alteration by oligo recombination provides novel assays for studying cellular processes. Single-strand exonucleases inhibit oligo recombination, and by mutating all four known exonucleases recombination is increased. Increasing the oligo concentration or addition of non-specific carrier oligo titrates out the exonucleases. In a model for oligo recombination, λ Beta protein anneals the oligo to complementary single-strand DNA at the replication fork. Mismatches are created and the methyl-directed mismatch repair (MMR) system acts to eliminate the mismatches inhibiting recombination. Three ways to evade MMR through oligo design include, in addition to the desired change 1) a C~C mismatch six bp from that change, 2) four or more adjacent mismatches, or 3) mismatches at four or more consecutive wobble positions. The latter proves useful for making high frequency changes that alter only the target amino-acid sequence and even allows modification of essential genes. Efficient uptake of DNA is important for oligo-mediated recombination. Uptake of oligos or plasmids is growth media-dependent and is 10,000-fold reduced for cells grown in minimal vs rich medium. Genome-wide engineering technologies utilizing recombineering will benefit from both optimized recombination frequencies and a greater understanding of how biological processes such as DNA replication and cell division impact recombinants formed at multiple chromosomal loci. Recombination events at multiple loci in individual cells are described here. PMID:21256136

  2. Charge transport in nitro substituted oligo(phenylene-ethynylene) molecules

    NASA Astrophysics Data System (ADS)

    Cabassi, Marco Alberto

    2007-12-01

    This thesis presents research aimed at tackling two issues in the field of molecular electronics. The first issue is the large range of molecular conductance values reported by various research groups for identical molecules. This is addressed by studying the same molecule in dissimilar environments. The second issue is experimental uncertainty---whether the observed effects are inherent to the molecule or due to external causes. This is addressed by performing in-situ spectroscopy of the molecule as part of its electrical characterization. Oligo(phenylene-ethynylene)s are a well studied class of molecules in the field of molecular electronics, and this work focuses on charge transport through nitro substituted oligo(phenylene-ethynylene) molecules. The electrical characterization of these molecules was performed utilizing two testbeds. An electromigrated break-junction testbed was used to probe individual molecules, while a nanowire molecular junction testbed was used to probe self-assembled monolayers of the molecule. Experiments performed on individual molecules revealed a temperature dependent transition in the dominant charge transport mechanism. Above 50K, hopping is the dominant charge transport mechanism, while below 50K direct tunneling is the dominant charge transport mechanism. Experiments performed on self-assembled monolayers did not reveal any temperature dependent transitions. The dominant charge transport mechanism appears to be direct tunneling throughout the temperature range investigated. The results also indicate that molecules embedded in a self-assembled monolayer have significantly lower conductance than individual molecules. This is primarily due to a second charge transport mechanism (hopping) that opens up above 50K that is available only to individual molecules, and secondarily due to better potential screening properties of the self-assembled monolayers. Inelastic electron tunneling spectra obtained for the molecules in a self

  3. Oligo-fucoidan prevents renal tubulointerstitial fibrosis by inhibiting the CD44 signal pathway.

    PubMed

    Chen, Cheng-Hsien; Sue, Yuh-Mou; Cheng, Chung-Yi; Chen, Yen-Cheng; Liu, Chung-Te; Hsu, Yung-Ho; Hwang, Pai-An; Huang, Nai-Jen; Chen, Tso-Hsiao

    2017-01-18

    Tubulointerstitial fibrosis is recognized as a key determinant of progressive chronic kidney disease (CKD). Fucoidan, a sulphated polysaccharide extracted from brown seaweed, exerts beneficial effects in some nephropathy models. The present study evaluated the inhibitory effect of oligo-fucoidan (800 Da) on renal tubulointerstitial fibrosis. We established a mouse CKD model by right nephrectomy with transient ischemic injury to the left kidney. Six weeks after the surgery, we fed the CKD mice oligo-fucoidan at 10, 20, and 100 mg/kg/d for 6 weeks and found that the oligo-fucoidan doses less than 100 mg/kg/d improved renal function and reduced renal tubulointerstitial fibrosis in CKD mice. Oligo-fucoidan also inhibited pressure-induced fibrotic responses and the expression of CD44, β-catenin, and TGF-β in rat renal tubular cells (NRK-52E). CD44 knockdown downregulated the expression of β-catenin and TGF-β in pressure-treated cells. Additional ligands for CD44 reduced the anti-fibrotic effect of oligo-fucoidan in NRK-52E cells. These data suggest that oligo-fucoidan at the particular dose prevents renal tubulointerstitial fibrosis in a CKD model. The anti-fibrotic effect of oligo-fucoidan may result from interfering with the interaction between CD44 and its extracellular ligands.

  4. Oligo-fucoidan prevents renal tubulointerstitial fibrosis by inhibiting the CD44 signal pathway

    PubMed Central

    Chen, Cheng-Hsien; Sue, Yuh-Mou; Cheng, Chung-Yi; Chen, Yen-Cheng; Liu, Chung-Te; Hsu, Yung-Ho; Hwang, Pai-An; Huang, Nai-Jen; Chen, Tso-Hsiao

    2017-01-01

    Tubulointerstitial fibrosis is recognized as a key determinant of progressive chronic kidney disease (CKD). Fucoidan, a sulphated polysaccharide extracted from brown seaweed, exerts beneficial effects in some nephropathy models. The present study evaluated the inhibitory effect of oligo-fucoidan (800 Da) on renal tubulointerstitial fibrosis. We established a mouse CKD model by right nephrectomy with transient ischemic injury to the left kidney. Six weeks after the surgery, we fed the CKD mice oligo-fucoidan at 10, 20, and 100 mg/kg/d for 6 weeks and found that the oligo-fucoidan doses less than 100 mg/kg/d improved renal function and reduced renal tubulointerstitial fibrosis in CKD mice. Oligo-fucoidan also inhibited pressure-induced fibrotic responses and the expression of CD44, β-catenin, and TGF-β in rat renal tubular cells (NRK-52E). CD44 knockdown downregulated the expression of β-catenin and TGF-β in pressure-treated cells. Additional ligands for CD44 reduced the anti-fibrotic effect of oligo-fucoidan in NRK-52E cells. These data suggest that oligo-fucoidan at the particular dose prevents renal tubulointerstitial fibrosis in a CKD model. The anti-fibrotic effect of oligo-fucoidan may result from interfering with the interaction between CD44 and its extracellular ligands. PMID:28098144

  5. Atomistic study on dithiolated oligo-phenylenevinylene gated device

    SciTech Connect

    Mahmoud, Ahmed Lugli, Paolo

    2014-11-28

    Thanks to their semiconducting behavior, conjugated molecules are considered as an attractive candidate for future electronic devices. Understanding the charge transport characteristics through such molecules for different device applications would accelerate the progress in the field of molecular electronics. In addition, it would become more feasible to introduce/enhance specific properties of molecular devices. This theoretical paper focuses on atomistic simulation and characterization of novel molecular FET employing dithiolated oligo-phenylenevinylene molecules. The simulation is validated by its agreement with the experimental measurements conducted on the same molecules. The employed molecule has oxygen linkers, which are responsible for the strongly nonlinear current characteristics on the molecular device. We perform a thorough atomistic device analysis to illustrate the principles behind the nonlinear current characteristics and the gating effect.

  6. Oligo and Poly-thiophene/Zno Hybrid Nanowire Solar Cells

    SciTech Connect

    Briseno, Alejandro L.; Holcombe, Thomas W.; Boukai, Akram I.; Garnett, Erik C.; Shelton, Steve W.; Frechet, Jean J. M.; Yang, Peidong

    2009-11-03

    We demonstrate the basic operation of an organic/inorganic hybrid single nanowire solar cell. End-functionalized oligo- and polythiophenes were grafted onto ZnO nanowires to produce p-n heterojunction nanowires. The hybrid nanostructures were characterized via absorption and electron microscopy to determine the optoelectronic properties and to probe the morphology at the organic/inorganic interface. Individual nanowire solar cell devices exhibited well-resolved characteristics with efficiencies as high as 0.036percent, Jsc = 0.32 mA/cm2, Voc = 0.4 V, and a FF = 0.28 under AM 1.5 illumination with 100 mW/cm2 light intensity. These individual test structures will enable detailed analysis to be carried out in areas that have been difficult to study in bulk heterojunction devices.

  7. OligoFaktory: a visual tool for interactive oligonucleotide design.

    PubMed

    Schretter, Colas; Milinkovitch, Michel C

    2006-01-01

    The OligoFaktory is a set of tools for the design, on an arbitrary number of target sequences, of high-quality long oligonucleotide for micro-array, of primer pair for PCR, of siRNA and more. The user-centered interface exists in two flavours: a web portal and a standalone software for Mac OS X Tiger. A unified presentation of results provides overviews with distribution charts and relative location bar graphs, as well as detailed features for each oligonucleotide. Input and output files conform to a common XML interchange file format to allow both automatic generation of input data, archiving, and post-processing of results. The design pipeline can use BLAST servers to evaluate specificity of selected oligonucleotides. The web portal http://ueg.ulb.ac.be/oligofaktory/; the software for Macintosh: http://www.oligofaktory.org/

  8. Oligo(3,6-phenanthrene ethynylenes): synthesis, characterization, and photoluminescence.

    PubMed

    Li, Jichao; Hu, Gongfang; Wang, Ningning; Hu, Tao; Wen, Qiaodong; Lu, Ping; Wang, Yanguang

    2013-04-05

    A series of highly fluorescent, oligo(3,6-phenanthrene ethynylenes) (F1-F7) were synthesized, and their photophysical behavior was systematically investigated. They emitted light with highly emissive quantum yields, up to 0.92. Emissive wavelengths of these compounds relied on the number of phenanthrene blocks existing in the oligomers. Red-shifted emissions were observed as the number of phenanthrenes increased. On the basis of theoretical calculations, helical structures could be formed for F4-F7, indicating that the excimer emissions might be observed for F4-F7 due to the intramolecular π-π stackings of phenanthrenes in the helical structures. However, excimer emissions were only observed for F5-F7 in dilute cyclohexane and for F6 and F7 in dilute methylene chloride, respectively. No excimer emission was observed for F4-F7 in dilute tetrahydrofuran due to the degree of solvation.

  9. Metabolic engineering for amino-, oligo-, and polysugar production in microbes.

    PubMed

    Hossain, Gazi Sakir; Shin, Hyun-Dong; Li, Jianghua; Wang, Miao; Du, Guocheng; Chen, Jian; Liu, Long

    2016-03-01

    Amino-, oligo-, and polysugars are important for both medicinal and industrial applications. Microbial processes used in production of such sugars are not only carbon-intensive and energy-demanding processes but also have other distinct disadvantages such as low productivity, low yields, and by-product contamination. Therefore, metabolic engineering has emerged as an effective tool for developing engineered strains to deliver production strategies for many valuable sugars, which were previously difficult to manufacture by other means, in necessary amounts to support their applications. In this review, the recent strategies used for metabolic engineering are summarized and future prospects of this technique are discussed. We hope that this review will contribute to the development of functional and high-value sugar production by metabolic engineering strategies.

  10. Expression profiling of microRNA using oligo DNA arrays

    PubMed Central

    Liu, Chang-Gong; Spizzo, Riccardo; Calin, George Adrian; Croce, Carlo Maria

    2012-01-01

    After 12 years from its first application, microarray technology has become the reference technique to monitor gene expression of thousands of genes in the same experiment. In the past few years an increasing amount of evidence showed the importance of non coding RNA (ncRNA) in different human diseases. The microRNAs (miRNAs) are one of the groups of ncRNA. They are small RNA fragments, 19–25 nucleotides long, with a main regulatory function on both protein coding genes and non-coding RNAs. The application of microarray platforms applied to miRNA profiling determined their deregulation in virtually all human diseases that have been studied. We previously developed a custom miRNA microarray platform, and here we describe the protocol we used to work with it including the oligo design strategy, the microaray printing protocol, the target-probe hybridization and the signal detection. PMID:18158129

  11. Pharmacologic Studies on the In Vitro Bronchodilating Vasoactive Actions of Oligo-PGB.

    DTIC Science & Technology

    1986-08-01

    also examined the dose response curve to OVA in the presence of pyrilamine (histamine H,-receptor antagonist) alone or in combination with indomethacin... response curve to oligo-PGB will be the best protocol to study this relationship. To exclude the possiblity that the oligo-PGB relaxation could be due...in the presence of indomethacin vv: ich showed a greater degree of relaxation at 10-5M than at 10-6M of oligo-PGB. We suggest that the complete dose

  12. Murine protein which binds preferentially to oligo-C-rich single-stranded nucleic acids.

    PubMed Central

    Goller, M; Funke, B; Gehe-Becker, C; Kröger, B; Lottspeich, F; Horak, I

    1994-01-01

    Two single-stranded nucleic acid binding proteins mCBP and mCTBP were identified by means of their binding to a potential recombination hotspot in LTRs of mouse retro-transposons. Both are nuclear proteins of 35 and 55 kDa respectively. mCBP binds preferentially to oligo dC, mCTBP to oligo dCdT. mCBP was purified and its cDNA was isolated and sequenced. Images PMID:8208614

  13. Achieving targeted and quantifiable alteration of mRNA splicing with Morpholino oligos

    SciTech Connect

    Morcos, Paul A. . E-mail: pmorcos@gene-tools.com

    2007-06-29

    This work represents the first guide for using steric-block antisense oligos as tools for effective and targeted modification of RNA splicing. Comparison of several steric-block oligo types shows the properties of Morpholinos provide significant advantages over other potential splice-blocking oligos. The procedures and complications of designing effective splice-blocking Morpholino oligos are described. The design process requires complete pre-mRNA sequence for defining suitable targets, which usually generate specific predictable messengers. To validate the targeting procedure, the level and nature of transcript alteration is characterized by RT-PCR analysis of splice modification in a {beta}-globin splice model system. An oligo-walking study reveals that while U1 and U2 small nuclear RiboNucleoProtein (snRNP) binding sites are the most effective targets for blocking splicing, inclusion of these sites is not required to achieve effective splice modifications. The most effective targeting strategy employs simultaneously blocking snRNP binding sites and splice-junctions. The work presented here continues to be the basis for most of the successful Morpholino oligos designed for the worldwide research community to block RNA splicing.

  14. Postoperative oligo-recurrence of non-small-cell lung cancer: clinical features and survival†.

    PubMed

    Hishida, Tomoyuki; Yoshida, Junji; Aokage, Keiju; Nagai, Kanji; Tsuboi, Masahiro

    2016-03-01

    Postoperative recurrences of non-small-cell lung cancer (NSCLC) are usually disseminated and systemic. Recently, the concept of oligo-recurrence, which is theoretically curable by definitive local therapy (DLT), has been proposed in several cancers. The aim of this study was to clarify clinical features and outcomes of patients with postoperative oligo-recurrence of NSCLC. From 3275 patients with resected pathological stage IA-IIIB NSCLC between 1993 and 2011, a total of 768 patients who developed recurrence were included in this study. Oligo-recurrence was defined as 1-3 loco-regional or distant recurrent lesions restricted to a single organ. Other recurrences were classified as poly-recurrence. Second primary lung cancers and suspected lesions were excluded. DLT included surgery, stereotactic radiotherapy and radiotherapy with a 45 Gy or higher dose, performed with curative intent. Oligo-recurrence was identified in 162 (21%) patients, mainly as a solitary recurrence (n = 129, 80%) in regional lymph nodes, brain, lung, bone and adrenal gland, and the proportion of patients with oligo-recurrence increased gradually year by year. The patients with oligo-recurrence had more early-staged disease at initial surgery and a longer time to recurrence than those with poly-recurrence. The entire population of oligo-recurrence patients had better post-recurrence survival (PRS) than those with poly-recurrence (5-year PRS: 32.9 vs 9.9%, P < 0.001). For oligo-recurrence, DLT was totally conducted in 105 (65%) patients as initial treatment. Multivariate analyses revealed that the initial DLT was associated with improved PRS [odds ratio (OR) 0.44; 95% confidence interval (CI) 0.29-0.68]. The recurrence location and initial pathological stage did not affect PRS. The 5-year PRS and postoperative progression-free survival rates after DLT were 38.6 and 22.3%, respectively. Of the 10 long-term (≥5-year) progression-free survivors, 9 were those with a solitary recurrence. Initial DLT

  15. Mechanism of T-oligo-induced cell cycle arrest in Mia-PaCa pancreatic cancer cells.

    PubMed

    Rankin, Andrew M; Sarkar, Sibaji; Faller, Douglas V

    2012-06-01

    DNA oligonucleotides with sequence homology to human telomeric DNA (T-oligo) induce cell cycle arrest, followed by apoptosis, senescence, or autophagy in a human cancer cell type-specific manner. T-oligo has potential as a new therapeutic strategy in oncology because of its ability to target certain types of tumor cells while sparing normal ones. In the present study, we demonstrate the T-oligo-induced S-phase cell cycle arrest in four pancreatic cancer cell lines. To further contribute to the mechanistic understanding of T-oligo, we also identify cyclin dependent kinase 2 (cdk2) as a functional mediator in the T-oligo-induced cell cycle arrest of pancreatic cancer cells. Ectopic expression of a constitutively active cdk2 mutant abrogates T-oligo-induced cell cycle arrest in these tumor cells while knockdown of cdk2 expression alone recapitulates the T-oligo effect. Finally, we demonstrate the dispensability of T-oligo-induced ATM/ATR-mediated DNA damage response-signaling pathways, which have long been considered functional in the T-oligo signaling mechanism.

  16. Oligo(L-lysine)-induced titanium dioxide: Effects of consecutive lysine on precipitation

    NASA Astrophysics Data System (ADS)

    Ahn, Sungjun; Park, Sangwoo; Lee, Sang-Yup

    2011-11-01

    Biomineralization of metal oxide utilizes biomolecular substances, such as peptides and proteins, to induce mineralization of metal precursors in a mild aqueous solution. In this study, we investigated biomineralization of an abiological substance, titanium dioxide (TiO 2), by oligo(L-lysine). Specifically, we systemically studied the influence of the number of consecutive lysine on TiO 2 precipitation. Oligo(L-lysine) was chosen as a homopeptide lysine source whose lysine quantity was adjusted. When oligo(L-lysine) contains more than three consecutive lysine, it induces notably fast precipitation, while single and dilysine do not readily form TiO 2 precipitates. Precipitation of TiO 2 was promoted with the length of oligo(L-lysine). The oligo(L-lysine) was associated with TiO 2 precipitate, which was confirmed by spectroscopic and thermogravitational analyses. The outcomes of this research provide a plausible rationale for explaining precipitation of the Ti precursor that is highly dependent on peptide sequences.

  17. PROBEmer: a web-based software tool for selecting optimal DNA oligos

    PubMed Central

    Emrich, Scott J.; Lowe, Mary; Delcher, Arthur L.

    2003-01-01

    PROBEmer (http://probemer.cs.loyola.edu) is a web-based software tool that enables a researcher to select optimal oligos for PCR applications and multiplex detection platforms including oligonucleotide microarrays and bead-based arrays. Given two groups of nucleic-acid sequences, a target group and a non-target group, the software identifies oligo sequences that occur in members of the target group, but not in the non-target group. To help predict potential cross hybridization, PROBEmer computes all near neighbors in the non-target group and displays their alignments. The software has been used to obtain genus-specific prokaryotic probes based on the 16S rRNA gene, gene-specific probes for expression analyses and PCR primers. In this paper, we describe how to use PROBEmer, the computational methods it employs, and experimental results for oligos identified by this software tool. PMID:12824409

  18. Design of smart oligo(ethylene glycol)-based biocompatible hybrid microgels loaded with magnetic nanoparticles.

    PubMed

    Boularas, Mohamed; Gombart, Emilie; Tranchant, Jean-François; Billon, Laurent; Save, Maud

    2015-01-01

    This article reports a rational strategy for preparing smart oligo(ethylene glycol)-based hybrid microgels loaded with high content of homogeneously distributed preformed magnetic nanoparticles (NPs) (up to 33 wt%). The strategy is based on the synthesis of biocompatible multiresponsive microgels by precipitation copolymerization of di(ethylene glycol) methyl ether methacrylate, oligo(ethylene glycol) methyl ether methacrylate, methacrylic acid, and oligo(ethylene glycol)diac-rylate. An aqueous dispersion of preformed magnetic NPs is straightforwardly loaded into the microgels. Robust monodisperse thermoresponsive magnetic microgels are produced, exhibiting a constant value of the volume phase transition temperature whatever the NPs content. The homogeneous microstructure of the initial stimuli-responsive biocompatible microgels plays a crucial role for the design of unique well-defined ethylene glycol-based thermoresponsive hybrid microgels. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. A note on temperature-dependent band narrowing in oligo-acene crystals

    NASA Astrophysics Data System (ADS)

    Hannewald, K.; Stojanovic, V. M.; Bobbert, P. A.

    2004-03-01

    We present a theoretical description of polaron band narrowing in oligo-acene crystals due to electron-lattice interaction. The analysis is based on a model which takes both local and nonlocal contributions to the electron-phonon coupling into account. Different approximation schemes are discussed and compared. The theory is supplemented by quantitative ab initio calculations of the temperature dependence of polaron bandwidths in oligo-acene crystals which show the important role of in-plane nonlocal electron-phonon coupling.

  20. The Trypanosoma cruzi Satellite DNA OligoC-TesT and Trypanosoma cruzi Kinetoplast DNA OligoC-TesT for Diagnosis of Chagas Disease: A Multi-cohort Comparative Evaluation Study

    PubMed Central

    De Winne, Koen; Büscher, Philippe; Luquetti, Alejandro O.; Tavares, Suelene B. N.; Oliveira, Rodrigo A.; Solari, Aldo; Zulantay, Ines; Apt, Werner; Diosque, Patricio; Monje Rumi, Mercedes; Gironès, Nuria; Fresno, Manuel; Lopez-Velez, Rogelio; Perez-Molina, José A.; Monge-Maillo, Begoña; Garcia, Lineth; Deborggraeve, Stijn

    2014-01-01

    Background The Trypanosoma cruzi satellite DNA (satDNA) OligoC-TesT is a standardised PCR format for diagnosis of Chagas disease. The sensitivity of the test is lower for discrete typing unit (DTU) TcI than for TcII-VI and the test has not been evaluated in chronic Chagas disease patients. Methodology/Principal Findings We developed a new prototype of the OligoC-TesT based on kinetoplast DNA (kDNA) detection. We evaluated the satDNA and kDNA OligoC-TesTs in a multi-cohort study with 187 chronic Chagas patients and 88 healthy endemic controls recruited in Argentina, Chile and Spain and 26 diseased non-endemic controls from D.R. Congo and Sudan. All specimens were tested in duplicate. The overall specificity in the controls was 99.1% (95% CI 95.2%–99.8%) for the satDNA OligoC-TesT and 97.4% (95% CI 92.6%–99.1%) for the kDNA OligoC-TesT. The overall sensitivity in the patients was 67.9% (95% CI 60.9%–74.2%) for the satDNA OligoC-TesT and 79.1% (95% CI 72.8%–84.4%) for the kDNA OligoC-Test. Conclusions/Significance Specificities of the two T. cruzi OligoC-TesT prototypes are high on non-endemic and endemic controls. Sensitivities are moderate but significantly (p = 0.0004) higher for the kDNA OligoC-TesT compared to the satDNA OligoC-TesT. PMID:24392177

  1. The Trypanosoma cruzi satellite DNA OligoC-TesT and Trypanosoma cruzi kinetoplast DNA OligoC-TesT for diagnosis of Chagas disease: a multi-cohort comparative evaluation study.

    PubMed

    De Winne, Koen; Büscher, Philippe; Luquetti, Alejandro O; Tavares, Suelene B N; Oliveira, Rodrigo A; Solari, Aldo; Zulantay, Ines; Apt, Werner; Diosque, Patricio; Monje Rumi, Mercedes; Gironès, Nuria; Fresno, Manuel; Lopez-Velez, Rogelio; Perez-Molina, José A; Monge-Maillo, Begoña; Garcia, Lineth; Deborggraeve, Stijn

    2014-01-01

    The Trypanosoma cruzi satellite DNA (satDNA) OligoC-TesT is a standardised PCR format for diagnosis of Chagas disease. The sensitivity of the test is lower for discrete typing unit (DTU) TcI than for TcII-VI and the test has not been evaluated in chronic Chagas disease patients. We developed a new prototype of the OligoC-TesT based on kinetoplast DNA (kDNA) detection. We evaluated the satDNA and kDNA OligoC-TesTs in a multi-cohort study with 187 chronic Chagas patients and 88 healthy endemic controls recruited in Argentina, Chile and Spain and 26 diseased non-endemic controls from D.R. Congo and Sudan. All specimens were tested in duplicate. The overall specificity in the controls was 99.1% (95% CI 95.2%-99.8%) for the satDNA OligoC-TesT and 97.4% (95% CI 92.6%-99.1%) for the kDNA OligoC-TesT. The overall sensitivity in the patients was 67.9% (95% CI 60.9%-74.2%) for the satDNA OligoC-TesT and 79.1% (95% CI 72.8%-84.4%) for the kDNA OligoC-Test. Specificities of the two T. cruzi OligoC-TesT prototypes are high on non-endemic and endemic controls. Sensitivities are moderate but significantly (p = 0.0004) higher for the kDNA OligoC-TesT compared to the satDNA OligoC-TesT.

  2. Combinatorial enzyme technology: Conversion of pectin to oligo species and its effect on microbial growth

    USDA-ARS?s Scientific Manuscript database

    Plant cell wall polysaccharides, which consist of polymeric backbones with various types of substitution, were studied using the concept of combinatorial enzyme technology for conversion of agricultural fibers to functional products. Using citrus pectin as the starting substrate, an active oligo spe...

  3. Combinatorial enzyme technology: Conversion of pectin to oligo species and its effect on microbial growth

    USDA-ARS?s Scientific Manuscript database

    Plant cell wall polysaccharides, which consist of polymeric backbones with various types of substitution, were studied using the concept of combinatorial enzyme technology for conversion of agricultural fibers to functional products. Using citrus pectin as the starting substrate, an active oligo spe...

  4. Pharmacologic Studies on the In Vitro Bronchodilating Vasoactive Actions of Oligo-PGB (Prostaglandin B)

    DTIC Science & Technology

    1988-01-06

    of indomethacin which showed a greater de,.,ee of relaxation at 10-5M than at 10 6M of oligo-PGB. We suggest t eit the complete dose - response curve to...to further increase the responses of O-PGB-treated tissues (figure 7). We also examined the dose response curve to OVA in the presence of pyrilamine

  5. On the hybrid glassy carbon electrode/OligoThiophene/Ag(NP) interface.

    PubMed

    Tassinari, Francesco; Tancini, Erik; Innocenti, Massimo; Schenetti, Luisa; Fontanesi, Claudio

    2012-11-06

    GC/OligoThiophene/Ag(NP) hybrid interfaces are synthesized and characterized: GC is the glassy carbon surface; OligoThiophene stands for both an ultrathin bithiophene grafted film and a 4-Br-Bithiophene grafted polymer; Ag(NP) stands for silver nanoparticles. The hybrid interface preparation involves different steps: first, the electrode surface is functionalized through a combination of electrochemically assisted grafting (under reduction regime) and polymerization (under oxidation regime); then, silver nanoparticles are chemisorbed by dipping. In particular, an ultrathin film of grafted bithiophene can be obtained by applying one cyclic voltammetry reduction cycle (GC/BT surface), while subsequent cyclic voltammetry cycling under oxidation regime yields an immobilized 4Br-Bithiophene polymer (GC/4BrBT surface). AFM and TEM images were recorded to investigate the morphology and chemical composition of the Ag(NP). Fe(II)/Fe(III) cyclic voltammetry, Zn underpotential deposition (UPD), XPS, LA-ICP-MS, and Raman techniques were exploited to characterize both the GC/OligoThiophene and GC/OligoThiophene/Ag(NP) interfaces. Theoretical calculation, at the B3LYP/6-311G** level of the theory, enabled rationalization of the electroreduction mechanism and the Raman results.

  6. Synthesis, electronic properties and self-assembly on Au{111} of thiolated (oligo)phenothiazines

    PubMed Central

    Franz, Adam W; Stoycheva, Svetlana; Himmelhaus, Michael

    2010-01-01

    Summary (Oligo)phenothiazinyl thioacetates, synthesized by a one-pot sequence, are electrochemically oxidizable and highly fluorescent. SAMs can be readily formed from thiols prepared by in situ deprotection of the thioacetates in the presence of a gold-coated silicon wafer. Monolayer formation is confirmed by ellipsometry and the results compared to those obtained by force field and DFT calculations. PMID:20703376

  7. Maillard reaction products of rice protein hydrolysates with mono-, oligo- and polysaccharides

    USDA-ARS?s Scientific Manuscript database

    Rice protein, a byproduct of rice syrup production, is abundant but, its lack of functionality prevents its wide use as a food ingredient. Maillard reaction products of (MRPs) hydrolysates from the limited hydrolysis of rice protein (LHRP) and various mono-, oligo- and polysaccharides were evaluat...

  8. Transcriptomic and proteomic approach to identify differentially expressed genes and proteins in Arabidopsis thaliana mutants lacking chloroplastic 1 and cytosolic FBPases reveals several levels of metabolic regulation.

    PubMed

    Soto-Suárez, Mauricio; Serrato, Antonio J; Rojas-González, José A; Bautista, Rocío; Sahrawy, Mariam

    2016-12-01

    During the photosynthesis, two isoforms of the fructose-1,6-bisphosphatase (FBPase), the chloroplastidial (cFBP1) and the cytosolic (cyFBP), catalyse the first irreversible step during the conversion of triose phosphates (TP) to starch or sucrose, respectively. Deficiency in cyFBP and cFBP1 isoforms provokes an imbalance of the starch/sucrose ratio, causing a dramatic effect on plant development when the plastidial enzyme is lacking. We study the correlation between the transcriptome and proteome profile in rosettes and roots when cFBP1 or cyFBP genes are disrupted in Arabidopsis thaliana knock-out mutants. By using a 70-mer oligonucleotide microarray representing the genome of Arabidopsis we were able to identify 1067 and 1243 genes whose expressions are altered in the rosettes and roots of the cfbp1 mutant respectively; whilst in rosettes and roots of cyfbp mutant 1068 and 1079 genes are being up- or down-regulated respectively. Quantitative real-time PCR validated 100% of a set of 14 selected genes differentially expressed according to our microarray analysis. Two-dimensional (2-D) gel electrophoresis-based proteomic analysis revealed quantitative differences in 36 and 26 proteins regulated in rosettes and roots of cfbp1, respectively, whereas the 18 and 48 others were regulated in rosettes and roots of cyfbp mutant, respectively. The genes differentially expressed and the proteins more or less abundant revealed changes in protein metabolism, RNA regulation, cell signalling and organization, carbon metabolism, redox regulation, and transport together with biotic and abiotic stress. Notably, a significant set (25%) of the proteins identified were also found to be regulated at a transcriptional level. This transcriptomic and proteomic analysis is the first comprehensive and comparative study of the gene/protein re-adjustment that occurs in photosynthetic and non-photosynthetic organs of Arabidopsis mutants lacking FBPase isoforms.

  9. Arabidopsis hybrid speciation processes

    PubMed Central

    Schmickl, Roswitha; Koch, Marcus A.

    2011-01-01

    The genus Arabidopsis provides a unique opportunity to study fundamental biological questions in plant sciences using the diploid model species Arabidopsis thaliana and Arabidopsis lyrata. However, only a few studies have focused on introgression and hybrid speciation in Arabidopsis, although polyploidy is a common phenomenon within this genus. More recently, there is growing evidence of significant gene flow between the various Arabidopsis species. So far, we know Arabidopsis suecica and Arabidopsis kamchatica as fully stabilized allopolyploid species. Both species evolved during Pleistocene glaciation and deglaciation cycles in Fennoscandinavia and the amphi-Beringian region, respectively. These hybrid studies were conducted either on a phylogeographic scale or reconstructed experimentally in the laboratory. In our study we focus at a regional and population level. Our research area is located in the foothills of the eastern Austrian Alps, where two Arabidopsis species, Arabidopsis arenosa and A. lyrata ssp. petraea, are sympatrically distributed. Our hypothesis of genetic introgression, migration, and adaptation to the changing environment during the Pleistocene has been confirmed: We observed significant, mainly unidirectional gene flow between the two species, which has given rise to the tetraploid A. lyrata. This cytotype was able to escape from the narrow ecological niche occupied by diploid A. lyrata ssp. petraea on limestone outcrops by migrating northward into siliceous areas, leaving behind a trail of genetic differentiation. PMID:21825128

  10. Anion induced modulation of self-assembly and optical properties in urea end-capped oligo(p-phenylenevinylene)s.

    PubMed

    Varghese, Reji; George, Subi J; Ajayaghosh, Ayyappanpillai

    2005-02-07

    The non-emissive supramolecular assembly of urea end-capped oligo(p-phenylenevinylene) flourophores turned strongly emissive in the presence of tetrabutylammonium flouride which has implications in the anion controlled design of supramolecular architectures with tunable emission properties.

  11. Superexchange contributions to distance dependence of electron transfer/transport: exchange and electronic coupling in oligo(para-phenylene)- and oligo(2,5-thiophene)-bridged donor-bridge-acceptor biradical complexes.

    PubMed

    Kirk, Martin L; Shultz, David A; Stasiw, Daniel E; Lewis, Geoffrey F; Wang, Guangbin; Brannen, Candice L; Sommer, Roger D; Boyle, Paul D

    2013-11-13

    The preparation and characterization of three new donor-bridge-acceptor biradical complexes are described. Using variable-temperature magnetic susceptibility, EPR hyperfine coupling constants, and the results of X-ray crystal structures, we evaluate both exchange and electronic couplings as a function of bridge length for two quintessential molecular bridges: oligo(para-phenylene), β = 0.39 Å(-1) and oligo(2,5-thiophene), β = 0.22 Å(-1). This report represents the first direct comparison of exchange/electronic couplings and distance attenuation parameters (β) for these bridges. The work provides a direct measurement of superexchange contributions to β, with no contribution from incoherent hopping. The different β values determined for oligo(para-phenylene) and oligo(2,5-thiophene) are due primarily to the D-B energy gap, Δ, rather than bridge-bridge electronic couplings, H(BB). This is supported by the fact that the H(BB) values extracted from the experimental data for oligo(para-phenylene) (H(BB) = 11,400 cm(-1)) and oligo(2,5-thiophene) (12,300 cm(-1)) differ by <10%. The results presented here offer unique insight into the intrinsic molecular factors that govern H(DA) and β, which are important for understanding the electronic origin of electron transfer and electron transport mediated by molecular bridges.

  12. Oligo(dA-dT)-dependent signal amplification for the detection of proteins in cells.

    PubMed

    Hanaki, Ken-ichi; Ohka, Seii; Yamamoto, Kenji; Nomoto, Akio; Yoshikura, Hiroshi

    2004-05-01

    An ultrasensitive protein detection system in situ named the ImmunoAT-tailing method was developed. It consists of three elementary processes: (i) detection of a protein by a primary antibody and a biotinylated secondary antibody; (ii) linking of biotinylated 15-base oligo(dA-dT) to the biotinylated immunocomplex via streptavidin; and (iii) self-priming elongation of oligo(dA-dT) by the Klenow fragment, 3' to 5' exo-. After the elongation reaction in the presence of dATP, dTTP, and dye-labeled dUTP, the protein was labeled with a large number of the dye molecules. The poly(dA-dT) elongated without the labeled nucleotides was detected by 4',6-diamidino-2-phenylindole (DAPI) staining. By combining the different labelings, double staining was possible. This ImmunoAT-tailing method has a specificity and sensitivity higher than that of tyramide signal amplification.

  13. Thermosensitivity of bile acid-based oligo(ethylene glycol) stars in aqueous solutions.

    PubMed

    Strandman, Satu; Le Dévédec, Frantz; Zhu, X X

    2011-08-03

    Amphiphilic star-shaped oligo(ethylene glycol)s with a hydrophobic bile acid core and varying number of hydrophilic arms have been made. Their thermal behavior in aqueous solutions depends on the number rather than the length of the arms. The two-armed lithocholate derivative showed the strongest tendency for association and exhibited the lowest cloud point (79 °C) of the oligomers made, as well as another phase separation at a lower temperature (31 °C). The "double thermosensitivity" arising both from the salt-dependent LCST of the oligo(ethylene glycol) segments and the temperature-responsive self-assembly of amphiphilic bile acid derivative provides an interesting path in the design of bile acid-based smart materials. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. alpha-DNA X: alpha and beta tetrathymidilates covalently linked to oxazolopyridocarbazolium (OPC): comparative stabilization of oligo beta-[dT]:oligo beta-[dA] and oligo alpha-[dT]:oligo beta-[dA] duplexes by the intercalating agent.

    PubMed Central

    Bazile, D; Gautier, C; Rayner, B; Imbach, J L; Paoletti, C; Paoletti, J

    1989-01-01

    The influence of the intercalating oxazolopyridocarbazolium (HOPC) on the stabilization of modified oligonucleotides: alpha-T4c5OPC or beta-T4c5OPC associated to beta-oligo (dA) was studied. It appears that the situation is different from what has been observed for the interaction of these modified oligonucleotides with poly (rA). The higher free energy of formation of the alpha-T4c5OPC :beta-oligo(dA), when compared to beta-T4c5OPC, is essentially due to the overall stability added to this system by the intercalator. This enhanced stability comes from a higher number of binding sites of HOPC for the alpha:beta duplex together with a lower van't Hoff energy of formation of the alpha:beta duplex. PMID:2798125

  15. Assessing the Sporicidal Activity of Oligo-p-phenylene Ethynylenes and Their Role as Bacillus Germinants.

    PubMed

    Pappas, Harry C; Lovchik, Julie A; Whitten, David G

    2015-04-21

    A wide range of oligo-p-phenylene ethynylenes has been shown to exhibit good biocidal activity against both Gram-negative and Gram-positive bacteria. While cell death may occur in the dark, these biocidal compounds are far more effective in the light as a result of their ability to sensitize the production of cell-damaging reactive oxygen species. In these studies, the interactions of a specific cationic oligo-p-phenylene ethynylene with spore-forming Bacillus atrophaeus and Bacillus anthracis Sterne have been investigated. Flow cytometry assays are used to rapidly monitor cell death as well as spore germination. This compound effectively killed Bacillus anthracis Sterne vegetative cells (over 4 log reduction), presumably by severe perturbations of the bacterial cell wall and cytoplasmic membrane, while also acting as an effective spore germinant in the dark. While 2 log reduction of B. anthracis Sterne spores was observed, it is hypothesized that further killing could be achieved through enhanced germination.

  16. Expanding The Scope Of Oligo-pyrrolinone-pyrrolidines As Protein-protein Interface Mimics

    PubMed Central

    Raghuraman, Arjun; Xin, Dongyue; Perez, Lisa M.; Burgess, Kevin

    2013-01-01

    Oligo-pyrrolinone-pyrrolidines (generic structure 1) have the potential to interfere with protein-protein interactions (PPIs), but to reduce this to practice it is necessary to be able to synthesize these structures with a variety of different side-chains corresponding to genetically encoded proteins. This paper describes expansion of the synthetic scope of 1, the difficulties encountered in this process, particularly issues with epimerization and slow coupling rates, and methods to overcome them. Finally, spectroscopic and physicochemical properties as well as proteolytic stabilities of molecules in this series were measured; these data highlight the suitability of oligo-pyrrolinone-pyrrolidines for the development of pharmacological probes or pharmaceutical leads. PMID:23654284

  17. Exploring Redox States, Doping and Ordering of Electroactive Star-Shaped Oligo(aniline)s.

    PubMed

    Mills, Benjamin M; Fey, Natalie; Marszalek, Tomasz; Pisula, Wojciech; Rannou, Patrice; Faul, Charl F J

    2016-11-14

    We have prepared a simple star-shaped oligo(aniline) (TDPB) and characterised it in detail by MALDI-TOF MS, UV/Vis/NIR spectroscopy, time-dependent DFT, cyclic voltammetry and EPR spectroscopy. TDPB is part of an underdeveloped class of π-conjugated molecules with great potential for organic electronics, display and sensor applications. It is redox active and reacts with acids to form radical cations. Acid-doped TDPB shows behaviour similar to discotic liquid crystals, with X-ray scattering investigations revealing columnar self-assembled arrays. The combination of unpaired electrons and supramolecular stacking suggests that star-shaped oligo(aniline)s like TDPB have the potential to form conducting nanowires and organic magnetic materials.

  18. Exploring Redox States, Doping and Ordering of Electroactive Star‐Shaped Oligo(aniline)s

    PubMed Central

    Mills, Benjamin M.; Fey, Natalie; Marszalek, Tomasz; Pisula, Wojciech; Rannou, Patrice

    2016-01-01

    Abstract We have prepared a simple star‐shaped oligo(aniline) (TDPB) and characterised it in detail by MALDI‐TOF MS, UV/Vis/NIR spectroscopy, time‐dependent DFT, cyclic voltammetry and EPR spectroscopy. TDPB is part of an underdeveloped class of π‐conjugated molecules with great potential for organic electronics, display and sensor applications. It is redox active and reacts with acids to form radical cations. Acid‐doped TDPB shows behaviour similar to discotic liquid crystals, with X‐ray scattering investigations revealing columnar self‐assembled arrays. The combination of unpaired electrons and supramolecular stacking suggests that star‐shaped oligo(aniline)s like TDPB have the potential to form conducting nanowires and organic magnetic materials. PMID:27723154

  19. Porphyrin-beta-oligo-ethynylenephenylene-[60]fullerene triads: synthesis and electrochemical and photophysical characterization of the new porphyrin-oligo-PPE-[60]fullerene systems.

    PubMed

    Lembo, Angelo; Tagliatesta, Pietro; Guldi, Dirk M; Wielopolski, Mateusz; Nuccetelli, Marzia

    2009-03-05

    The synthesis and electrochemical and photophysical studies of new electron donor-acceptor arrays, bearing porphyrins covalently linked to fullerene, are described. In the reported investigation, phenyleneethynylene subunits were chosen as a linking bridge to guarantee a high conjugation degree between the donor (i.e., porphyrin), the molecular bridge (i.e., oligo-phenyleneethynylenes), and the acceptor (i.e., fullerene). To enhance the electronic interactions through the extended pi-system, the molecular bridge has been directly linked to the beta-pyrrole position of the porphyrin ring, generating a new example of donor-bridge-acceptor systems where, for the first time, the meso-phenyl ring of the macrocycle is not used to hold the "bridge" between porphyrin and fullerene moieties. This modification allows altering the chemical and physical properties of the tetrapyrrole ring. Steady-state and time-resolved fluorescence studies together with transient absorption measurements reveal that in nonpolar media (i.e., toluene) transduction of singlet excited-state energy governs the excited-state deactivation, whereas in polar media (i.e., tetrahydrofuran) charge transfer prevails generating a long-lived radical ion pair state. The lifetimes hereof range from 300 to 700 ns. The study also sheds light onto the wirelike behavior of the oligo-phenyleneethynylene bridges, for which a damping factor (beta) of 0.11 +/- 0.05 A(-1) has been determined in the current study.

  20. Seasonal Variability of Meiofaunal Abundance in the Oligo-mesohaline Area of the Gironde Estuary, France

    NASA Astrophysics Data System (ADS)

    Santos, P. J. P.; Castel, J.; Souza-Santos, L. P.

    1996-11-01

    The seasonality of meiofauna abundance was examined at an intertidal mud flat located in the oligo-mesohaline reach of the Gironde Estuary, France. Samples were collected weekly for 1 year at two stations located at the lower and the upper level of the mud flat (Stations L and H, respectively). Clear seasonal variations were evident for the meiofauna at both stations. Multivariate analysis revealed that meiofaunal composition, as well as biomass, was mainly regulated by temperature and salinity. Meiofaunal abundances were dominated by harpacticoid copepods at Station H and by nematodes at Station L, with meiofaunal biomass dominated by harpacticoid copepods at both stations, an unusual situation in estuarine muddy sediments. The meiofaunal community response to salinity occurs both as a chronic effect and as an anticipation to estuarine water salinity changes, thus suggesting that the animals response to this factor in oligo-mesohaline areas can also be an acute response to local heavy rains which can influence the meiofauna due to both variations of interstitial salinity and by erosion. Microphytobenthic resources, as estimated by chlorophyll aand pheopigment concentrations, had no strong influence on either meiofauna composition or biomass. Furthermore, evidence is given that microphytobenthic food supply is not a limiting factor to the benthic fauna in the oligo-mesohaline area of the Gironde Estuary.

  1. Digging into the low molecular weight peptidome with the OligoNet web server.

    PubMed

    Liu, Youzhong; Forcisi, Sara; Lucio, Marianna; Harir, Mourad; Bahut, Florian; Deleris-Bou, Magali; Krieger-Weber, Sibylle; Gougeon, Régis D; Alexandre, Hervé; Schmitt-Kopplin, Philippe

    2017-09-15

    Bioactive peptides play critical roles in regulating many biological processes. Recently, natural short peptides biomarkers are drawing significant attention and are considered as "hidden treasure" of drug candidates. High resolution and high mass accuracy provided by mass spectrometry (MS)-based untargeted metabolomics would enable the rapid detection and wide coverage of the low-molecular-weight peptidome. However, translating unknown masses (<1 500 Da) into putative peptides is often limited due to the lack of automatic data processing tools and to the limit of peptide databases. The web server OligoNet responds to this challenge by attempting to decompose each individual mass into a combination of amino acids out of metabolomics datasets. It provides an additional network-based data interpretation named "Peptide degradation network" (PDN), which unravels interesting relations between annotated peptides and generates potential functional patterns. The ab initio PDN built from yeast metabolic profiling data shows a great similarity with well-known metabolic networks, and could aid biological interpretation. OligoNet allows also an easy evaluation and interpretation of annotated peptides in systems biology, and is freely accessible at https://daniellyz200608105.shinyapps.io/OligoNet/ .

  2. Structure-activity relationships of oligo-beta-glucoside elicitors of phytoalexin accumulation in soybean.

    PubMed Central

    Cheong, J J; Birberg, W; Fügedi, P; Pilotti, A; Garegg, P J; Hong, N; Ogawa, T; Hahn, M G

    1991-01-01

    The abilities of a family of chemically synthesized oligo-beta-glucosides, ranging in size from hexamer to decamer, to induce phytoalexin accumulation in soybean cotyledons were investigated to determine which structural elements of the oligoglucosides are important for their biological activity. The results of the biological assays established that the following structural motif is necessary for the oligo-beta-glucosides to have high elicitor activity: [formula; see text] The branched trisaccharide at the nonreducing end of the oligoglucosides was found to be essential for maximum elicitor activity. Substitution of either the nonreducing terminal backbone glucosyl residue or the side-chain glucosyl residue closest to the nonreducing end with glucosaminyl or N-acetylglucosaminyl residues reduced the elicitor activity of the oligoglucosides between 10-fold and 10,000-fold. Elicitor activity was also reduced 1000-fold if the two side-chain glucosyl residues were attached to adjacent backbone glucosyl residues rather than to glucosyl residues separated by an unbranched residue. In contrast, modifications of the reducing terminal glucosyl residue of an elicitor-active hepta-beta-glucoside by conjugation with tyramine and subsequent iodination had no significant effect on the elicitor activity of the hepta-beta-glucoside. These results demonstrate that oligo-beta-glucosides must have a specific structure to trigger the signal transduction pathway, which ultimately leads to the de novo synthesis of phytoalexins in soybean. PMID:1840904

  3. The Arabidopsis Circadian System

    PubMed Central

    McClung, C. Robertson; Salomé, Patrice A.; Michael, Todd P.

    2002-01-01

    Rhythms with periods of approximately 24 hr are widespread in nature. Those that persist in constant conditions are termed circadian rhythms and reflect the activity of an endogenous biological clock. Plants, including Arabidopsis, are richly rhythmic. Expression analysis, most recently on a genomic scale, indicates that the Arabidopsis circadian clock regulates a number of key metabolic pathways and stress responses. A number of sensitive and high-throughput assays have been developed to monitor the Arabidopsis clock. These assays have facilitated the identification of components of plant circadian systems through genetic and molecular biological studies. Although much remains to be learned, the framework of the Arabidopsis circadian system is coming into focus. Dedication This review is dedicated to the memory of DeLill Nasser, a wonderful mentor and an unwavering advocate of both Arabidopsis and circadian rhythms research. PMID:22303209

  4. The RNA-binding protein repertoire of Arabidopsis thaliana

    PubMed Central

    Marondedze, Claudius; Thomas, Ludivine; Serrano, Natalia L.; Lilley, Kathryn S.; Gehring, Chris

    2016-01-01

    RNA-binding proteins (RBPs) have essential roles in determining the fate of RNA from synthesis to decay and have been studied on a protein-by-protein basis, or computationally based on a number of well-characterised RNA-binding domains. Recently, high-throughput methods enabled the capture of mammalian RNA-binding proteomes. To gain insight into the role of Arabidopsis thaliana RBPs at the systems level, we have employed interactome capture techniques using cells from different ecotypes grown in cultures and leaves. In vivo UV-crosslinking of RNA to RBPs, oligo(dT) capture and mass spectrometry yielded 1,145 different proteins including 550 RBPs that either belong to the functional category ‘RNA-binding’, have known RNA-binding domains or have orthologs identified in mammals, C. elegans, or S. cerevisiae in addition to 595 novel candidate RBPs. We noted specific subsets of RBPs in cultured cells and leaves and a comparison of Arabidopsis, mammalian, C. elegans, and S. cerevisiae RBPs reveals a common set of proteins with a role in intermediate metabolism, as well as distinct differences suggesting that RBPs are also species and tissue specific. This study provides a foundation for studies that will advance our understanding of the biological significance of RBPs in plant developmental and stimulus specific responses. PMID:27405932

  5. Specific analogues uncouple transport, signalling, oligo-ubiquitination and endocytosis in the yeast Gap1 amino acid transceptor

    PubMed Central

    Van Zeebroeck, Griet; Rubio-Texeira, Marta; Schothorst, Joep; Thevelein, Johan M

    2014-01-01

    The Saccharomyces cerevisiae amino acid transceptor Gap1 functions as receptor for signalling to the PKA pathway and concomitantly undergoes substrate-induced oligo-ubiquitination and endocytosis. We have identified specific amino acids and analogues that uncouple to certain extent signalling, transport, oligo-ubiquitination and endocytosis. l-lysine, l-histidine and l-tryptophan are transported by Gap1 but do not trigger signalling. Unlike l-histidine, l-lysine triggers Gap1 oligo-ubiquitination without substantial induction of endocytosis. Two transported, non-metabolizable signalling agonists, β-alanine and d-histidine, are strong and weak inducers of Gap1 endocytosis, respectively, but both causing Gap1 oligo-ubiquitination. The non-signalling agonist, non-transported competitive inhibitor of Gap1 transport, l-Asp-γ-l-Phe, induces oligo-ubiquitination but no discernible endocytosis. The Km of l-citrulline transport is much lower than the threshold concentration for signalling and endocytosis. These results show that molecules can be transported without triggering signalling or substantial endocytosis, and that oligo-ubiquitination and endocytosis do not require signalling nor metabolism. Oligo-ubiquitination is required, but apparently not sufficient to trigger endocytosis. In addition, we demonstrate intracellular cross-induction of endocytosis of transport-defective Gap1Y395C by ubiquitination- and endocytosis-deficient Gap1K9R,K16R. Our results support the concept that different substrates bind to partially overlapping binding sites in the same general substrate-binding pocket of Gap1, triggering divergent conformations, resulting in different conformation-induced downstream processes. PMID:24852066

  6. Specific analogues uncouple transport, signalling, oligo-ubiquitination and endocytosis in the yeast Gap1 amino acid transceptor.

    PubMed

    Van Zeebroeck, Griet; Rubio-Texeira, Marta; Schothorst, Joep; Thevelein, Johan M

    2014-07-01

    The Saccharomyces cerevisiae amino acid transceptor Gap1 functions as receptor for signalling to the PKA pathway and concomitantly undergoes substrate-induced oligo-ubiquitination and endocytosis. We have identified specific amino acids and analogues that uncouple to certain extent signalling, transport, oligo-ubiquitination and endocytosis. L-lysine, L-histidine and L-tryptophan are transported by Gap1 but do not trigger signalling. Unlike L-histidine, L-lysine triggers Gap1 oligo-ubiquitination without substantial induction of endocytosis. Two transported, non-metabolizable signalling agonists, β-alanine and D-histidine, are strong and weak inducers of Gap1 endocytosis, respectively, but both causing Gap1 oligo-ubiquitination. The non-signalling agonist, non-transported competitive inhibitor of Gap1 transport, L-Asp-γ-L-Phe, induces oligo-ubiquitination but no discernible endocytosis. The Km of L-citrulline transport is much lower than the threshold concentration for signalling and endocytosis. These results show that molecules can be transported without triggering signalling or substantial endocytosis, and that oligo-ubiquitination and endocytosis do not require signalling nor metabolism. Oligo-ubiquitination is required, but apparently not sufficient to trigger endocytosis. In addition, we demonstrate intracellular cross-induction of endocytosis of transport-defective Gap1(Y395C) by ubiquitination- and endocytosis-deficient Gap1(K9R,K16R). Our results support the concept that different substrates bind to partially overlapping binding sites in the same general substrate-binding pocket of Gap1, triggering divergent conformations, resulting in different conformation-induced downstream processes.

  7. The antimicrobial effects of the alginate oligomer OligoG CF-5/20 are independent of direct bacterial cell membrane disruption

    PubMed Central

    Pritchard, Manon F.; Powell, Lydia C.; Khan, Saira; Griffiths, Peter C.; Mansour, Omar T.; Schweins, Ralf; Beck, Konrad; Buurma, Niklaas J.; Dempsey, Christopher E.; Wright, Chris J.; Rye, Philip D.; Hill, Katja E.; Thomas, David W.; Ferguson, Elaine L.

    2017-01-01

    Concerns about acquisition of antibiotic resistance have led to increasing demand for new antimicrobial therapies. OligoG CF-5/20 is an alginate oligosaccharide previously shown to have antimicrobial and antibiotic potentiating activity. We investigated the structural modification of the bacterial cell wall by OligoG CF-5/20 and its effect on membrane permeability. Binding of OligoG CF-5/20 to the bacterial cell surface was demonstrated in Gram-negative bacteria. Permeability assays revealed that OligoG CF-5/20 had virtually no membrane-perturbing effects. Lipopolysaccharide (LPS) surface charge and aggregation were unaltered in the presence of OligoG CF-5/20. Small angle neutron scattering and circular dichroism spectroscopy showed no substantial change to the structure of LPS in the presence of OligoG CF-5/20, however, isothermal titration calorimetry demonstrated a weak calcium-mediated interaction. Metabolomic analysis confirmed no change in cellular metabolic response to a range of osmolytes when treated with OligoG CF-5/20. This data shows that, although weak interactions occur between LPS and OligoG CF-5/20 in the presence of calcium, the antimicrobial effects of OligoG CF-5/20 are not related to the induction of structural alterations in the LPS or cell permeability. These results suggest a novel mechanism of action that may avoid the common route in acquisition of resistance via LPS structural modification. PMID:28361894

  8. Injectable biodegradable hybrid hydrogels based on thiolated collagen and oligo(acryloyl carbonate)-poly(ethylene glycol)-oligo(acryloyl carbonate) copolymer for functional cardiac regeneration.

    PubMed

    Xu, Guohui; Wang, Xiaolin; Deng, Chao; Teng, Xiaomei; Suuronen, Erik J; Shen, Zhenya; Zhong, Zhiyuan

    2015-03-01

    Injectable biodegradable hybrid hydrogels were designed and developed based on thiolated collagen (Col-SH) and multiple acrylate containing oligo(acryloyl carbonate)-b-poly(ethylene glycol)-b-oligo(acryloyl carbonate) (OAC-PEG-OAC) copolymers for functional cardiac regeneration. Hydrogels were readily formed under physiological conditions (37°C and pH 7.4) from Col-SH and OAC-PEG-OAC via a Michael-type addition reaction, with gelation times ranging from 0.4 to 8.1 min and storage moduli from 11.4 to 55.6 kPa, depending on the polymer concentrations, solution pH and degrees of substitution of Col-SH. The collagen component in the hybrid hydrogels retained its enzymatic degradability against collagenase, and the degradation time of the hydrogels increased with increasing polymer concentration. In vitro studies showed that bone marrow mesenchymal stem cells (BMSCs) exhibited rapid cell spreading and extensive cellular network formation on these hybrid hydrogels. In a rat infarction model, the infarcted left ventricle was injected with PBS, hybrid hydrogels, BMSCs or BMSC-encapsulating hybrid hydrogels. Echocardiography demonstrated that the hybrid hydrogels and BMSC-encapsulating hydrogels could increase the ejection fraction at 28 days compared to the PBS control group, resulting in improved cardiac function. Histology revealed that the injected hybrid hydrogels significantly reduced the infarct size and increased the wall thickness, and these were further improved with the BMSC-encapsulating hybrid hydrogel treatment, probably related to the enhanced engraftment and persistence of the BMSCs when delivered within the hybrid hydrogel. Thus, these injectable hybrid hydrogels combining intrinsic bioactivity of collagen, controlled mechanical properties and enhanced stability provide a versatile platform for functional cardiac regeneration.

  9. Parallel vs. anti-parallel orientation in a curdlan/oligo(dA) complex as estimated by a FRET technique.

    PubMed

    Numata, Munenori; Koumoto, Kazuya; Mizu, Masami; Sakurai, Kazuo; Shinkai, Seiji

    2005-06-21

    We already found that beta-1,3-glucan polysaccharides form polymeric complexes with certain polynucleotides, but the parallel vs. anti-parallel orientation in those complexes had remained unsolved. In this paper, this controversial problem has been discussed for curdlan/oligo(dA) complexes utilizing two different energy transfer techniques. The first system consists of a combination of fluorescein-labeled curdlan and 3'-(or 5'-)tetramethyl-rhodamine (TAMRA)-labeled oligo(dA). The second system utilizes gold nanoparticles: that is, two curdlan chains were linked by a disulfide bond and after complexation with oligo(dA), the complex was immobilized on gold nanoparticles. In this system, TAMRA was attached to the 3'(or 5') end of oligo(dA) and the gold particle acted as a fluorescence quencher (energy acceptor). These experiments have led us to conclude that in the curdlan/oligo(dA) complex, parallel orientation is more favourable than anti-parallel orientation. These findings have enabled us to envision a clearer image for the complexation mode between beta-1,3-glucan polysaccharides and polynucleotides.

  10. Microarray long oligo probe designing for Escherichia coli: an in-silico DNA marker extraction.

    PubMed

    Behzadi, Payam; Najafi, Ali; Behzadi, Elham; Ranjbar, Reza

    2016-01-01

    Urinary tract infections are predominant diseases which may be caused by different pathogenic microorganisms, particularly Escherichia coli (E.coli). DNA microarray technology is an accurate, rapid, sensitive, and specific diagnostic tool which may lead to definite diagnosis and treatment of several infectious diseases. DNA microarray is a multi-process method in which probe designing plays an important. Therefore, the authors of the present study have tried to design a range of effective and proper long oligo microarray probes for detection and identification of different strains of pathogenic E.coli and in particular, uropathogenic E.coli (UPEC). E.coli O26 H11 11368 uid41021 was selected as the standard strain for probe designing. This strain encompasses the largest nucleotide sequence and the most number of genes among other pathogenic strains of E.coli. For performing this in silico survey, NCBI database, GReview Server, PanSeq Server, Oligoanalyzer tool, and AlleleID 7.7 were used to design accurate, appropriate, effective, and flexible long oligo microarray probes. Moreover, the genome of E.coli and its closely related microorganisms were compared. In this study, 15 long oligo microarray probes were designed for detecting and identifying different strains of E.coli such as UPEC. These probes possessed the best physico-chemical characteristics. The functional and structural properties of the designed probes were recognized by practical tools and softwares. The use of reliable advanced technologies and methodologies for probe designing guarentees the high quality of microarray probes and makes DNA microarray technology more flexible and an effective diagnostic technique.

  11. Oligo-Recurrence of Osteosarcoma Patients: Treatment Strategies for Pulmonary Metastases.

    PubMed

    Iwata, Shintaro; Yonemoto, Tsukasa; Iizasa, Toshihiko; Niibe, Yuzuru; Kamoda, Hiroto; Ishii, Takeshi

    2015-12-01

    Distant metastases from osteosarcoma most commonly occur in the lungs. Osteosarcoma can be cured by complete surgical resection of all metastatic lesions if the number is limited (oligo-recurrence: ≤ 5 metastatic or recurrent lesions with controlled primary lesions). This study aimed to clarify the prognostic factors for osteosarcoma patients with pulmonary metastasis and determine their oligo-recurrence status. Patients with conventional osteosarcoma who underwent definitive surgery for the primary lesion and at least one thoracotomy for pulmonary metastases were recruited to this retrospective study. Clinicopathological information was collected on each thoracotomy from 1976 to 2011, and was then analyzed statistically. We counted the number of resected nodules that were pathologically confirmed as metastatic lesions from osteosarcoma. In total, 151 thoracotomies in 71 patients were analyzed. Forty-seven patients (66 %) underwent up to two thoracotomies, and the maximum number of thoracotomies was six. The median number of resected nodules on each thoracotomy was two, and the median total size of metastatic lesions was 20 mm. Incomplete surgical remission [relative risk (RR) 3.42], a less than 1-year interval from a previous thoracotomy (RR 1.97), more than three resected nodules (RR 2.42); and total size of more than 30 mm for pulmonary metastases (RR 2.19) were independent predictors of increased risk of tumor death by multivariate analysis. We propose that factors contributing to oligo-recurrence of patients with pulmonary metastatic osteosarcoma include complete surgical remission, an interval from a previous thoracotomy, number of resected nodules, and total size of pulmonary metastases.

  12. Carbon ion radiotherapy for oligo-recurrent lung metastases from colorectal cancer: a feasibility study.

    PubMed

    Takahashi, Wataru; Nakajima, Mio; Yamamoto, Naoyoshi; Yamada, Shigeru; Yamashita, Hideomi; Nakagawa, Keiichi; Tsuji, Hiroshi; Kamada, Tadashi

    2014-03-01

    The purpose of this study was to evaluate the efficacy and feasibility of carbon ion radiotherapy (CIRT) for oligo-recurrent lung tumors from colorectal cancer (CRC). From May 1997 to October 2012, 34 consecutive patients with oligo-recurrent pulmonary metastases from CRC were treated with CIRT. The patients were not surgical candidates for medical reasons or patient refusal. Using a respiratory-gated technique, carbon ion therapy was delivered with curative intent using 4 coplanar beam angles. A median dose of 60 GyE (range, 44-64.8 GyE) was delivered to the planning target volume (PTV), with a median daily dose of 15 GyE (range, 3.6-44 GyE). Treatment outcome was analyzed in terms of local control rate (LCR), survival rate, and treatment-related complications. In total, 34 patients with 44 oligo-recurrent pulmonary lesions were treated with CIRT. Median follow-up period was 23.7 months. The 2- and 3-year actuarial LCRs of the treated patients were 85.4% ± 6.2% and 85.4% ± 6.2%, respectively. Overall survival was 65.1% ± 9.5% at 2 years, and 50.1% ± 10.5% at 3 years. Although survival rates were relatively worse in the subsets of patients aged<63 years or with early metastasis (< 36 months after resection of primary site), these factors were not significantly correlated with overall survival (P=0.13 and 0.19, respectively). All treatment-related complications were self-limited, without any grade 3-5 toxicity. CIRT is one of the most effective nonsurgical treatments for colorectal lung metastases, which are relatively resistant to stereotactic body radiotherapy. CIRT is considered to be the least invasive approach even in patients who have undergone repeated prior thoracic metastasectomies.

  13. Smart poly(oligo(propylene glycol) methacrylate) hydrogel prepared by gamma radiation

    NASA Astrophysics Data System (ADS)

    Suljovrujic, E.; Micic, M.

    2015-01-01

    The synthesis of poly(oligo(propylene glycol) methacrylate) (POPGMA) from functionalised oligo(propylene glycol) methacrylate (OPGMA) monomers by gamma radiation-induced radical polymerisation is reported for the first time; POPGMA homopolymeric hydrogel with oligo(propylene glycol) (OPG) pendant chains, as a non-linear PPGMA-analogue, was synthesised from an monomer-solvent (OPGMA375-water/ethanol) mixture at different irradiation doses (5, 10, 25, and 40 kGy). Determination of the gel fraction was conducted after synthesis. The swelling properties of the POPGMA hydrogel were preliminarily investigated over wide pH (2.2-9.0) and temperature (4-70 °C) ranges. Additional characterisation of structure and properties was conducted by UV-vis and Fourier transform infrared (FTIR) spectroscopy as well as by differential scanning calorimetry (DSC). In order to evaluate the potential for biomedical applications, biocompatibility (cytocompatibility and haemolytic activity) studies were performed as well. Sol-gel conversion was relatively high for all irradiation doses, indicating radiation-induced synthesis as a good method for fabricating this hydrogel. Thermoresponsiveness and variations in swelling capacity as a result of thermosensitive OPG pendant chains with a lower critical solution temperature (LCST) were mainly observed below room temperature; thus, the volume phase transition temperature (VPTT) of POPGMA homopolymeric hydrogel is about 15 °C. Furthermore, POPGMA has satisfactory biocompatibility. The results indicate that the hydrogels with propylene glycol pendant chains can be easily prepared by gamma radiation and have potential for different applications as smart and biocompatible polymers.

  14. Structural and electronic properties of oligo- and polythiophenes modified by substituents

    PubMed Central

    Rittmeyer, Simon P

    2012-01-01

    Summary The electronic and structural properties of oligo- and polythiophenes that can be used as building blocks for molecular electronic devices have been studied by using periodic density functional theory calculations. We have in particular focused on the effect of substituents on the electronic structure of thiophenes. Whereas singly bonded substituents, such as methyl, amino or nitro groups, change the electronic properties of thiophene monomers and dimers, they hardly influence the band gap of polythiophene. In contrast, phenyl-substituted polythiophenes as well as vinyl-bridged polythiophene derivatives exhibit drastically modified band gaps. These effects cannot be explained by simple electron removal or addition, as calculations for charged polythiophenes demonstrate. PMID:23365804

  15. Polar stationary phases based on poly(oligo ethylene glycol)diacrylates for capillary gas chromatography

    NASA Astrophysics Data System (ADS)

    Shiryaeva, V. E.; Popova, T. P.; Korolev, A. A.; Kanat'eva, A. Yu.; Kurganov, A. A.

    2017-08-01

    New stationary phases for capillary columns in GC are synthesized and studied. The phases are prepared by depositing oligo(ethylene glycol)diacrylates on the column walls and subsequent polymerization (crosslinking) in the presence of peroxide initiators. It is shown that stationary phases based on monomers with molecular weights of 10 kDa or higher exhibit separation properties similar to those of conventional stationary phases based on polyethylene glycol (PEG); however, their thermal stability is higher because they have a higher degree of crosslinking and a more ordered structure of the crosslinked polymers than the respective parameters of phases based on native PEG.

  16. Development and validation of a flax (Linum usitatissimum L.) gene expression oligo microarray.

    PubMed

    Fenart, Stéphane; Ndong, Yves-Placide Assoumou; Duarte, Jorge; Rivière, Nathalie; Wilmer, Jeroen; van Wuytswinkel, Olivier; Lucau, Anca; Cariou, Emmanuelle; Neutelings, Godfrey; Gutierrez, Laurent; Chabbert, Brigitte; Guillot, Xavier; Tavernier, Reynald; Hawkins, Simon; Thomasset, Brigitte

    2010-10-21

    Flax (Linum usitatissimum L.) has been cultivated for around 9,000 years and is therefore one of the oldest cultivated species. Today, flax is still grown for its oil (oil-flax or linseed cultivars) and its cellulose-rich fibres (fibre-flax cultivars) used for high-value linen garments and composite materials. Despite the wide industrial use of flax-derived products, and our actual understanding of the regulation of both wood fibre production and oil biosynthesis more information must be acquired in both domains. Recent advances in genomics are now providing opportunities to improve our fundamental knowledge of these complex processes. In this paper we report the development and validation of a high-density oligo microarray platform dedicated to gene expression analyses in flax. Nine different RNA samples obtained from flax inner- and outer-stems, seeds, leaves and roots were used to generate a collection of 1,066,481 ESTs by massive parallel pyrosequencing. Sequences were assembled into 59,626 unigenes and 48,021 sequences were selected for oligo design and high-density microarray (Nimblegen 385K) fabrication with eight, non-overlapping 25-mers oligos per unigene. 18 independent experiments were used to evaluate the hybridization quality, precision, specificity and accuracy and all results confirmed the high technical quality of our microarray platform. Cross-validation of microarray data was carried out using quantitative qRT-PCR. Nine target genes were selected on the basis of microarray results and reflected the whole range of fold change (both up-regulated and down-regulated genes in different samples). A statistically significant positive correlation was obtained comparing expression levels for each target gene across all biological replicates both in qRT-PCR and microarray results. Further experiments illustrated the capacity of our arrays to detect differential gene expression in a variety of flax tissues as well as between two contrasted flax varieties

  17. Development and validation of a flax (Linum usitatissimum L.) gene expression oligo microarray

    PubMed Central

    2010-01-01

    Background Flax (Linum usitatissimum L.) has been cultivated for around 9,000 years and is therefore one of the oldest cultivated species. Today, flax is still grown for its oil (oil-flax or linseed cultivars) and its cellulose-rich fibres (fibre-flax cultivars) used for high-value linen garments and composite materials. Despite the wide industrial use of flax-derived products, and our actual understanding of the regulation of both wood fibre production and oil biosynthesis more information must be acquired in both domains. Recent advances in genomics are now providing opportunities to improve our fundamental knowledge of these complex processes. In this paper we report the development and validation of a high-density oligo microarray platform dedicated to gene expression analyses in flax. Results Nine different RNA samples obtained from flax inner- and outer-stems, seeds, leaves and roots were used to generate a collection of 1,066,481 ESTs by massive parallel pyrosequencing. Sequences were assembled into 59,626 unigenes and 48,021 sequences were selected for oligo design and high-density microarray (Nimblegen 385K) fabrication with eight, non-overlapping 25-mers oligos per unigene. 18 independent experiments were used to evaluate the hybridization quality, precision, specificity and accuracy and all results confirmed the high technical quality of our microarray platform. Cross-validation of microarray data was carried out using quantitative qRT-PCR. Nine target genes were selected on the basis of microarray results and reflected the whole range of fold change (both up-regulated and down-regulated genes in different samples). A statistically significant positive correlation was obtained comparing expression levels for each target gene across all biological replicates both in qRT-PCR and microarray results. Further experiments illustrated the capacity of our arrays to detect differential gene expression in a variety of flax tissues as well as between two contrasted

  18. Comparative study of the interaction of meso-tetrakis (N-para-trimethyl-anilium) porphyrin (TMAP) in its free base and Fe derivative form with oligo(dA.dT)15 and oligo(dG.dC)15.

    PubMed

    Bathaie, S Zahra; Ajloo, Davood; Daraie, Marzieh; Ghadamgahi, Maryam

    2015-01-01

    Interaction between a cationic porphyrin and its ferric derivative with oligo(dA.dT)15 and oligo(dG.dC)15 was studied by UV-vis spectroscopy, resonance light scattering (RLS), and circular dichroism (CD) at different ionic strengths; molecular docking and molecular dynamics simulation were also used for completion. Followings are the observed changes in the spectral properties of meso-tetrakis (N-para-trimethyl-anilium) porphyrin (TMAP), as a free-base porphyrin with no axial ligand, and its Fe derivative (FeTMAP) upon interaction with oligo(dA.dT)15 and oligo(dG.dC)15: (1) the substantial red shift and hypochromicity at the Soret maximum in the UV-vis spectra; (2) the increased RLS intensity by increasing the ionic strength; and (3) an intense bisignate excitonic CD signal. All of them are the reasons for TMAP and FeTMAP binding to oligo(dA.dT)15 and oligo(dG.dC)15 with the outside binding mode, accompanied by the self-stacking of the ligands along the oligonucleotide helix. The CD results demonstrated a drastic change from excitonic in monomeric behavior at higher ionic strengths, which indicates the groove binding of the ligands with oligonucleotides. Molecular docking also confirmed the groove binding mode of the ligands and estimated the binding constants and energies of the interactions. Their interaction trend was further confirmed by molecular dynamics technique and structure parameters obtained from simulation. It showed that TMAP reduced the number of intermolecular hydrogen bonds and increased the solvent accessible surface area in the oligonucleotide. The self-aggregation of ligands at lower concentrations was also confirmed.

  19. On-Flow Synthesis of Co-Polymerizable Oligo-Microspheres and Application in ssDNA Amplification

    PubMed Central

    Lee, Se Hee; Lee, Jae Ha; Lee, Ho Won; Kim, Yang-Hoon; Jeong, Ok Chan; Ahn, Ji-Young

    2016-01-01

    We fabricated droplet-based microfluidic platform for copolymerizable microspheres with acrydite modified DNA probe. The copolymerizable 3-D polyacrylamide microspheres were successfully produced from microcontinuous-flow synthesis with on-channel solidification. DNA copolymerization activity, surface presentation and thermostability were assessed by using fluorescent labeled complementary probe. The binding performance was only visible on the surface area of oligo-microspheres. We show that the resulting oligo-microspheres can be directly integrated into a streamlined microsphere-PCR protocol for amplifying ssDNA. Our microspheres could be utilized as a potential material for ssDNA analysis such as DNA microarray and automatic DNA SELEX process. PMID:27447941

  20. Solid support synthesis of all-Rp-oligo(ribonucleoside phosphorothioate)s.

    PubMed Central

    Almer, H; Stawinski, J; Strömberg, R

    1996-01-01

    The first method for solid support synthesis of all-Rp-oligo(ribonucleoside phosphorothioate)s is presented as well as attempts to increase the stereoselectivity of the key step in this approach. The synthetic strategy consists of (i) a solid support synthesis procedure, using 5'-O-(4-methoxytriphenylmethyl)-2'-O-tert-butyldimethylsilyl-ri bon ucleoside 3'-H- phosphonates, that due to stereoselectivity in the condensation step, gives oligomers with mostly Sp-H-phosphonate diesters (72-89% under standard conditions), (ii) stereospecific sulfurization with S8 in pyridine to produce oligo(ribonucleoside phosphorothioate)s enriched with internucleosidic linkages of Rp configuration, (iii) treatment of the deprotected oligonucleotides with the enzyme Nuclease P1 from Penicillium citrinum, that specifically catalyses cleavage of Sp-phosphorothioate diester linkages, which leaves a mixture of oligomers having all internucleosidic linkages as Rp-phosphorothioates, and finally (iv) isolation and HPLC purification of the full length all-Rp oligomer. Mixed sequences containing the four common nucleosidic residues up to the chain length of a heptamer were synthesized. Change of N-4-protection on the cytidine building block from propionyl to N-methylpyrrolidin-2-ylidene gave a slightly improved diastereoselectivity in H-phosphonate diester formation. Increased selectivity up to 99+% was obtained with the guanosine building block when the amount of pyridine in the coupling step was reduced. PMID:8871563

  1. Esters of oligo-(glycerol carbonate-glycerol): New biobased oligomeric surfactants.

    PubMed

    Holmiere, Sébastien; Valentin, Romain; Maréchal, Philippe; Mouloungui, Zéphirin

    2017-02-01

    Glycerol carbonate is one of the most potentially multifunction glycerol-derived compounds. Glycerol is an important by-product of the oleochemical industry. The oligomerization of glycerol carbonate, assisted by the glycerol, results in the production of polyhydroxylated oligomers rich in linear carbonate groups. The polar moieties of these oligomers (Mw<1000Da) were supplied by glycerol and glycerol carbonate rather than ethylene oxide as in most commercial surfactants. The insertion of linear carbonate groups into the glycerol-based skeleton rendered the oligomers amphiphilic, resulting in a decrease in air/water surface tension to 57mN/m. We improved the physical and chemical properties of the oligomers, by altering the type of acylation reaction and the nature of the acyl donor. The polar head is constituted of homo-oligomers and hetero-oligomers. Homo-oligomers are oligoglycerol and/or oligocarbonate, hetero-oligomers are oligo(glycerol-glycerol carbonate). Coprah oligoesters had the best surfactant properties (CMC<1mg/mL, πcmc<30mN/m), outperforming molecules of fossil origin, such as ethylene glycol monododecyl ether, glycol ethers and fatty acid esters of sorbitan polyethoxylates. The self-assembling properties of oligocarbonate esters were highlighted by their ability to stabilize inverse and multiple emulsions. The oligo-(glycerol carbonate-glycerol ether) with relatively low molecular weights showed properties of relatively high-molecular weight molecules, and constitute a viable "green" alternative to ethoxylated surfactants.

  2. Synthesis of Hetero-bifunctional, End-Capped Oligo-EDOT Derivatives.

    PubMed

    Spicer, Christopher D; Booth, Marsilea A; Mawad, Damia; Armgarth, Astrid; Nielsen, Christian B; Stevens, Molly M

    2017-01-12

    Conjugated oligomers of 3,4-ethylenedioxythiophene (EDOT) are attractive materials for tissue engineering applications and as model systems for studying the properties of the widely used polymer poly(3,4-ethylenedioxythiophene). We report here the facile synthesis of a series of keto-acid end-capped oligo-EDOT derivatives (n = 2-7) through a combination of a glyoxylation end-capping strategy and iterative direct arylation chain extension. Importantly, these structures not only represent the longest oligo-EDOTs reported but are also bench stable, in contrast to previous reports on such oligomers. The constructs reported here can undergo subsequent derivatization for integration into higher-order architectures, such as those required for tissue engineering applications. The synthesis of hetero-bifunctional constructs, as well as those containing mixed-monomer units, is also reported, allowing further complexity to be installed in a controlled manner. Finally, we describe the optical and electrochemical properties of these oligomers and demonstrate the importance of the keto-acid in determining their characteristics.

  3. Hydrophilization of poly(caprolactone) copolymers through introduction of oligo(ethylene glycol) moieties.

    PubMed

    Wurth, Jonathan J; Blumenthal, Nils R; Shastri, V Prasad

    2014-01-01

    In this study, a new family of poly(ε-caprolactone) (PCL) copolymers that bear oligo(ethylene glycol) (OEG) moieties is described. The synthesis of three different oligo(ethylene glycol) functionalized epoxide monomers derived from 2-methyl-4-pentenoic acid, and their copolymerization with ε-caprolactone (CL) to poly(CL-co-OEG-MPO) copolymers is presented. The statistical copolymerization initiated with SnOct2/BnOH yielded the copolymers with varying OEG content and composition. The linear relationship between feed ratio and incorporation of the OEG co-monomer enables control over backbone functional group density. The introduction of OEG moieties influenced both the thermal and the hydrophilic characteristics of the copolymers. Both increasing OEG length and backbone content resulted in a decrease in static water contact angle. The introduction of OEG side chains in the PCL copolymers had no adverse influence on MC-3TE3-E1 cell interaction. However, changes to cell form factor (Φ) were observed. While unmodified PCL promoted elongated (anisotropic) morphologies (Φ = 0.094), PCL copolymer with tri-ethylene glycol side chains at or above seven percent backbone incorporation induced more isotropic cell morphologies (Φ = 0.184) similar to those observed on glass controls (Φ = 0.151).

  4. Vascular development in Arabidopsis.

    PubMed

    Ye, Zheng-Hua; Freshour, Glenn; Hahn, Michael G; Burk, David H; Zhong, Ruiqin

    2002-01-01

    Vascular tissues, xylem and phloem, form a continuous network throughout the plant body for transport of water, minerals, and food. Characterization of Arabidopsis mutants defective in various aspects of vascular formation has demonstrated that Arabidopsis is an ideal system for investigating the molecular mechanisms controlling vascular development. The processes affected in these mutants include initiation or division of procambium or vascular cambium, formation of continuous vascular cell files, differentiation of procambium or vascular cambium into vascular tissues, cell elongation, patterned secondary wall thickening, and biosynthesis of secondary walls. Identification of the genes affected by some of these mutations has revealed essential roles in vascular development for a cytokinin receptor and several factors mediating auxin transport or signaling. Mutational studies have also identified a number of Arabidopsis mutants defective in leaf venation pattern or vascular tissue organization in stems. Genetic evidence suggests that the vascular tissue organization is regulated by the same positional information that determines organ polarity.

  5. Submergence Confers Immunity Mediated by the WRKY22 Transcription Factor in Arabidopsis[W

    PubMed Central

    Hsu, Fu-Chiun; Chou, Mei-Yi; Chou, Shu-Jen; Li, Ya-Ru; Peng, Hsiao-Ping; Shih, Ming-Che

    2013-01-01

    Transcriptional control plays an important role in regulating submergence responses in plants. Although numerous genes are highly induced during hypoxia, their individual roles in hypoxic responses are still poorly understood. Here, we found that expression of genes that encode members of the WRKY transcription factor family was rapidly and strongly induced upon submergence in Arabidopsis thaliana, and this induction correlated with induction of a large portion of innate immunity marker genes. Furthermore, prior submergence treatment conferred higher resistance to the bacterial pathogen Pseudomonas syringae in Arabidopsis. Among the WRKY genes tested, WRKY22 had the highest level of induction during the early stages of submergence. Compared with the wild type, WRKY22 T-DNA insertion mutants wrky22-1 and wrky22-2 had lower disease resistance and lower induction of innate immunity markers, such as FLG22-INDUCED RECEPTOR-LIKE KINASE1 (FRK1) and WRKY53, after submergence. Furthermore, transcriptomic analyses of wrky22-2 and chromatin immunoprecipitation identified several potential targets of WRKY22, which included genes encoding a TIR domain–containing protein, a plant peptide hormone, and many OLIGO PEPTIDE TRANSPORTER genes, all of which may lead to induction of innate immunity. In conclusion, we propose that submergence triggers innate immunity in Arabidopsis via WRKY22, a response that may protect against a higher probability of pathogen infection either during or after flooding. PMID:23897923

  6. Luminescent oligo(ethylene glycol)-functionalized cyclometalated platinum(II) complexes: cellular characterization and mitochondria-specific localization.

    PubMed

    Guo, Zhengqing; Tong, Wah-Leung; Chan, Michael C W

    2014-02-18

    A readily tunable series of non-planar oligo(ethylene glycol)-substituted phosphorescent Pt(II) complexes has been investigated as live cell imaging agents; suitable structural modifications can give good cellular uptake, traceable mitochondria-specific localization and potent cytotoxic characteristics towards HeLa cells.

  7. The Oligo Fucoidan Inhibits Platelet-Derived Growth Factor-Stimulated Proliferation of Airway Smooth Muscle Cells

    PubMed Central

    Yang, Chao-Huei; Tsao, Chiung-Fang; Ko, Wang-Sheng; Chiou, Ya-Ling

    2016-01-01

    In the pathogenesis of asthma, the proliferation of airway smooth muscle cells (ASMCs) is a key factor in airway remodeling and causes airway narrowing. In addition, ASMCs are also the effector cells of airway inflammation. Fucoidan extracted from marine brown algae polysaccharides has antiviral, antioxidant, antimicrobial, anticlotting, and anticancer properties; however, its effectiveness for asthma has not been elucidated thus far. Platelet-derived growth factor (PDGF)-treated primary ASMCs were cultured with or without oligo-fucoidan (100, 500, or 1000 µg/mL) to evaluate its effects on cell proliferation, cell cycle, apoptosis, and Akt, ERK1/2 signaling pathway. We found that PDGF (40 ng/mL) increased the proliferation of ASMCs by 2.5-fold after 48 h (p < 0.05). Oligo-fucoidan reduced the proliferation of PDGF-stimulated ASMCs by 75%–99% after 48 h (p < 0.05) and induced G1/G0 cell cycle arrest, but did not induce apoptosis. Further, oligo-fucoidan supplementation reduced PDGF-stimulated extracellular signal-regulated kinase (ERK1/2), Akt, and nuclear factor (NF)-κB phosphorylation. Taken together, oligo-fucoidan supplementation might reduce proliferation of PDGF-treated ASMCs through the suppression of ERK1/2 and Akt phosphorylation and NF-κB activation. The results provide basis for future animal experiments and human trials. PMID:26761017

  8. The Oligo Fucoidan Inhibits Platelet-Derived Growth Factor-Stimulated Proliferation of Airway Smooth Muscle Cells.

    PubMed

    Yang, Chao-Huei; Tsao, Chiung-Fang; Ko, Wang-Sheng; Chiou, Ya-Ling

    2016-01-09

    In the pathogenesis of asthma, the proliferation of airway smooth muscle cells (ASMCs) is a key factor in airway remodeling and causes airway narrowing. In addition, ASMCs are also the effector cells of airway inflammation. Fucoidan extracted from marine brown algae polysaccharides has antiviral, antioxidant, antimicrobial, anticlotting, and anticancer properties; however, its effectiveness for asthma has not been elucidated thus far. Platelet-derived growth factor (PDGF)-treated primary ASMCs were cultured with or without oligo-fucoidan (100, 500, or 1000 µg/mL) to evaluate its effects on cell proliferation, cell cycle, apoptosis, and Akt, ERK1/2 signaling pathway. We found that PDGF (40 ng/mL) increased the proliferation of ASMCs by 2.5-fold after 48 h (p < 0.05). Oligo-fucoidan reduced the proliferation of PDGF-stimulated ASMCs by 75%-99% after 48 h (p < 0.05) and induced G₁/G₀ cell cycle arrest, but did not induce apoptosis. Further, oligo-fucoidan supplementation reduced PDGF-stimulated extracellular signal-regulated kinase (ERK1/2), Akt, and nuclear factor (NF)-κB phosphorylation. Taken together, oligo-fucoidan supplementation might reduce proliferation of PDGF-treated ASMCs through the suppression of ERK1/2 and Akt phosphorylation and NF-κB activation. The results provide basis for future animal experiments and human trials.

  9. OligoG CF-5/20 Disruption of Mucoid Pseudomonas aeruginosa Biofilm in a Murine Lung Infection Model

    PubMed Central

    Song, Zhijun; Ciofu, Oana; Onsøyen, Edvar; Rye, Philip D.; Høiby, Niels

    2016-01-01

    Biofilm growth is a universal survival strategy for bacteria, providing an effective and resilient approach for survival in an otherwise hostile environment. In the context of an infection, a biofilm provides resistance and tolerance to host immune defenses and antibiotics, allowing the biofilm population to survive and thrive under conditions that would destroy their planktonic counterparts. Therefore, the disruption of the biofilm is a key step in eradicating persistent bacterial infections, as seen in many types of chronic disease. In these studies, we used both in vitro minimum biofilm eradication concentration (MBEC) assays and an in vivo model of chronic biofilm infection to demonstrate the biofilm-disrupting effects of an alginate oligomer, OligoG CF-5/20. Biofilm infections were established in mice by tracheal instillation of a mucoid clinical isolate of Pseudomonas aeruginosa embedded in alginate polymer beads. The disruption of the biofilm by OligoG CF-5/20 was observed in a dose-dependent manner over 24 h, with up to a 2.5-log reduction in CFU in the infected mouse lungs. Furthermore, in vitro assays showed that 5% OligoG CF-5/20 significantly reduced the MBEC for colistin from 512 μg/ml to 4 μg/ml after 8 h. These findings support the potential for OligoG CF-5/20 as a biofilm disruption agent which may have clinical value in reducing the microbial burden in chronic biofilm infections. PMID:26833153

  10. Arabidopsis brassinosteroid signaling pathway.

    PubMed

    Belkhadir, Youssef; Wang, Xuelu; Chory, Joanne

    2006-12-05

    Plants control their size through the action of several phytohormones. One class of growth-promoting hormones is the brassinosteroids (BRs), the polyhydroxylated steroid hormones of plants. Here, we present the Arabidopsis-specific proteins that are the founding members of key BR signaling pathway components found in all plants. The genetic studies that identified these components are unique to Arabidopsis owing to its rapid generation time, sophisticated genetics, and facile transformation protocols, thereby highlighting the importance of a reference plant for understanding fundamental processes in all land plants.

  11. Carbon ion radiotherapy for oligo-recurrent lung metastases from colorectal cancer: a feasibility study

    PubMed Central

    2014-01-01

    Background The purpose of this study was to evaluate the efficacy and feasibility of carbon ion radiotherapy (CIRT) for oligo-recurrent lung tumors from colorectal cancer (CRC). Methods From May 1997 to October 2012, 34 consecutive patients with oligo-recurrent pulmonary metastases from CRC were treated with CIRT. The patients were not surgical candidates for medical reasons or patient refusal. Using a respiratory-gated technique, carbon ion therapy was delivered with curative intent using 4 coplanar beam angles. A median dose of 60 GyE (range, 44–64.8 GyE) was delivered to the planning target volume (PTV), with a median daily dose of 15 GyE (range, 3.6–44 GyE). Treatment outcome was analyzed in terms of local control rate (LCR), survival rate, and treatment-related complications. Results In total, 34 patients with 44 oligo-recurrent pulmonary lesions were treated with CIRT. Median follow-up period was 23.7 months. The 2- and 3-year actuarial LCRs of the treated patients were 85.4% ± 6.2% and 85.4% ± 6.2%, respectively. Overall survival was 65.1% ± 9.5% at 2 years, and 50.1% ± 10.5% at 3 years. Although survival rates were relatively worse in the subsets of patients aged < 63 years or with early metastasis (< 36 months after resection of primary site), these factors were not significantly correlated with overall survival (P = 0.13 and 0.19, respectively). All treatment-related complications were self-limited, without any grade 3–5 toxicity. Conclusions CIRT is one of the most effective nonsurgical treatments for colorectal lung metastases, which are relatively resistant to stereotactic body radiotherapy. CIRT is considered to be the least invasive approach even in patients who have undergone repeated prior thoracic metastasectomies. PMID:24581481

  12. EvOligo: A Novel Software to Design and Group Libraries of Oligonucleotides Applicable for Nucleic Acid-Based Experiments.

    PubMed

    Milewski, Marek C; Kamel, Karol; Kurzynska-Kokorniak, Anna; Chmielewski, Marcin K; Figlerowicz, Marek

    2017-03-15

    Experimental methods based on DNA and RNA hybridization, such as multiplex polymerase chain reaction, multiplex ligation-dependent probe amplification, or microarray analysis, require the use of mixtures of multiple oligonucleotides (primers or probes) in a single test tube. To provide an optimal reaction environment, minimal self- and cross-hybridization must be achieved among these oligonucleotides. To address this problem, we developed EvOligo, which is a software package that provides the means to design and group DNA and RNA molecules with defined lengths. EvOligo combines two modules. The first module performs oligonucleotide design, and the second module performs oligonucleotide grouping. The software applies a nearest-neighbor model of nucleic acid interactions coupled with a parallel evolutionary algorithm to construct individual oligonucleotides, and to group the molecules that are characterized by the weakest possible cross-interactions. To provide optimal solutions, the evolutionary algorithm sorts oligonucleotides into sets, preserves preselected parts of the oligonucleotides, and shapes their remaining parts. In addition, the oligonucleotide sets can be designed and grouped based on their melting temperatures. For the user's convenience, EvOligo is provided with a user-friendly graphical interface. EvOligo was used to design individual oligonucleotides, oligonucleotide pairs, and groups of oligonucleotide pairs that are characterized by the following parameters: (1) weaker cross-interactions between the non-complementary oligonucleotides and (2) more uniform ranges of the oligonucleotide pair melting temperatures than other available software products. In addition, in contrast to other grouping algorithms, EvOligo offers time-efficient sorting of paired and unpaired oligonucleotides based on various parameters defined by the user.

  13. Diketopyrrolopyrrole-based Conjugated Polymers Bearing Branched Oligo(Ethylene Glycol) Side Chains for Photovoltaic Devices.

    PubMed

    Chen, Xingxing; Zhang, Zijian; Ding, Zicheng; Liu, Jun; Wang, Lixiang

    2016-08-22

    Conjugated polymers are essential for solution-processable organic opto-electronic devices. In contrast to the great efforts on developing new conjugated polymer backbones, research on developing side chains is rare. Herein, we report branched oligo(ethylene glycol) (OEG) as side chains of conjugated polymers. Compared with typical alkyl side chains, branched OEG side chains endowed the resulting conjugated polymers with a smaller π-π stacking distance, higher hole mobility, smaller optical band gap, higher dielectric constant, and larger surface energy. Moreover, the conjugated polymers with branched OEG side chains exhibited outstanding photovoltaic performance in polymer solar cells. A power conversion efficiency of 5.37 % with near-infrared photoresponse was demonstrated and the device performance could be insensitive to the active layer thickness.

  14. Supramolecular hydrogels with reverse thermal gelation properties from (oligo)tyrosine containing block copolymers.

    PubMed

    Huang, Jin; Hastings, Conn L; Duffy, Garry P; Kelly, Helena M; Raeburn, Jaclyn; Adams, Dave J; Heise, Andreas

    2013-01-14

    Novel block copolymers comprising poly(ethylene glycol) (PEG) and an oligo(tyrosine) block were synthesized in different compositions by N-carboxyanhydride (NCA) polymerization. It was shown that PEG2000-Tyr(6) undergoes thermoresponsive hydrogelation at a low concentration range of 0.25-3.0 wt % within a temperature range of 25-50 °C. Cryogenic transmission electron microscopy (Cryo-TEM) revealed a continuous network of fibers throughout the hydrogel sample, even at concentrations as low as 0.25 wt %. Circular dichroism (CD) results suggest that better packing of the β-sheet tyrosine block at increasing temperature induces the reverse thermogelation. A preliminary assessment of the potential of the hydrogel for in vitro application confirmed the hydrogel is not cytotoxic, is biodegradable, and produced a sustained release of a small-molecule drug.

  15. Bis(aminoaryl) Carbon-Bridged Oligo(phenylenevinylene)s Expand the Limits of Electronic Couplings.

    PubMed

    Burrezo, Paula Mayorga; Lin, Nai-Ti; Nakabayashi, Koji; Ohkoshi, Shin-Ichi; Calzado, Eva M; Boj, Pedro G; Díaz García, María A; Franco, Carlos; Rovira, Concepciò; Veciana, Jaume; Moos, Michael; Lambert, Christoph; López Navarrete, Juan T; Tsuji, Hayato; Nakamura, Eiichi; Casado, Juan

    2017-03-06

    Carbon-bridged bis(aminoaryl) oligo(para-phenylenevinylene)s have been prepared and their optical, electrochemical, and structural properties analyzed. Their radical cations are class III and class II mixed-valence systems, depending on the molecular size, and they show electronic couplings which are among the largest for the self-exchange reaction of purely organic molecules. In their dication states, the antiferromagnetic coupling is progressively tuned with size from quinoidal closed-shell to open-shell biradicals. The data prove that the electronic coupling in the radical cations and the singlet-triplet gap in the dications show similar small attenuation factors, thus allowing charge/spin transfer over rather large distances. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Radiation grafting of oligo(ethylene glycol) ethyl ether methacrylate on polypropylene

    NASA Astrophysics Data System (ADS)

    Komasa, Justyna; Miłek, Andrzej; Ulański, Piotr; Rosiak, Janusz M.

    2014-01-01

    Oligo(ethylene glycol) ethyl ether methacrylate (OEGMA) can be grafted onto polypropylene (PP) films by post-irradiation grafting, forming a thermosensitive polymer layer, as indicated by FT-IR and contact angle measurements. In the first step, PP foils are irradiated by electron beam (5.5 kGy/min, up to 300 kGy) in the presence of air. Subsequently, the irradiated foils react with the monomer in oxygen-free solutions in isopropanol (up to 2 M of monomer) at 70 °C. Degree of grafting of OEGMA can be controlled by proper selection of absorbed dose, monomer concentration and reaction time. This work is a part of a broader project on thermosensitive materials facilitating cell growth and detachment for optimizing cell layer engineering techniques in the treatment of burn wounds.

  17. Improved anticoagulation of titanium by sequential immobilization of oligo(ethylene glycol) and 2-methacryloyloxyethyl phosphorylcholine.

    PubMed

    Pan, Chang-Jiang; Hou, Yan-Hua; Liu, Heng-Quan; Ding, Hong-Yan; Dong, Yun-Xiao

    2013-12-01

    Titanium and its alloys have been widely used for blood-contacting biomedical devices; however, their blood compatibility needs to be improved. In this study, titanium surface was modified by sequential immobilization of oligo(ethylene glycol) (OEG) and 2-methacryloyloxyethyl phosphorylcholine (MPC) to improve its anticoagulation. Water contact angle results showed an excellent hydrophilic surface after the immobilization. Attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR) confirmed that OEG and MPC were successfully immobilized on titanium surface. Static platelet adhesion and APTT (activated partial thromboplastin time) experiments suggested that the anticoagulation of titanium was significantly enhanced by the immobilization of OEG and further by subsequent MPC grafting. The approach in the present study opens up a window of promising an effective and efficient method to improve the anticoagulation of blood-contact biomedical devices such as coronary stents.

  18. Oligo-2'-deoxyribonucleotides containing uracil modified at the 5-position with linkers ending with guanidinium groups.

    PubMed

    Roig, Victoria; Asseline, Ulysse

    2003-04-16

    We report here the synthesis and binding studies of oligo-2'-deoxyribonucleotides (ODNs) containing 2'-deoxyuridines, modified at the 5-position by linkers ending with either one or two guanidinium groups. Comparison was made with ODNs containing 2'-deoxyuridines modified at the 5-position with linkers ending with either two or one amino groups. One or two modified 2'-deoxyuridines were incorporated into pyrimidine strands, and their influence on the stability of duplex (with both DNA and RNA targets) and triplex structures was studied. The strongest stabilization was obtained with modified ODNs containing guanidinium groups. This result confirms that the reduction of the global negative charge number on one strand is an important parameter in the stability of duplex and triplex structures.

  19. Fluorescence vesicles by self-assembly of oligo(biphenylene vinylene) bolaamphiphiles in n-hexane

    NASA Astrophysics Data System (ADS)

    Hwang, In-Wook; Kim, Yong-Rok

    2013-09-01

    Self-assembly of an oligo(biphenylene vinylene); OBPV bolaamphiphile with two polar coils of significantly long poly(propylene oxide); PPO (n = 21) at each end generated a fluorescent vesicle in apolar n-hexane. The vesicle efficiently produced trans-stilbene-like OBPV excimer emissions, as evidenced by an intense, redshifted, structured fluorescence spectrum with a long decay time of 5.0 ± 0.1 ns. An OBPV chromophore bound at both sides via a polar coil-to-coil interaction in apolar n-hexane was conducive to OBPV excimer emission, as evident from analysis of the spectroscopic data obtained from OBPVs with different PPO coil lengths (n = 13, 21, 34).

  20. Understanding the unconventional effects of halogenation on the luminescent properties of oligo(phenylene vinylene) molecules.

    PubMed

    Sun, Chun-Lin; Li, Jun; Geng, Hong-Wei; Li, Hui; Ai, Yong; Wang, Qiang; Pan, Shan-Lin; Zhang, Hao-Li

    2013-12-01

    It is commonly known that halogenation tends to decrease the luminescence quantum yield of an organic dye, owing to the high electronegativity and heavy-atom effect of the halogen atom. However, based on an investigation of the effects of halogenation on the luminescence of the oligo(phenylene vinylene) (OPV) framework, we demonstrate that halogenation can have positive impact on the solid-state fluorescence and electrochemiluminescence (ECL) properties of OPV derivatives. The chlorinated OPV exhibits a very high solid-state fluorescence quantum yield (91%), whilst the brominated analogue gives the highest ECL emission intensity. Time-dependent density functional theory calculations, natural bond orbital analysis, and natural transition orbital analysis were performed to assist the understanding of the origin of these positive halogenation effects, which provide insight into the rational design of highly luminescent halogenated organic materials for solid-state devices and ECL applications. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Novel antifouling oligo(ethylene glycol) methacrylate particles via surfactant-free emulsion polymerization.

    PubMed

    Buyukserin, Fatih; Camli, Sevket Tolga; Yavuz, Mustafa Selman; Budak, Gurer Guven

    2011-03-01

    The use of particle formulations with antifouling surface properties attracts increasing interest in several biotechnological applications. Majority of these studies utilize a poly(ethylene glycol) coating to render the corresponding surface nonrecognizable to biological macromolecules. Herein, we report a simple way to prepare novel antifouling colloids composed of oligo(ethylene glycol) backbones via surfactant-free emulsion polymerization. Monodisperse cross-linked poly(ethylene glycol) ethyl ether methacrylate particles were characterized by dynamic light scattering and transmission electron microscopy. The effects of monomer, cross-linker and initiator on particle characteristics were investigated. More importantly, a prominent blockage of bovine serum albumin adsorption was obtained for the poly(ethylene glycol)-based sub-micron (~200 nm) particles when compared with similar-sized poly(methyl methacrylate) counterparts.

  2. Surface-enhanced Raman scattering of a Ag/oligo(phenyleneethynylene)/Ag sandwich.

    PubMed

    Fletcher, Melissa; Alexson, D M; Prokes, Sharka; Glembocki, Orest; Vivoni, Alberto; Hosten, Charles

    2011-02-01

    α,ω-Dithiols are a useful class of compounds in molecular electronics because of their ability to easily adsorb to two metal surfaces, producing a molecular junction. We have prepared Ag nanosphere/oligo(phenyleneethynylene)/Ag sol (AgNS/OPE/Ag sol) and Ag nanowire/oligo(phenyleneethynylene)/Ag sol (AgNW/OPE/Ag sol) sandwiches to simulate the architecture of a molecular electronic device. This was achieved by self-assembly of OPE on the silver nanosurface, deprotection of the terminal sulfur, and deposition of Ag sol atop the monolayer. These sandwiches were then characterized by surface-enhanced Raman scattering (SERS) spectroscopy. The resulting spectra were compared to the bulk spectrum of the dimer and to the Ag nanosurface/OPE SERS spectra. The intensities of the SERS spectra in both systems exhibit a strong dependence on Ag deposition time and the results are also suggestive of intense interparticle coupling of the electromagnetic fields in both the AgNW/OPE/Ag and the AgNS/OPE/Ag systems. Three previously unobserved bands (1219, 1234, 2037 cm(-1)) arose in the SER spectra of the sandwiches and their presence is attributed to the strong enhancement of the electromagnetic field which is predicted from the COSMOL computational package. The 544 cm(-1) disulfide bond which is observed in the spectrum of solid OPE but is absent in the AgNS/OPE/Ag and AgNW/OPE/Ag spectra is indicative of chemisorption of OPE to the nanoparticles through oxidative dissociation of the disulfide bond.

  3. Neutral nickel ethylene oligo- and polymerization catalysts: towards computational catalyst prediction and design.

    PubMed

    Heyndrickx, Wouter; Occhipinti, Giovanni; Jensen, Vidar R

    2014-06-23

    DFT calculations have been used to elucidate the chain termination mechanisms for neutral nickel ethylene oligo- and polymerization catalysts and to rationalize the kind of oligomers and polymers produced by each catalyst. The catalysts studied are the (κ(2)-O,O)-coordinated (1,1,1,5,5,5-hexafluoro-2,4-acetylacetonato)nickel catalyst I, the (κ(2)-P,O)-coordinated SHOP-type nickel catalyst II, the (κ(2)-N,O)-coordinated anilinotropone and salicylaldiminato nickel catalysts III and IV, respectively, and the (κ(2)-P,N)-coordinated phosphinosulfonamide nickel catalyst V. Numerous termination pathways involving β-H elimination and β-H transfer steps have been investigated, and the most probable routes identified. Despite the complexity and multitude of the possible termination pathways, the information most critical to chain termination is contained in only few transition states. In addition, by consideration of the propagation pathway, we have been able to estimate chain lengths and discriminate between oligo- and polymerization catalysts. In agreement with experiment, we found the Gibbs free energy difference between the overall barrier for the most facile propagation and termination pathways to be close to 0 kcal mol(-1) for the ethylene oligomerization catalysts I and V, whereas values of at least 7 kcal mol(-1) in favor of propagation were determined for the polymerization catalysts III and IV. Because of the shared intermediates between the termination and branching pathways, we have been able to identify the preferred cis/trans regiochemistry of β-H elimination and show that a pronounced difference in σ donation of the two bridgehead atoms of the bidentate ligand can suppress hydride formation and thus branching. The degree of rationalization obtained here from a handful of key intermediates and transition states is promising for the use of computational methods in the screening and prediction of new catalysts of the title class.

  4. Oligo(p-phenylene ethynylene)-BODIPY derivatives: synthesis, energy transfer, and quantum-chemical calculations.

    PubMed

    Yin, Shouchun; Leen, Volker; Jackers, Carine; Beljonne, David; Van Averbeke, Bernard; Van der Auweraer, Mark; Boens, Noël; Dehaen, Wim

    2011-11-18

    The synthesis and energy-transfer properties of a series of oligo(p-phenylene ethynylene)-BODIPY (OPEB) cassettes are reported. A series of oligo(p-phenylene ethynylene)s (OPEs) with different conjugated chain lengths as energy donor subunit in the energy-transfer system were capped at both ends with BODIPY chromophores as energy-acceptor subunits. The effect of the conjugated chain of OPEs on energy transfer in the OPEB cassettes was investigated by UV/Vis and fluorescence spectroscopy and modeling. With increasing number n of phenyl acetylene units (n=1-7), the absorption and emission maxima of OPEn are bathochromically shifted. In the OPEBn analogues, the absorption maximum assigned to the BODIPY moieties is independent of the length of the OPE spacer. However, the relative absorption intensity of the BODIPY band decreases when the number of phenyl acetylene units is increased. The emission spectra of OPEBn are dominated by a band peaking at 613 nm, corresponding to emission of the BODIPY moieties, regardless of whether excitation is at 420 or 550 nm. Furthermore, a very small band is observed with a maximum between 450 and 500 nm, and its intensity relative to that of the BODIPY emission increases with increasing n, that is, the excited state of OPE subunits is efficiently quenched in OPEBn by energy transfer to the BODIPY moieties. Energy transfer (ET) from OPEn to BODIPY in OPEBn is very efficient (all Φ(ET) values are greater than 98 %) and only slightly decreases with increasing length of the OPE units. These results are supported by theoretical studies that show very high energy transfer efficiency (Φ(ET) >75 %) from the OPE spacer to the BODIPY end-groups for chains with up to 15-20 units. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Oligo-Miocene peatland ecosystems of the Gippsland Basin and modern analogues

    NASA Astrophysics Data System (ADS)

    Korasidis, Vera A.; Wallace, Malcolm W.; Wagstaff, Barbara E.; Holdgate, Guy R.

    2017-02-01

    A detailed examination of the brown coal facies preserved in the Latrobe Valley Morwell 1B seam indicates that the type of peat-forming environment and the associated hydrological regime are the main factors influencing the development of lithotypes in brown coal deposits. New palynological data from the Morwell 1B seam suggests that each respective lithotype in the lightening-upwards lithotype cycles was deposited in a particular depositional environment that was characterised by a distinct floral community. The laminated dark lithotype represents a fire-prone emergent marsh that grew on the margins of a coastal lagoon and/or freshwater swamp. This facies grades into the dark lithotype, representing the transition from a meadow marsh to a periodically flooded ombrogenous forested bog. The medium and lighter lithotypes are interpreted as being deposited in an angiosperm-dominated ombrogenous forest bog that was intolerant of fire. These peat-forming environments are interpreted as being largely controlled by moisture and relative depth to water table. Each environment produces distinct lithotypes and lightening-upwards cycles are interpreted as terrestrialization cycles. As the peat grew upwards and above the water table, less moist conditions prevailed and lighter lithotypes were produced. The observed change in colour, from darker to lighter lithotypes, results from the environment evolving from anaerobic/inundated to less anaerobic/less moist settings via terrestrialization. The thin and laterally extensive light and pale lithotypes that top the cycles are interpreted to represent a residual layer of concentrated, oxidation resistant peat-forming elements that result from intense weathering and aerobic degradation of the peats. At a generic level, modern lowland bogs of South Westland in New Zealand have remarkably similar floral/ecological gradients to those of the Oligo-Miocene Morwell 1B brown coal cycles in Australia. This suggests that modern New Zealand

  6. Starch Metabolism in Arabidopsis

    PubMed Central

    Streb, Sebastian; Zeeman, Samuel C.

    2012-01-01

    Starch is the major non-structural carbohydrate in plants. It serves as an important store of carbon that fuels plant metabolism and growth when they are unable to photosynthesise. This storage can be in leaves and other green tissues, where it is degraded during the night, or in heterotrophic tissues such as roots, seeds and tubers, where it is stored over longer time periods. Arabidopsis accumulates starch in many of its tissues, but mostly in its leaves during the day. It has proven to be a powerful genetic system for discovering how starch is synthesised and degraded, and new proteins and processes have been discovered. Such work has major significance for our starch crops, whose yield and quality could be improved by the application of this knowledge. Research into Arabidopsis starch metabolism has begun to reveal how its daily turnover is integrated into the rest of metabolism and adapted to the environmental conditions. Furthermore, Arabidopsis mutant lines deficient in starch metabolism have been employed as tools to study other biological processes ranging from sugar sensing to gravitropism and flowering time control. This review gives a detailed account of the use of Arabidopsis to study starch metabolism. It describes the major discoveries made and presents an overview of our understanding today, together with some as-yet unresolved questions. PMID:23393426

  7. Multi-centre evaluation of the speed-oligo Mycobacteria assay for differentiation of Mycobacterium spp. in clinical isolates.

    PubMed

    Hofmann-Thiel, Sabine; Turaev, Laziz; Alnour, Tarig; Drath, Lore; Müllerova, Maria; Hoffmann, Harald

    2011-12-19

    A new DNA line probe assay (Speed-oligo Mycobacteria, Vircell) has been launched for rapid differentiation of Mycobacterium spp. from cultures. Compared to other line-probe assays, Speed-oligo Mycobacteria covers a relatively limited spectrum of species but uses a simpler and faster dip-stick technique. The present multi-centre, multi-country study aimed at evaluating the utility and usability of Speed-oligo Mycobacteria in routine mycobacteriology diagnostics. Results from Speed-oligo Myobacteria were compared to those from Genotype CM (HAIN lifescience, Nehren, Germany), another line-probe assay. Speed-oligo Mycobacteria assay was performed in three main steps: 1) DNA extraction from cultured material 2) PCR amplification of the target gene and an internal control and 3) hybridization of the PCR products to specific probes by means of a dip-stick. Two hundred forty-two clinical isolates were recovered from consecutive positive mycobacterial cultures at two German (IML Gauting, Bioscientia Ingelheim), one Czech (KLINLAB Prague), and at a Sudanese (Khartoum) laboratory. All Mycobacterium species covered by the assay were reliably recognized. The rate of false positive results was 1.2% and concerned only the species M. marinum and M. peregrinum. The identification rate, i.e. the proportion of isolates which was correctly differentiated to the level of species or complex by the assay, differed significantly among laboratories being 94.9%, 90.7%, and 75.0% at the study sites IML Gauting, KLINLAB Prague and Bioscientia Ingelheim, respectively. This difference was caused by different spectra of NTM species encountered by the laboratory centres in daily routine diagnostics. Speed-oligo Mycobacteria assay was proved a rapid and easy-to-perform alternative to conventional line-probe assays. The assay showed excellent sensitivity with regard to identification of genus Mycobacterium and species/complexes covered by the test. However, due to its relatively limited spectrum of

  8. Automated solid-phase synthesis of high capacity oligo-dT cellulose for affinity purification of poly-A tagged biomolecules.

    PubMed

    Sau, Sujay P; Larsen, Andrew C; Chaput, John C

    2014-12-15

    Affinity purification of poly-adenylated biomolecules using solid supports that are derivatized with poly-thymidine oligonucleotides provides a powerful method for isolating cellular mRNA. These systems have also been used to purify mRNA-peptide fusions generated by RNA-display. However, the commercial source for high capacity oligo-dT cellulose was recently discontinued. To overcome this problem, we have developed a low cost solid-phase synthesis protocol to generate oligo-dT cellulose. Comparative binding studies indicate that chemically synthesized oligo-dT cellulose functions with superior loading capacity when compared to the discontinued product. We suggest that this method could be used to synthesize oligo-dT resin for routine purification of poly-adenylated biomolecules. Copyright © 2014 Elsevier Ltd. All rights reserved.

  9. Arabidopsis assay for mutagenicity.

    PubMed

    Gichner, T; Badayev, S A; Demchenko, S I; Relichová, J; Sandhu, S S; Usmanov, P D; Usmanova, O; Velemínský, J

    1994-10-16

    Four laboratories, two in the Czech Republic (Brno and Prague) and two in the CIS (Moscow and Duschanbe), participated in the International Programme on Chemical Safety's (IPCS) collaborative study to evaluate the utility of the most commonly used plant test systems, including the Arabidopsis thaliana assay, for assessing the mutagenic potential of environmental agents. Out of the five compounds evaluated in the Arabidopsis assay, three compounds, i.e., ethyl methanesulfonate, N-methyl-N-nitrosourea, and azidoglycerol, were reported to be mutagenic by all four participating laboratories. Sodium azide (NaN3) demonstrated a negative response in all four laboratories, whereas maleic hydrazide was reported to be weakly mutagenic by one laboratory and nonmutagenic by the other three laboratories.

  10. Analysis of 14-3-3 Family Member Function in Xenopus Embryos by Microinjection of Antisense Morpholino Oligos

    NASA Astrophysics Data System (ADS)

    Lau, Jeffrey M. C.; Muslin, Anthony J.

    The 14-3-3 intracellular phosphoserine/threonine-binding proteins are adapter molecules that regulate signal transduction, cell cycle, nutrient sensing, apoptotic, and cytoskeletal pathways. There are seven 14-3-3 family members, encoded by separate genes, in vertebrate organisms. To evaluate the role of individual 14-3-3 proteins in vertebrate embryonic development, we utilized an antisense morpholino oligo microinjection technique in Xenopus laevis embryos. By use of this method, we showed that embryos lacking specific 14-3-3 proteins displayed unique phenotypic abnormalities. Specifically, embryos lacking 14-3-3 τ exhibited gastrulation and axial patterning defects, but embryos lacking 14-3-3 γ exhibited eye defects without other abnormalities, and embryos lacking 14-3-3 ζ appeared completely normal. These and other results demonstrate the power and specificity of the morpholino antisense oligo microinjection technique.

  11. A Star-shaped Oligo(phenylenevinylene) Liquid Crystal Host with an Anthracene Guest-A Double Nanosegregating Supermesogen.

    PubMed

    Maier, Philipp; Grüne, Matthias; Lehmann, Matthias

    2017-01-23

    Hexasubstituted C3 -symmetric benzenes with three elongated shape-persistent oligo(phenylenevinylene) arms and three pyridyl hydrogen-bond acceptors have been synthesized. These mesogens assemble in a double-helical columnar liquid crystal (LC) structure, owing to the compensation of free spaces between conjugated arms by dimer formation. The void is filled also by up to three anthracene carboxylic acids as guests forming hydrogen bonded supermesogens assembling in columnar LC and soft-crystal phases. Thin film fluorescence and solid-state NMR spectroscopy imply a transition from a disordered columnar LC to an unexpected double nanosegregated morphology of a filled soft columnar crystal phase. An additional intracolumnar separation of anthracene and oligo(phenylenevinylene) chromophores occurs, separate to the general segregation of aliphatic and aromatic building blocks in LC structures. The new type of supermesogens will enable the rational design of host-guest double cables with a wide range of different conjugated building blocks.

  12. Engineering oligo(ethylene glycol) based nonfouling surfaces and microstructures for biomedical applications

    NASA Astrophysics Data System (ADS)

    Ma, Hongwei

    This thesis presents the initial development of oligo(ethylene glycol) (OEG) based "nonfouling"---protein and cell resistant---coatings that can be applied to a wide range of biomedical applications. The hypothesis underlying this work is that a high density of OEG will eliminate nonspecific protein adsorption thus reduce or eradicate undesired surface phenomena, such as poor biocompatibility, which are direct consequences of the nonspecific protein adsorption. A generalized method for creating functionalized nonfouling surfaces was developed by combining two strategies, namely "Surface-Initiated Atom Transfer Radical Polymerization of Oligo(ethylene glycol) methyl methacrylate (SI-ATRP of OEGMA)" and "Modular design of initiator", demonstrated on gold (metallic materials), glass and silicon oxide (hydroxylated substrates). SI-ATRP was able to achieve an OEG coating with a density higher than all the pre-existing techniques could achieve. It also provided control over the coating thickness and architecture that are not easily controlled by other techniques. Thickness-density profile of poly(OEGMA) was constructed based on SI-ATRP from mixed SAMs on gold. For the first time, we constructed a map of protein resistance of PEG coated surfaces, which reveals the relationship between the poly(OEGMA) coatings and their protein adsorption. Besides its scientific implications, the practical use (from an engineering point of view) of these results is that the information shall be instructive in designing nonfouling surfaces by providing critical structural parameters. This thesis also demonstrates integration of SI-ATRP with micro and nano scale pattern fabrication, which further expands the applications of this technology. In vitro cell culturing on patterned surfaces confirmed that high-density OEG coatings were exceptionally nonfouling even in physiological milieu, which shows great promise for the in vivo study of OEG coatings. A prototype protein microarray was

  13. Fluorescent monitoring of copper-occupancy in His-ended catalytic oligo-peptides

    PubMed Central

    Inokuchi, Reina; Kawano, Tomonori

    2016-01-01

    ABSTRACT Controlled generation of reactive oxygen species (ROS) is widely beneficial to various medical, environmental, and agricultural studies. As inspired by the functional motifs in natural proteins, our group has been engaged in development of catalytically active oligo-peptides as minimum-sized metalloenzymes for generation of superoxide anion, an active member of ROS. In such candidate molecules, catalytically active metal-binding minimal motif was determined to be X-X-H, where X can be most amino acids followed by His. Based on above knowledge, we have designed a series of minimal copper-binding peptides designated as GnH series peptides, which are composed of oligo-glycyl chains ended with C-terminal His residue such as GGGGGH sequence (G5H). In order to further study the role of copper binding to the peptidic catalysts sharing the X-X-H motif such as G5H-conjugated peptides, we should be able to score the occupancy of the peptide population by copper ion in the reaction mixture. Here, model peptides with Cu-binding affinity which show intrinsic fluorescence due to tyrosyl residue (Y) in the UV region (excitation at ca. 230 and 280 nm, and emission at ca. 320 nm) were synthesized to score the effect of copper occupancy. Synthesized peptides include GFP-derived fluorophore sequence, TFSYGVQ (designated as Gfp), and Gfp sequence fused to C-terminal G5H (Gfp-G5H). In addition, two Y-containing tri-peptides derived from natural GFP fluorophores, namely, TYG and SYG were fused to the G5H (TYG-G5H and SYG-G5H). Conjugation of metal-binding G5H sequence to GFP-fluorophore peptide enhanced the action of Cu2+ on quenching of intrinsic fluorescence due to Y residue. Two other Y-containing peptides, TYG-G5H and SYG-G5H, also showed intrinsic fluorescence which is sensitive to addition of Cu2+. There was linear relationship between the loading of Cu2+ and the quenching of fluorescence in these peptide, suggesting that Cu2+-dependent quenching of Y

  14. Fluorescent monitoring of copper-occupancy in His-ended catalytic oligo-peptides.

    PubMed

    Inokuchi, Reina; Kawano, Tomonori

    2016-01-01

    Controlled generation of reactive oxygen species (ROS) is widely beneficial to various medical, environmental, and agricultural studies. As inspired by the functional motifs in natural proteins, our group has been engaged in development of catalytically active oligo-peptides as minimum-sized metalloenzymes for generation of superoxide anion, an active member of ROS. In such candidate molecules, catalytically active metal-binding minimal motif was determined to be X-X-H, where X can be most amino acids followed by His. Based on above knowledge, we have designed a series of minimal copper-binding peptides designated as G n H series peptides, which are composed of oligo-glycyl chains ended with C-terminal His residue such as GGGGGH sequence (G5H). In order to further study the role of copper binding to the peptidic catalysts sharing the X-X-H motif such as G5H-conjugated peptides, we should be able to score the occupancy of the peptide population by copper ion in the reaction mixture. Here, model peptides with Cu-binding affinity which show intrinsic fluorescence due to tyrosyl residue (Y) in the UV region (excitation at ca. 230 and 280 nm, and emission at ca. 320 nm) were synthesized to score the effect of copper occupancy. Synthesized peptides include GFP-derived fluorophore sequence, TFSYGVQ (designated as Gfp), and Gfp sequence fused to C-terminal G5H (Gfp-G5H). In addition, two Y-containing tri-peptides derived from natural GFP fluorophores, namely, TYG and SYG were fused to the G5H (TYG-G5H and SYG-G5H). Conjugation of metal-binding G5H sequence to GFP-fluorophore peptide enhanced the action of Cu(2+) on quenching of intrinsic fluorescence due to Y residue. Two other Y-containing peptides, TYG-G5H and SYG-G5H, also showed intrinsic fluorescence which is sensitive to addition of Cu(2+). There was linear relationship between the loading of Cu(2+) and the quenching of fluorescence in these peptide, suggesting that Cu(2+)-dependent quenching of Y

  15. Postdiffusion of oligo-peptide within exponential growth multilayer films for localized peptide delivery.

    PubMed

    Wang, Xuefei; Ji, Jian

    2009-10-06

    The multilayers of poly(L-lysine) (PLL) and hyaluronic acid (HA) were constructed by alternating deposition of PLL at high pH and HA at low pH. The exponential growth of the multilayer was proved to be amplified by increasing the pH difference between the two deposition solutions. The exponential growth multilayers of PLL/HA assembled at different pH were utilized as reservoirs for loading a trans-activating transcriptional factor (TAT) peptide. The confocal laser scanning microscopy (CLSM) results indicated that the FITC-labeled TAT could diffuse throughout the exponentially growing PLL/HA film. The amount of peptide embedded within multilayer could be adjusted by both multilayer assembly pH and the TAT loading pH. Compared with (PLL/HA 6.5/6.5)5 multilayer (PLL/HA a/b means that the multilayer film was constructed by using PLL at pH a and HA at pH b), the (PLL/HA 9.5/2.9)5 film can be loaded with more TAT peptide at the same loading pH 6.5. The excess of positively charged TAT peptide within (PLL/HA 9.5/2.9)5 film could not only be ascribed to its extraordinary thickness but also be attributed to its uncompensated negative charge density enhanced by the pH difference between film buildup and peptide loading process. Increasing of the TAT loading pH from 6.5 to 9.5, which increases the pH difference between multilayer assembly and peptide loading process, enhances the uncompensated charge density within (PLL/HA 9.5/2.9)5 film and elevates the peptide density from 13.8 to 25.0 microg/cm2. Compared with direct layer-by-layer assembly of TAT and HA, the postdiffusion of TAT into (PLL/HA 9.5/2.9)5 film was loaded much more peptide. The postdiffusion of peptide into a rapid growth multilayer can be more favorable to load and sustainedly release functional oligo-peptide. The cell culture results indicated that the TAT embedded within the film maintained the ability to traverse across the Hep G2 cell membrane. The functionalized (PLL/HA 9.5/2.9)5 TAT 9.5 film was more

  16. Oligo-Miocene Deposition Along the Eastern Margin of the Altiplano Plateau, Salla, Bolivia

    NASA Astrophysics Data System (ADS)

    Leier, A. L.; Long, S.; McQuarrie, N.

    2006-12-01

    The Eastern Cordillera of the Bolivian Andes forms the eastern boundary of the Altiplano plateau, an internally- drained hinterland basin that occupies an area of 150,000 km2 and has an average elevation of 4 km. Almost all tectonic models of the region indicate an important causal relationship existed between early Tertiary deformation in the Eastern Cordillera and initial development of the Altiplano plateau. We examined Oligo- Miocene strata deposited along the eastern margin of the Altiplano plateau and within the Eastern Cordillera near the village of Salla (100 km south of La Paz) to constrain the depositional and deformational history of the region. Stratigraphic units in the study area consist of the Oligocene Luribay Conglomerate and the overlying Oligo-Miocene Salla Beds. The Luribay Conglomerate comprises up to 500 m of pebble- to boulder- conglomerate with interbedded coarse-grained sandstone. Clast-compositions, thicknesses, facies, and paleocurrent directions vary considerably between outcrop exposures. Conglomerate beds were deposited by gravity flows in alluvial fan settings and by traction transport in fluvial systems. Growth strata within the Luribay Conglomerate record syn-deformational deposition. The overlying Salla Beds consist of roughly 500 m of clay- and siltstone, with minor amounts of sandstone and rare conglomerate lenses. Extensive evidence of pedogenesis within the succession suggests the region was characterized by well-drained interfluve environments during Late Oligocene-Early Miocene time. Although the Salla Beds are folded and faulted, they are generally less deformed than the underlying Luribay Conglomerate. Deposition near Salla commenced during Oligocene time in a number of discrete basins separated from one another by topographic highs, which were produced by upper crustal folding and faulting in the west verging portion of the Andean fold-thrust belt. Sediments within these basins were derived from local sources and deposited

  17. sigReannot: an oligo-set re-annotation pipeline based on similarities with the Ensembl transcripts and Unigene clusters

    PubMed Central

    Casel, Pierrot; Moreews, François; Lagarrigue, Sandrine; Klopp, Christophe

    2009-01-01

    Background Microarray is a powerful technology enabling to monitor tens of thousands of genes in a single experiment. Most microarrays are now using oligo-sets. The design of the oligo-nucleotides is time consuming and error prone. Genome wide microarray oligo-sets are designed using as large a set of transcripts as possible in order to monitor as many genes as possible. Depending on the genome sequencing state and on the assembly state the knowledge of the existing transcripts can be very different. This knowledge evolves with the different genome builds and gene builds. Once the design is done the microarrays are often used for several years. The biologists working in EADGENE expressed the need of up-to-dated annotation files for the oligo-sets they share including information about the orthologous genes of model species, the Gene Ontology, the corresponding pathways and the chromosomal location. Results The results of SigReannot on a chicken micro-array used in the EADGENE project compared to the initial annotations show that 23% of the oligo-nucleotide gene annotations were not confirmed, 2% were modified and 1% were added. The interest of this up-to-date annotation procedure is demonstrated through the analysis of real data previously published. Conclusion SigReannot uses the oligo-nucleotide design procedure criteria to validate the probe-gene link and the Ensembl transcripts as reference for annotation. It therefore produces a high quality annotation based on reference gene sets. PMID:19615116

  18. Salvage radiotherapy for regional lymph node oligo-recurrence after radical surgery of non-small cell lung cancer.

    PubMed

    Seol, Ki Ho; Lee, Jeong Eun; Cho, Joon Yong; Lee, Deok Heon; Seok, Yangki; Kang, Min Kyu

    2017-09-14

    Currently, evidence-based guidelines for salvage therapy to treat mediastinal lymph node (LN) oligo-recurrence in post-resection non-small cell lung cancer (NSCLC) are limited. In patients previously treated by surgery without irradiation, radiotherapy (RT) might be safely utilized. We evaluate the clinical outcomes of salvage RT for patients with LN oligo-recurrence that developed after radical surgery for NSCLC. Thirty-one patients with stage I-IIIA NSCLC who developed regional LN oligo-recurrence between 2008 and 2013 were reviewed. The median time from surgery to recurrence was 12 months. Fifteen patients (48.4%) had single LN recurrence. All patients were irradiated by 3-dimensional conformal RT at the recurrent LN area with daily fractions of 2-3 Gy, with a median dose of 66 Gy (range 51-66). Sixteen patients also received chemotherapy. After salvage RT, 16 patients achieved a complete response, nine a partial response, and six had stable disease. The median follow-up was 14 months (range 3-76). One and two-year in-field control rates were 88.4% and 75.8%, respectively. One and two-year progression-free survival rates were 73.1% and 50.9%, respectively. Progression sites were predominantly distant. Ten of the 31 patients (32.3%) met the revised Response Evaluation Criteria for Solid Tumors for a complete response by the final follow-up. Recurrent LN size (<3 vs. ≥3 cm) was a significant prognostic factor for progression-free survival (P = 0.013). Salvage RT for patients with regional LN oligo-recurrence after radical surgery was an effective treatment option with an acceptable level of toxicity. © 2017 The Authors. Thoracic Cancer published by China Lung Oncology Group and John Wiley & Sons Australia, Ltd.

  19. Preparation of Reactive Oligo(p-Phenylene Vinylene) Materials for Spatial Profiling of the Chemical Reactivity of Intracellular Compartments.

    PubMed

    Nie, Chenyao; Li, Shengliang; Wang, Bing; Liu, Libing; Hu, Rong; Chen, Hui; Lv, Fengting; Dai, Zhihui; Wang, Shu

    2016-05-01

    An oligo(p-phenylene vinylene) derivative (OPV-pfp) functionalized with pentafluorophenol active ester is designed and synthesized. The high reactivity of OPV-pfp with biological small molecules or macromolecules containing amino groups under physiological conditions leads to spectral changes of OPV-pfp; thus, spatial reactivity discrimination for different subcellular structures inside cells is realized by triggering and imaging the fluorescence signal change of the OPV-pfp.

  20. Effect of Backbone Design on Hybridization Thermodynamics of Oligo-nucleic Acids: A Coarse-Grained Molecular Dynamics Simulation Study

    NASA Astrophysics Data System (ADS)

    Ghobadi, Ahmadreza F.; Jayaraman, Arthi

    DNA hybridization is the basis of various bio-nano technologies, such as DNA origami and assembly of DNA-functionalized nanoparticles. A hybridized double stranded (ds) DNA is formed when complementary nucleobases on hybridizing strands exhibit specific and directional hydrogen bonds through canonical Watson-Crick base-pairing interactions. In recent years, the need for cheaper alternatives and significant synthetic advances have driven design of DNA mimics with new backbone chemistries. However, a fundamental understanding of how these backbone modifications in the oligo-nucleic acids impact the hybridization and melting behavior of the duplex is still lacking. In this talk, we present our recent findings on impact of varying backbone chemistry on hybridization of oligo-nucleic acid duplexes. We use coarse-grained molecular dynamics simulations to isolate the effect of strand flexibility, electrostatic interactions and nucleobase spacing on the melting curves for duplexes with various strand sequences and concentrations. Since conjugation of oligo-nucleic acids with polymers serve as building blocks for thermo-responsive polymer networks and gels, we also present the effect of such conjugation on hybridization thermodynamics and polymer conformation.

  1. A Call for the Aggressive Treatment of Oligometastatic and Oligo-Recurrent Non-Small Cell Lung Cancer

    PubMed Central

    Patel, Pretesh R.; Yoo, David S.; Niibe, Yuzuru; Urbanic, James J.; Salama, Joseph K.

    2012-01-01

    Metastatic non-small cell lung cancer (NSCLC) carries a dismal prognosis. Clinical evidence suggests the existence of an intermediate, or oligometastatic, state when metastases are limited in number and/or location. In addition, following initial curative therapy, many patients present with limited metastatic disease, or oligo-recurrence. Metastasis-directed, anti-cancer therapies may benefit these patients. A growing evidence-base supports the use of hypofractionated, image-guided radiotherapy (HIGRT) for a variety of malignant conditions including inoperable stage I NSCLC and many metastatic sites. When surgical resection is not possible, HIGRT offers an effective alternative for local treatment of limited metastatic disease. Early studies have produced promising results when HIGRT was delivered to all known sites of disease in patients with oligometastatic/oligo-recurrent NSCLC. In a population of patients formerly considered rapidly terminal, these studies report five year overall survival rates of 13–22%. HIGRT for metastatic NSCLC warrants further study. We call for large, intergroup, and even international randomized trials incorporating HIGRT and other metastasis-directed therapies into the treatment of patients with oligometastatic/oligo-recurrent NSCLC. PMID:23125927

  2. T. cruzi OligoC-TesT: A Simplified and Standardized Polymerase Chain Reaction Format for Diagnosis of Chagas Disease

    PubMed Central

    Deborggraeve, Stijn; Coronado, Ximena; Solari, Aldo; Zulantay, Ines; Apt, Werner; Mertens, Pascal; Laurent, Thierry; Leclipteux, Thierry; Stessens, Tim; Dujardin, Jean-Claude; Herdewijn, Piet; Büscher, Philippe

    2009-01-01

    Background PCR has evolved into one of the most promising tools for T. cruzi detection in the diagnosis and control of Chagas disease. However, general use of the technique is hampered by its complexity and the lack of standardization. Methodology We here present the development and phase I evaluation of the T. cruzi OligoC-TesT, a simple and standardized dipstick format for detection of PCR amplified T. cruzi DNA. The specificity and sensitivity of the assay were evaluated on blood samples from 60 Chagas non-endemic and 48 endemic control persons and on biological samples from 33 patients, 7 reservoir animals, and 14 vectors collected in Chile. Principal Findings The lower detection limits of the T. cruzi OligoC-TesT were 1 pg and 1 to 10 fg of DNA from T. cruzi lineage I and II, respectively. The test showed a specificity of 100% (95% confidence interval [CI]: 96.6%–100%) on the control samples and a sensitivity of 93.9% (95% CI: 80.4%–98.3%), 100% (95% CI: 64.6%–100%), and 100% (95% CI: 78.5%–100%) on the human, rodent, and vector samples, respectively. Conclusions The T. cruzi OligoC-TesT showed high sensitivity and specificity on a diverse panel of biological samples. The new tool is an important step towards simplified and standardized molecular diagnosis of Chagas disease. PMID:19503815

  3. Difference of carboxybetaine and oligo(ethylene glycol) moieties in altering hydrophobic interactions: a molecular simulation study.

    PubMed

    Shao, Qing; White, Andrew D; Jiang, Shaoyi

    2014-01-09

    Polycarboxybetaine and poly(ethylene glycol) materials resist nonspecific protein adsorption but differ in influencing biological functions such as enzymatic activity. To investigate this difference, we studied the influence of carboxybetaine and oligo(ethylene glycol) moieties on hydrophobic interactions using molecular simulations. We employed a model system composed of two non-polar plates and studied the potential of mean force of plate-plate association in carboxybetaine, (ethylene glycol)4, and (ethylene glycol)2 solutions using well-tempered metadynamics simulations. Water, trimethylamine N-oxide, and urea solutions were used as reference systems. We analyzed the variation of the potential of mean force in various solutions to study how carboxybetaine and oligo(ethylene glycol) moieties influence the hydrophobic interactions. To study the origin of their influence, we analyzed the normalized distributions of moieties and water molecules using molecular dynamics simulations. The simulation results showed that oligo(ethylene glycol) moieties repel water molecules away from the non-polar plates and weaken the hydrophobic interactions. Carboxybetaine moieties do not repel water molecules away from the plates and therefore do not influence the hydrophobic interactions.

  4. Tidal dynamics and mangrove carbon sequestration during the Oligo-Miocene in the South China Sea

    NASA Astrophysics Data System (ADS)

    Collins, Daniel S.; Avdis, Alexandros; Allison, Peter A.; Johnson, Howard D.; Hill, Jon; Piggott, Matthew D.; Hassan, Meor H. Amir; Damit, Abdul Razak

    2017-06-01

    Modern mangroves are among the most carbon-rich biomes on Earth, but their long-term (>=106 years) impact on the global carbon cycle is unknown. The extent, productivity and preservation of mangroves are controlled by the interplay of tectonics, global sea level and sedimentation, including tide, wave and fluvial processes. The impact of these processes on mangrove-bearing successions in the Oligo-Miocene of the South China Sea (SCS) is evaluated herein. Palaeogeographic reconstructions, palaeotidal modelling and facies analysis suggest that elevated tidal range and bed shear stress optimized mangrove development along tide-influenced tropical coastlines. Preservation of mangrove organic carbon (OC) was promoted by high tectonic subsidence and fluvial sediment supply. Lithospheric storage of OC in peripheral SCS basins potentially exceeded 4,000 Gt (equivalent to 2,000 p.p.m. of atmospheric CO2). These results highlight the crucial impact of tectonic and oceanographic processes on mangrove OC sequestration within the global carbon cycle on geological timescales.

  5. Oligo-dT selected spermatozoal transcript profiles differ among higher and lower fertility dairy sires.

    PubMed

    Card, C J; Krieger, K E; Kaproth, M; Sartini, B L

    2017-02-01

    Spermatozoal messenger RNA (mRNA) has the potential as a molecular marker for sire fertility because this population can reflect gene expression that occurred during spermatogenesis and may have a functional role in early embryonic development. The goal of this study was to compare the oligo-dT selected spermatozoal transcript profiles of higher fertility (Conception Rate (CR) 1.8-3.5) and lower fertility (CR -2.9 to -0.4) sires using Ribonucleic Acid Sequencing (RNA-Seq). A total of 3227 transcripts and 5366 transcripts were identified in the higher and lower fertility populations, respectively. While common transcripts between the two populations were identified (2422 transcripts), several transcripts were also unique to the fertility populations including 805 transcripts that were unique to the higher fertility population and 2944 transcripts that were unique to the lower fertility population. From gene ontological analysis, the transcripts unique to each fertility population differed in Biological Processes (BP), including enrichment of regulatory transcripts for growth and protein kinase activity in the higher fertility bulls. Biological variation in transcript presence among individual sires was also found. Of the candidate fertility spermatozoal transcripts chosen from the RNA-Seq population analysis reported here and previous publications, COX7C was negatively correlated with sire fertility. Using high-throughput sequencing, candidate spermatozoal transcripts were identified for further study as potential markers for sire fertility. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. Preparation, composition analysis and antioxidant activities of konjac oligo-glucomannan.

    PubMed

    Liu, Jianhua; Xu, Qiuhong; Zhang, Jingjing; Zhou, Xuxia; Lyu, Fei; Zhao, Peicheng; Ding, Yuting

    2015-10-05

    Konjac oligo-glucomannan (KOG) was prepared by degradation of konjac glucomannan (KG) using β-mannanase. The hydrolysis process was monitored by the viscosity of the enzymatic hydrolysates. Factors affecting the enzymatic hydrolysis of KG were investigated, and the optimum hydrolysis conditions were as follows: time 2h; temperature 50°C; pH 6.0; and enzymatic concentration 150 U/g. Under these optimized conditions, minimum viscosity (31.9 mPa·s) of the hydrolasate was obtained. The average degree of polymerization (DP) of the resulting KOG was approximately equal to 5.2. The results of Fourier transform infrared (FTIR) spectra of KG and KOG indicated that KG was successfully degraded. In addition, their antioxidant activities were evaluated by determination of hydroxyl radical (•OH) and 1,1-diphenyl-2-picrylhrazyl radical (•DPPH) scavenging activity, and determination of reducing power. The results showed that KOG exhibited significant antioxidant activities. Taken together, this study suggested that KOG could potentially be used as a natural antioxidant. Copyright © 2015 Elsevier Ltd. All rights reserved.

  7. The role of varicocele sclerotherapy in men with severe oligo-astheno-teratozoospermia.

    PubMed

    Ghanem, Mazen A; Safan, Manal A; Ghanem, Ashraf A; Dohle, Gert R

    2011-11-01

    The aim of this study was to verify the role of antegrade scrotal sclerotherapy for the treatment of varicoceles in infertile men with severe oligo-astheno-teratozoospermia (OAT). The 59 patients with severe OAT in this study underwent antegrade scrotal sclerotherapy for the treatment of varicoceles. The outcome was assessed in terms of improvement in semen parameters and spontaneous conception rate. Semen parameters and reproductive hormones were evaluated before antegrade sclerotherapy (AS) and 6 months after AS. After an average follow-up time of 34.8±3.2 months, significant improvement was noted in the mean sperm concentration, motility and morphology in 36 patients (61%). Spontaneous pregnancy occurred in nine couples (15%). Six months after treatment, inhibin B levels were significantly higher (P<0.04), whereas follicle-stimulating hormone (FSH) levels were significantly lower (P<0.001) than before treatment. Antegrade internal spermatic vein sclerotherapy can significantly improve seminal parameters and hormonal parameters in men with severe OAT and may even result in spontaneous pregnancy in couples who would otherwise be candidates for intracytoplasmic sperm injection (ICSI).

  8. The Oligo-Miocene of Eil (NE Somalia): a prograding coral- Lepidocyclina system

    NASA Astrophysics Data System (ADS)

    Bosellini, A.; Russo, A.; Arush, M. A.; Cabdulqadir, M. M.

    The Oligo-Miocene succession of Eil is the product of a depositional regression and constitutes a 120-150 m thick depositional sequence that prograded seaward for at least 20-25 km. Its time-transgressive stratigraphy is documented physically by well exposed tangential clinoforms (previously considered as evidence of a tectonic coastal flexure) and biostratigraphically by the occurrence of calcareous nannoplankton, planktonic and benthonic foraminifera, and a rich coral fauna. The upper boundary of the sequence is indicated by a reefal toplap, which constitutes the flat surface of the Nogal Plateau. Age (Chattian to Burdigalian) and toplap relationships of the sequence indicate clearly that progradation took place after the Late Oligocene flooding which followed the strong fall of sea-level during the Chattian. Because of the horizontal geometry of the entire sedimentary system, it has been possible to make a clear environmental reconstruction and a facies model with original water depths. A worldwide Tertiary facies—the Lepidocyclina beds— was confined to the front of the reef, at depths ranging from 35-40 to 120-130 m.

  9. The role of varicocele sclerotherapy in men with severe oligo-astheno-teratozoospermia

    PubMed Central

    Ghanem, Mazen A; Safan, Manal A; Ghanem, Ashraf A; Dohle, Gert R

    2011-01-01

    The aim of this study was to verify the role of antegrade scrotal sclerotherapy for the treatment of varicoceles in infertile men with severe oligo-astheno-teratozoospermia (OAT). The 59 patients with severe OAT in this study underwent antegrade scrotal sclerotherapy for the treatment of varicoceles. The outcome was assessed in terms of improvement in semen parameters and spontaneous conception rate. Semen parameters and reproductive hormones were evaluated before antegrade sclerotherapy (AS) and 6 months after AS. After an average follow-up time of 34.8±3.2 months, significant improvement was noted in the mean sperm concentration, motility and morphology in 36 patients (61%). Spontaneous pregnancy occurred in nine couples (15%). Six months after treatment, inhibin B levels were significantly higher (P<0.04), whereas follicle-stimulating hormone (FSH) levels were significantly lower (P<0.001) than before treatment. Antegrade internal spermatic vein sclerotherapy can significantly improve seminal parameters and hormonal parameters in men with severe OAT and may even result in spontaneous pregnancy in couples who would otherwise be candidates for intracytoplasmic sperm injection (ICSI). PMID:21785440

  10. Masking autoprocessing of Clostridium difficile toxin A by the C-terminus combined repetitive oligo peptides

    PubMed Central

    Zhang, Yongrong; Hamza, Therwa; Gao, Si; Feng, Hanping

    2015-01-01

    Clostridium difficile toxin A and B (TcdA and TcdB) are the major virulence factors of the bacterium, both of which consist of two enzymatic domains: an effector glucosyltransferase domain (GTD) and a cysteine protease domain (CPD) responsible for autocleavage and release of GTD. Although the CPDs from both toxins share a similar structure and mechanism of hexakisphosphate (InsP6) -induced activation, TcdA is substantially less sensitive to the autocleavage as compared with TcdB. In this study, we provided evidence of inter-domain regulation of CPD activity of TcdA and its autoprocessing. The C-terminus combined repetitive oligo peptides (CROPs) of TcdA reduced the accessibility of TcdB CPD to its substrate in a chimeric toxin TxB-Ar, consequently blocking autoprocessing. Moreover, interference of antibodies with the CROPs of full-length TcdA efficiently enhanced its GTD release. In conclusion, by utilizing chimeric toxins and specific antibodies, we identified that the CROPs of TcdA plays a crucial role in controlling the InsP6-mediated activation of CPD and autocleavage of GTD. Our data provides insights on the molecular mode of action of the C. difficile toxins. PMID:25725153

  11. Correlation of length of linear oligo(ethanamino) amides with gene transfer and cytotoxicity.

    PubMed

    Scholz, Claudia; Kos, Petra; Leclercq, Laurent; Jin, Xiaoyun; Cottet, Hervé; Wagner, Ernst

    2014-09-01

    The optimization of synthetic carriers for gene transfer remains a major challenge. Cationic polymers such as polyethylenimine (PEI) often show increasing gene transfer activity with increasing molecular weight, but this favorable effect is accompanied by an undesired increase in cytotoxicity. Moreover, the polydispersity of polymers prevents accurate determination of optimum size. Herein we describe the step-by-step elongation of precise linear oligo(ethanamino) amides by making use of the artificial amino acid succinoyl-tetraethylene pentamine (Stp) for solid-phase-assisted synthesis. This procedure enabled us to identify the optimal oligomer Stp30-W (8.4 kDa) with a length of 30 Stp units, with which effective gene transfer occurs in the absence of cytotoxicity. The transfection efficiency of Stp30-W exceeded that of standard linear PEI (22 kDa) by sixfold; nevertheless, Stp30-W exhibited tenfold lower cytotoxicity. In addition to the lower molecular weight, the succinate spacer between the oligoamine units may also contribute to the favorable biocompatibility. The cytotoxicity of the cationic polymer PEI is a major concern for use as a carrier for gene delivery, so this comparison between linear PEI and the new Stp oligomers is particularly relevant.

  12. Development of Electrically Conductive Oligo(polyethylene Glycol) Fumarate-Polypyrrole Hydrogels for Nerve Regeneration

    PubMed Central

    Runge, M. Brett; Dadsetan, Mahrokh; Baltrusaitis, Jonas; Ruesink, Terry; Lu, Lichun; Windebank, Anthony J.; Yaszemski, Michael J.

    2014-01-01

    Electrically conductive hydrogel composites consisting of oligo(polyethylene glycol) fumarate (OPF) and polypyrrole (PPy) were developed for applications in nerve regeneration. OPF-PPy scaffolds were synthesized using three different anions: naphthalene-2-sulfonic acid sodium salt (NSA), dodecylbenzenesulfonic acid sodium salt (DBSA), and dioctyl sulfosuccinate sodium salt (DOSS). Scaffolds were characterized by ATR-FTIR, XPS, AFM, dynamic mechanical analysis, electrical resistivity measurements, and swelling experiments. OPF-PPy scaffolds were shown to consist of up to 25 mol% polypyrrole with a compressive modulus ranging from 265 to 323 kPa and a sheet resistance ranging from 6 to 30 × 103 Ohms/square. In vitro studies using PC12 cells showed OPF-PPy materials had no cytotoxicity and PC12 cells showed distinctly better cell attachment and an increase in the percent of neurite bearing cells on OPF-PPy materials compared to OPF. The neurite lengths of PC12 cells were significantly higher on OPF-PPyNSA and OPF-PPyDBSA. These results show that electrically conductive OPF-PPy hydrogels are promising candidates for future applications in nerve regeneration. PMID:20942380

  13. Ladder Oligo(m-aniline)s: Derivatives of Azaacenes with Cross-Conjugated [pi]-Systems

    SciTech Connect

    Rajca, Andrzej; Boraty; #324; ski, Przemys; #322; aw J.; Olankitwanit, Arnon; Shiraishi, Kouichi; Pink, Maren; Rajca, Suchada

    2012-04-30

    We describe the synthesis and electronic properties of ladder oligomers of poly(m-aniline) that may be considered as derivatives of azaacenes with cross-conjugated {pi}-systems. Syntheses of ladder oligo(m-aniline)s with 9 and 13 collinearly fused six-membered rings employed Pd-catalyzed aminations and Friedel-Crafts-based ring closures. Structures were confirmed by either X-ray crystallography or correlations between DFT-computed and experimental spectroscopic data such as {sup 1}H, {sup 13}C, and {sup 15}N NMR chemical shifts and electronic absorption spectra. All compounds have planar 'azaacene' moieties. The experimental band gaps E{sub g} {approx} 3.5-3.65 eV, determined by the UV-vis absorption onsets, were in agreement with the TD-DFT-computed vertical excitation energies to the S{sub 1} state. Fluorescence quantum yields of up to 20% were found. Electrochemically estimated HOMO energies of -4.8 eV suggested propensity for a facile one-electron oxidation and just sufficient environmental stability toward oxygen (O{sub 2}). For two oligomers with 'tetraazanonacene' moieties, potentials of E{sup 4+/3+} {approx} 1.6-1.7 V vs SCE were determined for four-electron oxidation to the corresponding tetraradical tetracations.

  14. Toward Multiple Conductance Pathways with Heterocycle-Based Oligo(phenyleneethynylene) Derivatives.

    PubMed

    Miguel, Delia; Álvarez de Cienfuegos, Luis; Martín-Lasanta, Ana; Morcillo, Sara P; Zotti, Linda A; Leary, Edmund; Bürkle, Marius; Asai, Yoshihiro; Jurado, Rocío; Cárdenas, Diego J; Rubio-Bollinger, Gabino; Agraït, Nicolás; Cuerva, Juan M; González, M Teresa

    2015-11-04

    In this paper, we have systematically studied how the replacement of a benzene ring by a heterocyclic compound in oligo(phenyleneethynylene) (OPE) derivatives affects the conductance of a molecular wire using the scanning tunneling microscope-based break junction technique. We describe for the first time how OPE derivatives with a central pyrimidine ring can efficiently link to the gold electrode by two pathways presenting two different conductance G values. We have demonstrated that this effect is associated with the presence of two efficient conductive pathways of different length: the conventional end-to-end configuration, and another with one of the electrodes linked directly to the central ring. This represents one of the few examples in which two defined conductive states can be set up in a single molecule without the aid of an external stimulus. Moreover, we have observed that the conductance through the full length of the heterocycle-based OPEs is basically unaffected by the presence of the heterocycle. All these results and the simplicity of the proposed molecules push forward the development of compounds with multiple conductance pathways, which would be a breakthrough in the field of molecular electronics.

  15. N-Monosubstituted Methoxy-oligo(ethylene glycol) Carbamate Ester Prodrugs of Resveratrol.

    PubMed

    Mattarei, Andrea; Azzolini, Michele; Zoratti, Mario; Biasutto, Lucia; Paradisi, Cristina

    2015-09-03

    Resveratrol is a natural polyphenol with many interesting biological activities. Its pharmacological exploitation in vivo is, however, hindered by its rapid elimination via phase II conjugative metabolism at the intestinal and, most importantly, hepatic levels. One approach to bypass this problem relies on prodrugs. We report here the synthesis, characterization, hydrolysis, and in vivo pharmacokinetic behavior of resveratrol prodrugs in which the OH groups are engaged in an N-monosubstituted carbamate ester linkage. As promoiety, methoxy-oligo(ethylene glycol) groups (m-OEG) (CH₃-[OCH₂CH₂]n-) of defined chain length (n = 3, 4, 6) were used. These are expected to modulate the chemico-physical properties of the resulting derivatives, much like longer poly(ethylene glycol) (PEG) chains, while retaining a relatively low MW and, thus, a favorable drug loading capacity. Intragastric administration to rats resulted in the appearance in the bloodstream of the prodrug and of the products of its partial hydrolysis, confirming protection from first-pass metabolism during absorption.

  16. Antibacterial Properties of an Oligo-Acyl-Lysyl Hexamer Targeting Gram-Negative Species

    PubMed Central

    Zaknoon, Fadia; Goldberg, Keren; Sarig, Hadar; Epand, Raquel F.; Epand, Richard M.

    2012-01-01

    Toward developing new tools for fighting resistance to antibiotics, we investigated the antibacterial properties of a new decanoyl-based oligo-acyl-lysyl (OAK) hexamer, aminododecanoyl-lysyl-[aminodecanoyl-lysyl]5 (α12-5α10). The OAK exhibited preferential activity against Gram-negative bacteria (GNB), as determined using 36 strains, including diverse species, with an MIC90 of 6.2 μM. The OAK's bactericidal mode of action was associated with rapid membrane depolarization and cell permeabilization, suggesting that the inner membrane was the primary target, whereas the observed binding affinity to lipoteichoic acid suggested that inefficacy against Gram-positive species resulted from a cell wall interaction preventing α12-5α10 from reaching internal targets. Interestingly, perturbation of the inner membrane structure and function was preserved at sub-MIC values. This prompted us to assess the OAK's effect on the proton motive force-dependent efflux pump AcrAB-TolC, implicated in the low sensitivity of GNB to various antibiotics, including erythromycin. We found that under sub-MIC conditions, wild-type Escherichia coli was significantly more sensitive to erythromycin (the MIC dropped by >10-fold), unlike its acr-deletion mutant. Collectively, the data suggest a useful approach for treating GNB infections through overcoming antibiotic efflux. PMID:22751534

  17. Oligo(phenylenevinylene) hybrids and self-assemblies: versatile materials for excitation energy transfer.

    PubMed

    Praveen, Vakayil K; Ranjith, Choorikkat; Bandini, Elisa; Ajayaghosh, Ayyappanpillai; Armaroli, Nicola

    2014-06-21

    Oligo(phenylenevinylene)s (OPVs) are extensively investigated π-conjugated molecules that exhibit absorption and fluorescence in the UV-Vis spectral region, which can be widely tuned by chemical functionalisation and external control (e.g. solvent, temperature, pH). Further modulation of the optoelectronic properties of OPVs is possible by supramolecular aggregation, primarily driven by hydrogen bonding or π-stacking interactions. In recent years, extensive research work has been accomplished in exploiting the unique combination of the structural and electronic properties of OPVs, most of which has been targeted at the preparation of molecules and materials featuring photoinduced energy transfer. This review intends to offer an overview of the multicomponent arrays and self-assembled materials based on OPV which have been designed to undergo energy transfer by means of a thorough choice of excitation donor-acceptor partners. We present a few selected examples of photoactive dyads and triads containing organic moieties (e.g. fullerene, phenanthroline) as well as coordination compounds (Cu(I) complexes). We then focus more extensively on self-assembled materials containing suitably functionalised OPVs that lead to hydrogen bonded aggregates, helical structures, gels, nanoparticles, vesicles, mesostructured organic-inorganic hybrid films, functionalised nanoparticles and quantum dots. In most cases, these materials exhibit luminescence whose colour and intensity is related to the efficiency and direction of the energy transfer processes.

  18. Patients with isolated oligo/hypodontia caused by RUNX2 duplication.

    PubMed

    Molin, Arnaud; Lopez-Cazaux, Serena; Pichon, Olivier; Vincent, Marie; Isidor, Bertrand; Le Caignec, Cédric

    2015-06-01

    Loss-of-function mutations of RUNX2 are responsible for cleidocranial dysplasia, an autosomal dominant disorder characterized by delayed closure of cranial sutures, aplastic or hypoplastic clavicles, moderate short stature and supernumerary teeth. By contrast, an increased gene dosage is expected for duplication of the entire RUNX2 sequence and thus, a phenotype different from cleidocranial dysplasia. To date, two cousins with a duplication including the entire RUNX2 sequence in addition to MIR586, CLIC5 and the 5' half of SUPT3H have been reported. These patients presented with metopic synostosis and hypodontia. Here, we report on a family with an affected mother and three affected children. The four patients carried a 285 kb duplication identified by array comparative genomic hybridization. The duplication includes the entire sequence of RUNX2 and the 5' half of SUPT3H. We confirmed the duplication by real-time quantitative PCR in the four patients. Two children presented with the association of metopic craniosynostosis and oligo/hypodontia previously described, confirming the phenotype caused by RUNX2 duplication. Interestingly, the mother and one child had isolated hypodontia without craniosynostosis, broadening the phenotype observed in patients with such duplications.

  19. Overexpression of AtWRKY28 and AtWRKY75 in Arabidopsis enhances resistance to oxalic acid and Sclerotinia sclerotiorum.

    PubMed

    Chen, Xiaoting; Liu, Jun; Lin, Guifang; Wang, Airong; Wang, Zonghua; Lu, Guodong

    2013-10-01

    Based on Arabidopsis microarray, we found 8 WRKY genes were up-regulated with Oxalic acid (OA) challenge, AtWRKY28 and AtWRKY75 overexpression lines showed enhanced resistance to OA and Sclerotinia sclerotiorum. The WRKY transcription factors are involved in various plant physiological processes and most remarkably in coping with diverse biotic and abiotic stresses. Oxalic acid (OA) is an important pathogenicity-determinant of necrotrophic phytopathogenic fungi, such as Sclerotina sclerotiorum (S. sclerotiorum) and Botrytis cinerea (B. cinerea). The identification of differentially expressed genes under OA stress should facilitate our understanding of the pathogenesis mechanism of OA-producing fungi in host plants, and the mechanism of how plants respond to OA and pathogen infection. Based on Arabidopsis oligo microarray, we found 8 WRKY genes that were up-regulated upon OA challenge. The Arabidopsis plants overexpressing AtWRKY28 and AtWRK75 showed enhanced resistance to OA and S. sclerotiorum simultaneously. Furthermore, our results showed that overexpression of AtWRKY28 and AtWRK75 induced oxidative burst in host plants, which suppressed the hyphal growth of S. sclerotiorum, and consequently inhibited fungal infection. Gene expression profiling indicates that both AtWRKY28 and AtWRKY75 are transcriptional regulators of salicylic acid (SA)- and jasmonic acid/ethylene (JA/ET)-dependent defense signaling pathways, AtWRKY28 and AtWRKY75 mainly active JA/ET pathway to defend Arabidopsis against S. sclerotiorum and oxalic acid stress.

  20. Distributional patterns of decapod crustaceans in the circum-Mediterranean area during the Oligo-Miocene

    NASA Astrophysics Data System (ADS)

    Hyžný, Matúš

    2015-04-01

    . 80, 83-103. Harzhauser M., Kroh A., Mandic O., Piller W.E., Göhlich U., Reuter M. & Berning B. 2007: Biogeographic responses to geodynamics: a key study all around the Oligo-Miocene Tethyan Seaway. Zool. Anz. 246, 241-256. Harzhauser M., Mandic O. & Zuschin M. 2003: Changes in Paratethyan marine molluscs at the Early/Middle Miocene transition: diversity, palaeogeography and palaeoclimate. Acta Geol. Pol. 53, 323-339. Harzhauser M., Piller W.E. & Steininger F.F. 2002: Circum-Mediterranean Oligo/Miocene Biogeographic Evolution - the Gastropods' Point of View. Palaeogeogr., Palaeoclimatol., Palaeoecol. 183, 103-133. Müller P. 1979: The Indo-West-Pacific character of the Badenian decapod crustaceans of the Paratethys. In: VII International Congress on Mediterranean Neogene. Athens, September 27-October 2. Ann. Géol. Pays Hellén., Tome hors série 2, 865-869. Schweitzer C.E. 2001: Paleobiogeography of Cretaceous and Tertiary decapod crustaceans of the North Pacific Ocean. J. Paleontol. 75, 808-826. Studencka B., Gontsharova I.A. & Popov S.V. 1998: The bivalve faunas as a basis for reconstruction of the Middle Miocene history of the Paratethys. Acta Geol. Pol. 48, 285-342.

  1. Phylogenetic relationships of the Australian Oligo-Miocene ratite Emuarius gidju Casuariidae.

    PubMed

    Worthy, Trevor H; Hand, Suzanne J; Archer, Michael

    2014-03-01

    In Australia, ratites (Aves: Palaeognathae) are represented in the extant fauna by the family Casuariidae with 1 species of emu Dromaius novaehollandiae and 1 cassowary Casuarius casuarius. The Australian fossil record reveals no other extinct ratite families but there are a number of other casuariid species. Most significant of these, due to its Oligo-Miocene age and because it is known from abundant material, is Emuarius gidju. Here, we describe additional material and confirm that the taxon had a temporal range of Late Oligocene to Middle Miocene (approximately 24-15 Ma). We reveal new morphological details, including notably that the species had relatively much smaller eyes than D. novaehollandiae, in addition to a less well-developed cursorial ability, as inferred from its pelvic limb. In these respects, Emuarius is similar to Casuarius and suggest that it was adapted to denser vegetation than the open woodlands and grasslands that characterise much of Australia today and to which D. novaehollandiae, with its large eyes and enhanced cursorial ability, is strongly adapted. Emuarius was compared to and found to be distinct from the poorly provenanced Australian fossil species C. lydekkeri. We conducted a phylogenetic analysis of morphological data that robustly shows that E. gidju is the sister taxon of Dromaius and together these taxa form a clade that is sister to Casuarius. This indicates that the evolution towards enhanced cursorality that characterises Dromaius took place after the divergence of the emu-cassowary lineages and was likely not the driving mechanism of this divergence. Comparisons between D. novaehollandiae and D. baudinianus revealed no qualitative skeletal differences and we suggest that the latter taxon is best considered to be an island dwarf that should be taxonomically recognized at a subspecific level only. © 2013 International Society of Zoological Sciences, Institute of Zoology/Chinese Academy of Sciences and Wiley Publishing Asia Pty

  2. Crystalline oligo(ethylene sulfide) domains define highly stable supramolecular block copolymer assemblies.

    SciTech Connect

    Brubaker, Carrie E.; Velluto, Diana; Demurtas, Davide; Phelps, Edward A.; Hubbell, Jeffrey A.

    2015-07-01

    With proper control over copolymer design and solvation conditions, self-assembled materials display impressive morphological variety that encompasses nanoscale colloids as well as bulk three-dimensional architectures. Here we take advantage of both hydrophobicity and crystallinity to mediate supra-molecular self-assembly of spherical micellar, linear fibrillar, or hydrogel structures by a family of highly asymmetric poly(ethylene glycol)-b-oligo(ethylene sulfide) (PEG-OES) copolymers. Assembly structural polymorphism was achieved with modification of PEG-OES topology (linear versus multiarm) and with precise, monomer-by-monomer control of OES length. Notably, all three morphologies were accessed utilizing OES oligomers with degrees of polymerization as short as three. These exceptionally small assembly forming blocks represent the first application of ethylene sulfide oligomers in supramolecular materials. While the assemblies demonstrated robust aqueous stability over time, oxidation by hydrogen peroxide progressively converted ethylene sulfide residues to increasingly hydrophilic and amorphous sulfoxides and sulfones, causing morphological changes and permanent disassembly. We utilized complementary microscopic and spectroscopic techniques to confirm this chemical stimulus-responsive behavior in self-assembled PEG-OES colloidal dispersions and physical gels. In addition to inherent stimulus-responsive behavior, fibrillar assemblies demonstrated biologically relevant molecular delivery, as confirmed by the dose-dependent activation of murine bone marrow-derived dendritic cells following fibril-mediated delivery of the immunological adjuvant monophosphoryl lipid A. In physical gels composed of either linear or multiarm PEG-OES precursors, rheologic analysis also identified mechanical stimulus-responsive shear thinning behavior. Thanks to the facile preparation, user-defined morphology, aqueous stability, carrier functionality, and stimuli-responsive behaviors of

  3. Production of multi-, oligo- and single-pore membranes using a continuous ion beam

    NASA Astrophysics Data System (ADS)

    Apel, P. Yu.; Ivanov, O. M.; Lizunov, N. E.; Mamonova, T. I.; Nechaev, A. N.; Olejniczak, K.; Vacik, J.; Dmitriev, S. N.

    2015-12-01

    Ion track membranes (ITM) have attracted significant interest over the past two decades due to their numerous applications in physical, biological, chemical, biochemical and medical experimental works. A particular feature of ITM technology is the possibility to fabricate samples with a predetermined number of pores, including single-pore membranes. The present report describes a procedure that allowed for the production of multi-, oligo- and single-pore membranes using a continuous ion beam from an IC-100 cyclotron. The beam was scanned over a set of small diaphragms, from 17 to ∼1000 μm in diameter. Ions passed through the apertures and impinged two sandwiched polymer foils, with the total thickness close to the ion range in the polymer. The foils were pulled across the ion beam at a constant speed. The ratio between the transport speed and the scanning frequency determined the distance between irradiation spots. The beam intensity and the aperture diameters were adjusted such that either several, one or no ions passed through the diaphragms during one half-period of scanning. After irradiation, the lower foil was separated from the upper foil and was etched to obtain pores 6-8 μm in diameter. The pores were found using a color chemical reaction between two reagents placed on opposite sides of the foil. The located pores were further confirmed using SEM and optical microscopy. The numbers of tracks in the irradiation spots were consistent with the Poisson statistics. Samples with single or few tracks obtained in this way were employed to study fine phenomena in ion track nanopores.

  4. Oligo(ethylene glycol)-functionalized disiloxanes as electrolytes for lithium-ion batteries

    NASA Astrophysics Data System (ADS)

    Zhang, Zhengcheng; Dong, Jian; West, Robert; Amine, Khalil

    Functionalized disiloxane compounds were synthesized by attaching oligo(ethylene glycol) chains, -(CH 2CH 2O)- n, n = 2-7, via hydrosilation, dehydrocoupling, and nucleophilic substitution reactions and were examined as non-aqueous electrolyte solvents in lithium-ion cells. The compounds were fully characterized by 1H, 13C, and 29Si nuclear magnetic resonance (NMR) spectroscopy. Upon doping with lithium bis(oxalato)borate (LiBOB) or LiPF 6, the disiloxane electrolytes showed conductivities up to 6.2 × 10 -4 S cm -1 at room temperature. The thermal behavior of the electrolytes was studied by differential scanning calorimetry, which revealed very low glass transition temperatures before and after LiBOB doping and much higher thermal stability compared to organic carbonate electrolytes. Cyclic voltammetry measurements showed that disiloxane-based electrolytes with 0.8 M LiBOB salt concentration are stable to 4.7 V. The LiBOB/disiloxane combinations were found to be good electrolytes for lithium-ion cells; unlike LiPF 6, LiBOB can provide a good passivation film on the graphite anode. The LiPF 6/disiloxane electrolyte was enabled in lithium-ion cells by adding 1 wt% vinyl ethylene carbonate (VEC). Full cell performance tests with LiNi 0.80Co 0.15Al 0.05O 2 as the cathode and mesocarbon microbead (MCMB) graphite as the anode show stable cyclability. The results demonstrate that disiloxane-based electrolytes have considerable potential as electrolytes for use in lithium-ion batteries.

  5. High-throughput marker discovery in melon using a self-designed oligo microarray

    PubMed Central

    2010-01-01

    Background Genetic maps constitute the basis of breeding programs for many agricultural organisms. The creation of these maps is dependent on marker discovery. Melon, among other crops, is still lagging in genomic resources, limiting the ability to discover new markers in a high-throughput fashion. One of the methods used to search for molecular markers is DNA hybridization to microarrays. Microarray hybridization of DNA from different accessions can reveal differences between them--single-feature polymorphisms (SFPs). These SFPs can be used as markers for breeding purposes, or they can be converted to conventional markers by sequencing. This method has been utilized in a few different plants to discover genetic variation, using Affymetrix arrays that exist for only a few organisms. We applied this approach with some modifications for marker discovery in melon. Results Using a custom-designed oligonucleotide microarray based on a partial EST collection of melon, we discovered 6184 putative SFPs between the parents of our mapping population. Validation by sequencing of 245 SFPs from the two parents showed a sensitivity of around 79%. Most SFPs (81%) contained single-nucleotide polymorphisms. Testing the SFPs on another mapping population of melon confirmed that many of them are conserved. Conclusion Thousands of new SFPs that can be used for genetic mapping and molecular-assisted breeding in melon were discovered using a custom-designed oligo microarray. A portion of these SFPs are conserved and can be used in different breeding populations. Although improvement of the discovery rate is still needed, this approach is applicable to many agricultural systems with limited genomic resources. PMID:20426811

  6. Identification of three oligo-/polysaccharide-specific ligases in Yersinia enterocolitica.

    PubMed

    Pinta, Elise; Li, Zhilin; Batzilla, Julia; Pajunen, Maria; Kasanen, Tiina; Rabsztyn, Kamila; Rakin, Alexander; Skurnik, Mikael

    2012-01-01

    In lipopolysaccharide (LPS) biosynthesis of gram-negative bacteria the lipid A-core oligosaccharide (LA-core) and O-polysaccharide (O-PS) biosynthesis pathways proceed separately and converge in periplasmic space where the waaL-encoded ligase joins O-PS onto LA-core. Enterobacterial common antigen (ECA) biosynthesis follows that of O-PS except that ECA is usually ligated to phosphatidylglycerol (PG) and only rarely to LA-core. In Yersinia enterocolitica serotype O:3 LPS is composed of LA-inner core (IC) onto which a homopolymeric O-PS, a hexasaccharide called outer core (OC), and/or ECA are ligated. We found that an individual O:3 LPS molecule carries either OC or O-PS substitution but not both. Related to this, we identified three genes in Y. enterocolitica O:3 that all expressed O-PS ligase activity in the Escherichia coliΔwaaL mutant. The LPS phenotypes of Y. enterocolitica O:3 single, double and triple ligase mutants indicated that two of ligases, named as WaaL(os) and WaaL(ps) , had a preferred substrate specificity for OC and O-PS, respectively, although with some promiscuity between the ligases; the third ligase named as WaaL(xs) was not involved in LPS or ECA biosynthesis. In Y. enterocolitica O:8 the WaaL(os) homologue (Ye1727) ligated a single pentasaccharide O-unit to LA-IC suggesting that in both Y. enterocolitica O:3 and O:8 WaaL(os) is an oligosaccharide (OS)-specific ligase. Finally, Yersinia pestis and Y. pseudotuberculosis carry only the waaL(ps) gene, while either waaL(os) or waaL(xs) or both are additionally present in other Yersinia species. This is the first report on the presence of three different oligo-/polysaccharide-specific ligases in a single bacterium. © 2011 Blackwell Publishing Ltd.

  7. Tectonics and sedimentation of Oligo-Miocene Vasquez Formation, Soledad basin, southern California

    SciTech Connect

    Hendrix, E.D.

    1987-05-01

    The nonmarine Oligo-Miocene Vasquez Formation represents the earliest sedimentation within the Soledad basin. Basin analysis of this unit provides important clues to the tectonic regimen during the convergent/transform-margin transition in southern California during the mid-Tertiary. The Vasquez crops out in three separate subbasins or depocenters; from south to north, these are the Vasquez Rocks, Texas Canyon, and Charlie Canyon subbasins. Basaltic-andesitic volcanism and rapid subsidence punctuated the initial rifting event which generated the Vasquez Rocks half-graben and Texas Canyon graben. Small, thick alluvial fans were shed into these two subbasins, with sediment derived via erosion of local plutonic, metamorphic, and volcanic source terranes. A minimum of four discrete uplift events generated development of 250 to 600-m thick, upward-fining alluvial megacycles in both the Vasquez Rocks and Texas Canyon depocenters. In the absence of biostratigraphic control, these allocyclic megasequences provide a tangible means of lithostratigraphic correlation between these separate subbasins. A major uplift and drainage basin reorganization event subsequently modified the Vasquez depositional system, facilitating physical interconnection of the two southern subbasins. The northernmost subbasin, Charlie Canyon, is characterized by a single, thick, upward-coarsening alluvial fan sequence. There are no megacycles or clast suites to suggest interconnection with or evolutionary similarities to the other two depocenters. This sedimentologic uniqueness may support a mid-Tertiary palinspastic reconstruction which places the Charlie Canyon region 80-100 km northwest of its current location. Soledad basin rifting and Vasquez sedimentation are consistent with a tectonic model involving lithospheric extension north of the unstable Mendocino triple junction.

  8. Crystalline Oligo(ethylene sulfide) Domains Define Highly Stable Supramolecular Block Copolymer Assemblies.

    PubMed

    Brubaker, Carrie E; Velluto, Diana; Demurtas, Davide; Phelps, Edward A; Hubbell, Jeffrey A

    2015-07-28

    With proper control over copolymer design and solvation conditions, self-assembled materials display impressive morphological variety that encompasses nanoscale colloids as well as bulk three-dimensional architectures. Here we take advantage of both hydrophobicity and crystallinity to mediate supramolecular self-assembly of spherical micellar, linear fibrillar, or hydrogel structures by a family of highly asymmetric poly(ethylene glycol)-b-oligo(ethylene sulfide) (PEG-OES) copolymers. Assembly structural polymorphism was achieved with modification of PEG-OES topology (linear versus multiarm) and with precise, monomer-by-monomer control of OES length. Notably, all three morphologies were accessed utilizing OES oligomers with degrees of polymerization as short as three. These exceptionally small assembly forming blocks represent the first application of ethylene sulfide oligomers in supramolecular materials. While the assemblies demonstrated robust aqueous stability over time, oxidation by hydrogen peroxide progressively converted ethylene sulfide residues to increasingly hydrophilic and amorphous sulfoxides and sulfones, causing morphological changes and permanent disassembly. We utilized complementary microscopic and spectroscopic techniques to confirm this chemical stimulus-responsive behavior in self-assembled PEG-OES colloidal dispersions and physical gels. In addition to inherent stimulus-responsive behavior, fibrillar assemblies demonstrated biologically relevant molecular delivery, as confirmed by the dose-dependent activation of murine bone marrow-derived dendritic cells following fibril-mediated delivery of the immunological adjuvant monophosphoryl lipid A. In physical gels composed of either linear or multiarm PEG-OES precursors, rheologic analysis also identified mechanical stimulus-responsive shear thinning behavior. Thanks to the facile preparation, user-defined morphology, aqueous stability, carrier functionality, and stimuli-responsive behaviors of

  9. Dispersion of Vesicles Composed of Industrially Produced Alkyl (Oligo) Glucoside Using Diol-Boron Complexation.

    PubMed

    Aikawa, Tatsuo; Asano, Yuuka; Kondo, Takeshi; Yuasa, Makoto

    2016-07-01

    Alkyl (oligo)glucosides (AOG) are known to be environmentally compatible amphiphiles whose commercial applicability should be broadened. The present paper describes the preparation of molecular assemblies of industrially produced AOG, which is a mixture composed of different length of alkyl chains (C9-C12) with oligoglucoside moiety with a few (1-3) of glucose units. It was also described that regulation of the dispersibility of the molecular assemblies prepared by diol-boron complexation between the sugar moiety on AOG and boric acid in a dispersion medium. The molecular assembly of AOG was successfully formed by mixing AOG and cholesterols (CH). When using a suitable amount of CH (20-40 mol% with respect to AOG), the molecular assembly formed a vesicle structure. The dispersion ability of the resulting vesicle was dependent on both the boric acid concentration and pH of the dispersion medium. The light-scattering and ζ-potential measurements revealed that high concentrations (≥10 mM) of boric acid improved dispersibility the vesicles. In contrast, the vesicle agglomerated at low concentrations of boric acid (1-7.5 mM). In the absence of boric acid in dispersion medium, the vesicles were completely agglomerated. The optimum pH range for vesicle dispersion was found to be from neutral to basic (7.4-10.1). The (11)B NMR study revealed that borate ester formation occurred between boric acid and the diol of the sugar moiety on AOG vesicle. The present data suggest that borate ester formation that occurred on the surface of the vesicle provided negative charge to the vesicles, contributing to their dispersion via repulsive forces.

  10. The genesis of glaucony in the Oligo Miocene Torquay Group, southeastern Australia: petrographic and geochemical evidence

    NASA Astrophysics Data System (ADS)

    Kelly, Jonathan C.; Webb, John A.

    1999-04-01

    The Oligo-Miocene Torquay Group at Bird Rock, in southeastern Australia, comprises a sequence of fine-grained skeletal carbonates and argillaceous and glauconitic sandstones, which were deposited in a cool-water, mid-shelf environment. The Bird Rock glaucony consists predominantly of randomly interstratified glauconitic smectite, which constitutes bioclast infills and faecal pellet replacements. Petrographic and geochemical evidence indicates that the glaucony is autochthonous and comprises chemical components derived primarily from argillaceous matrix material; seawater is unlikely to be a significant source of ions. The glauconitization of the Bird Rock sediments occurred under sub-oxic partially reducing conditions, in the very shallow burial environment, and involved local iron redistribution. Sub-oxic conditions favour glauconitization because iron is stable in the soluble ferrous state and can be fixed in authigenic silicates due to the negligible concentrations of hydrogen sulphide. It is likely that localised acidic conditions were initiated during the glauconitization process; this acidity appears to have been buffered by the dissolution of bioclastic carbonate. The fact that glaucony predominantly occurs as bioclast infills and faecal pellet replacements implies that the physico-chemical conditions appropriate for glauconitization develop preferentially in such biogenic detritus. The development of appropriate micro-environments within such sediments probably relates to their physical confinement and/or high organic matter content. The Bird Rock glaucony developed during intervals of slow sedimentation and environmental quiescence associated with marine flooding events. These conditions facilitated glauconitization by allowing the favoured clay-rich sediments to accumulate and remain in the appropriate physico-chemical regime sufficiently long for the complex glauconitic structures to form.

  11. The effect of oligo(trimethylene carbonate) addition on the stiffness of acrylic bone cement

    PubMed Central

    Persson, Cecilia; López, Alejandro; Fathali, Hoda; Hoess, Andreas; Rojas, Ramiro; Ott, Marjam Karlsson; Hilborn, Jöns; Engqvist, Håkan

    2016-01-01

    Abstract With the increasing elderly population an increase in the number of bony fractures associated to age-related diseases such as osteoporosis also follows. The relatively high stiffness of the acrylic bone cements used in these patients has been suggested to give raise to a suboptimal load distribution surrounding the cement in vivo, and hence contribute to clinical complications, such as additional fractures. The aim of this study was to develop a low-modulus bone cement, based on currently used, commercially available poly(methyl methacrylate) (PMMA) cements for vertebroplasty. To this end, acrylate end-functionalized oligo(trimethylene carbonate) (oTMC) was incorporated into the cements, and the resulting compressive mechanical properties were evaluated, as well as the cytotoxic and handling properties of selected formulations. Sixteen wt%oTMC was needed in the vertebroplastic cement Osteopal V to achieve an elastic modulus of 1063 MPa (SD 74), which gave a corresponding compressive strength of 46.1 MPa (SD 1.9). Cement extracts taken at 1 and 12 hours gave a reduced MG-63 cell viability in most cases, while extracts taken at 24 hours had no significant effect on cell behavior. The modification also gave an increase in setting time, from 14.7 min (SD 1.7) to 18.0 min (SD 0.9), and a decrease in maximum polymerization temperature, from 41.5°C (SD 3.4) to 30.7°C (SD 1.4). While further evaluation of other relevant properties, such as injectability and in vivo biocompatibility, remains to be done, the results presented herein are promising in terms of approaching clinically applicable bone cements with a lower stiffness. PMID:26727581

  12. Foamed oligo(poly(ethylene glycol)fumarate) hydrogels as versatile prefabricated scaffolds for tissue engineering.

    PubMed

    Henke, Matthias; Baumer, Julia; Blunk, Torsten; Tessmar, Joerg

    2014-03-01

    Radically cross-linked hydrogels are frequently used as cell carriers due to their excellent biocompatibility and their tissue-like mechanical properties. Through frequent investigation, PEG-based polymers such as oligo(poly(ethylene glycol)fumarate [OPF] have proven to be especially suitable as cell carriers by encapsulating cells during hydrogel formation. In some cases, NaCl or biodegradable gelatin microparticles were added prior to cross-linking in order to provide space for the proliferating cells, which would otherwise stay embedded in the hydrogel matrix. However, all of these immediate cross-linking procedures involve time consuming sample preparation and sterilization directly before cell culture and often show notable swelling after their preparation. In this study, ready to use OPF-hydrogel scaffolds were prepared by gas foaming, freeze drying, individual packing into bags and subsequent γ-sterilization. The scaffolds could be stored and used "off-the-shelf" without any need for further processing prior to cell culture. Thus the handling was simplified and the sterility of the cell carrier was assured. Further improvement of the gel system was achieved using a two component injectable system, which may be used for homogenous injection molding in order to create individually shaped three dimensional scaffolds. In order to evaluate the suitability of the scaffolds for tissue engineering, constructs were seeded with juvenile bovine chondrocytes and cultured for 28 days. Cross-sections of the respective constructs showed an intense and homogenous red staining of GAG with safranin O, indicating a homogenous cell distribution within the scaffolds and the production of substantial amounts of GAG-rich matrix. Copyright © 2012 John Wiley & Sons, Ltd.

  13. Temperature-dependent control of Staphylococcus aureus biofilms and virulence by thermoresponsive oligo(N-vinylcaprolactam).

    PubMed

    Lee, Jin-Hyung; Kim, Yong-Guy; Lee, Kayeon; Kim, Seong-Cheol; Lee, Jintae

    2015-04-01

    Bacterial biofilms are associated with persistent infections because they are highly tolerant of antimicrobial agents, and in the case of Staphylococcus aureus, which is a leading cause of nosocomial infections because of its resistance to diverse antibiotics, biofilm formation is a known mechanism of drug resistance. In the present study, we investigated the ability of thermoresponsive oligo (N-vinylcaprolactam) (OVCL) to control biofilm formation by and the virulence of S. aureus. One synthetic and four commercial OVCLs (MW ≤ 240,000) at 50 µg/mL were found to increase S. aureus biofilm formation 7-fold at 25 °C, but to markedly inhibit S. aureus biofilm formation at 37 °C. Confocal and scanning electron microscopy confirmed the temperature-dependent effect of OVCL on S. aureus biofilms. It was found that the addition of OVCL to S. aureus culture caused cells to become dramatically more hydrophilic at 37 °C, which partially supports the biofilm reduction. Also, transcriptional analysis showed that OVCL temperature-dependently regulated biofilm-related genes (aur, agrA, and icaA) in S. aureus. In addition, it was found surface coatings containing OVCL effectively controlled S. aureus biofilm formation on solid glass surfaces. Furthermore, OVCL inhibited the hemolysis of human red blood cells by S. aureus at 37 °C and attenuated S. aureus virulence in the nematode Caenorhabditis elegans. These results suggest that OVCL has potential use for controlling bacterial biofilm formation and virulence.

  14. Rapid Synthesis of a Long Double-Stranded Oligonucleotide from a Single-Stranded Nucleotide Using Magnetic Beads and an Oligo Library

    PubMed Central

    Pengpumkiat, Sumate; Koesdjojo, Myra; Rowley, Erik R.; Mockler, Todd C.; Remcho, Vincent T.

    2016-01-01

    Chemical synthesis of oligonucleotides is a widely used tool in the field of biochemistry. Several methods for gene synthesis have been introduced in the growing area of genomics. In this paper, a novel method of constructing dsDNA is proposed. Short (28-mer) oligo fragments from a library were assembled through successive annealing and ligation processes, followed by PCR. First, two oligo fragments annealed to form a dsDNA molecule. The double-stranded oligo was immobilized onto magnetic beads (solid support) via streptavidin-biotin binding. Next, single-stranded oligo fragments were added successively through ligation to form the complete DNA molecule. The synthesized DNA was amplified through PCR and gel electrophoresis was used to characterize the product. Sanger sequencing showed that more than 97% of the nucleotides matched the expected sequence. Extending the length of the DNA molecule by adding single-stranded oligonucleotides from a basis set (library) via ligation enables a more convenient and rapid mechanism for the design and synthesis of oligonucleotides on the go. Coupled with an automated dispensing system and libraries of short oligo fragments, this novel DNA synthesis method would offer an efficient and cost-effective method for producing dsDNA. PMID:26930667

  15. Helix stability of oligoglycine, oligoalanine, and oligo-β-alanine dodecamers reflected by hydrogen-bond persistence.

    PubMed

    Liu, Chengyu; Ponder, Jay W; Marshall, Garland R

    2014-11-01

    Helices are important structural/recognition elements in proteins and peptides. Stability and conformational differences between helices composed of α- and β-amino acids as scaffolds for mimicry of helix recognition has become a theme in medicinal chemistry. Furthermore, helices formed by β-amino acids are experimentally more stable than those formed by α-amino acids. This is paradoxical because the larger sizes of the hydrogen-bonding rings required by the extra methylene groups should lead to entropic destabilization. In this study, molecular dynamics simulations using the second-generation force field, AMOEBA (Ponder, J.W., et al., Current status of the AMOEBA polarizable force field. J Phys Chem B, 2010. 114(8): p. 2549-64.) explored the stability and hydrogen-bonding patterns of capped oligo-β-alanine, oligoalanine, and oligoglycine dodecamers in water. The MD simulations showed that oligo-β-alanine has strong acceptor+2 hydrogen bonds, but surprisingly did not contain a large content of 3(12) -helical structures, possibly due to the sparse distribution of the 3(12) -helical structure and other structures with acceptor+2 hydrogen bonds. On the other hand, despite its backbone flexibility, the β-alanine dodecamer had more stable and persistent <3.0 Å hydrogen bonds. Its structure was dominated more by multicentered hydrogen bonds than either oligoglycine or oligoalanine helices. The 3(1) (PII) helical structure, prevalent in oligoglycine and oligoalanine, does not appear to be stable in oligo-β-alanine indicating its competition with other structures (stacking structure as indicated by MD analyses). These differences are among the factors that shape helical structural preferences and the relative stabilities of these three oligopeptides. © 2014 Wiley Periodicals, Inc.

  16. Transgenic Arabidopsis Gene Expression System

    NASA Technical Reports Server (NTRS)

    Ferl, Robert; Paul, Anna-Lisa

    2009-01-01

    The Transgenic Arabidopsis Gene Expression System (TAGES) investigation is one in a pair of investigations that use the Advanced Biological Research System (ABRS) facility. TAGES uses Arabidopsis thaliana, thale cress, with sensor promoter-reporter gene constructs that render the plants as biomonitors (an organism used to determine the quality of the surrounding environment) of their environment using real-time nondestructive Green Fluorescent Protein (GFP) imagery and traditional postflight analyses.

  17. Gene expression profiling in common cormorant liver with an oligo array: assessing the potential toxic effects of environmental contaminants.

    PubMed

    Nakayama, Kei; Iwata, Hisato; Kim, Eun-Young; Tashiro, Kosuke; Tanabe, Shinsuke

    2006-02-01

    To establish a monitoring system for gene expression profiles related to chemical contamination in wild common cormorants (Phalacrocorax carbo), the present study constructed an oligo array designed from expressed sequence tag (EST) sequences of the cormorant liver, where 1061 unique oligonucleotides were spotted. Common cormorants were collected from Lake Biwa, Japan in May 2001 and 2002. With the use of this oligo array, gene expression profiles in the liver of individual specimens were evaluated. To determine the expression patterns of genes altered by environmental contaminants, relationships between concentrations of persistent organochlorines including polychlorinated dibenzo-p-dioxins, furans, polychlorinated biphenyls, 1,1,1-trichloro-2,2-bis(p-chlorophenyl)ethane and its metabolites (DDTs), hexachlorocyclohexane isomers (HCHs), chlordane compounds (CHLs), butyltins, and bisphenol A (BPA) and expression levels of each gene in the cormorant liver were examined using stepwise multiple regression analysis. The reliability of data obtained by the oligo array was further confirmed by quantifying the expression levels of certain genes using real-time RT-PCR. The 2,3,7,8-tetrachlorodibenzo-p-dioxin toxic equivalent (TEQ) level was positively correlated with both cytochrome P4501A4 and 1A5 gene expression. In addition, the mRNA level of an antioxidant enzyme, Cu/Zn superoxide dismutase, was negatively correlated with hepatic total TEQ. Other antioxidant enzymes, glutathione peroxidase 3 and glutathione S-transferase class mu, were negatively correlated with HCHs and BPA levels, respectively. The mRNA expression level of a nonenzymatic antioxidant, haptoglobin, was negatively but not significantly correlated with CHLs. These results led to a hypothesis that wild cormorant population may suffer from oxidative stress due to chemically induced formation of reactive oxygen species and subsequent reduction of antioxidant resistance. Thus, the cormorant oligo array may be

  18. Dissolved organic matter dynamics in the oligo/meso-haline zone of wetland-influenced coastal rivers

    NASA Astrophysics Data System (ADS)

    Maie, Nagamitsu; Sekiguchi, Satoshi; Watanabe, Akira; Tsutsuki, Kiyoshi; Yamashita, Youhei; Melling, Lulie; Cawley, Kaelin M.; Shima, Eikichi; Jaffé, Rudolf

    2014-08-01

    Wetlands are key components in the global carbon cycle and export significant amounts of terrestrial carbon to the coastal oceans in the form of dissolved organic carbon (DOC). Conservative behavior along the salinity gradient of DOC and chromophoric dissolved organic matter (CDOM) has often been observed in estuaries from their freshwater end-member (salinity = 0) to the ocean (salinity = 35). While the oligo/meso-haline (salinity < 10) tidal zone of upper estuaries has been suggested to be more complex and locally influenced by geomorphological and hydrological features, the environmental dynamics of dissolved organic matter (DOM) and the environmental drivers controlling its source, transport, and fate have scarcely been evaluated. Here, we investigated the distribution patterns of DOC and CDOM optical properties determined by UV absorbance at 254 nm (A254) and excitation-emission matrix (EEM) fluorescence coupled with parallel factor analysis (PARAFAC) along the lower salinity range (salinity < 10) of the oligo/meso-haline zone for three distinct wetland-influenced rivers; namely the Bekanbeushi River, a cool-temperate river with estuarine lake in Hokkaido, Japan, the Harney River, a subtropical river with tidally-submerged mangrove fringe in Florida, USA, and the Judan River, a small, acidic, tropical rainforest river in Borneo, Malaysia. For the first two rivers, a clear decoupling between DOC and A254 was observed, while these parameters showed similar conservative behavior for the third. Three distinct EEM-PARAFAC models established for each of the rivers provided similar spectroscopic characteristics except for some unique fluorescence features observed for the Judan River. The distribution patterns of PARAFAC components suggested that the inputs from plankton and/or submerged aquatic vegetation can be important in the Bekanbeushi River. Further, DOM photo-products formed in the estuarine lake were also found to be transported upstream. In the Harney River

  19. OligoPrep PVA support for oligonucleotide synthesis in columns on a scale up to 10 micromol.

    PubMed

    Aitken, Sheena; Anderson, Emma

    2007-01-01

    OligoPrep is a macroporous polyvinylacetate (PVA) biodegradable support that has been designed for cost-effective automated synthesis of oligonucleotides using standard phosphoramidite chemistry. Originally developed for large-scale oligonucleotide synthesis in beds and reactors, we present here its utility for medium-scale work of 1-10 micromol in column syntheses on standard DNA synthesizers. We show how an increase in scale, and, therefore, yield, can be achieved without significant increase in reagent quantity. Additional deblock and oxidation cycles can provide high coupling yields, and the use of concentrated ammonia in aqueous methylamine (AMA) for oligonucleotide cleavage and deprotection results in excellent recovery.

  20. Immobilization of Antibody on a Cyclic Olefin Copolymer Surface with Functionalizable, Non-Biofouling Poly[Oligo(Ethylene Glycol) Methacrylate].

    PubMed

    Jeong, Seung Pyo; Kang, Sung Min; Hong, Daewha; Lee, Hee-Yoon; Choi, Insung S; Ko, Sangwon; Lee, Jungkyu K

    2015-02-01

    We report a perfluoroaryl azide-based photoreaction for synthesizing functionalizable and nonbiofouling poly[oligo(ethylene glycol) methacrylate] (pOEGMA) films on a chemically inert COC substrate, and an estimation of a surface coverage of the antibody immobilized onto the surface with the immuno-gold nanoparticles. The processes were confirmed by water contact angle measurement, FT-IR spectroscopy, and FE-SEM. The strategy demonstrated in this work could be applied to functionalizations of other polymeric materials and determination of the binding capacity of analytes in biosensors and microfluidic devices.

  1. Antimicrobial oligo(p-phenylene-ethynylene) film deposited by resonant infrared matrix-assisted pulsed laser evaporation.

    PubMed

    Ge, Wangyao; Yu, Qian; López, Gabriel P; Stiff-Roberts, Adrienne D

    2014-04-01

    The antimicrobial oligomer, oligo(p-phenylene-ethynylene) (OPE), was deposited as thin films by resonant infrared matrix-assisted pulsed laser evaporation (RIR-MAPLE) on solid substrates and exhibited light-induced biocidal activity. The biocidal activity of OPE thin films deposited by spin-coating and drop-casting was also investigated for comparison. Enhanced bacterial attachment and biocidal efficiency of the film deposited by RIR-MAPLE were observed and attributed to nanoscale surface topography of the thin film. Copyright © 2014 Elsevier B.V. All rights reserved.

  2. Optimization of Aqueous SI-ATRP Grafting of Poly(Oligo(Ethylene Glycol) Methacrylate) Brushes from Benzyl Chloride Macroinitiator Surfaces.

    PubMed

    Rodda, Andrew E; Ercole, Francesca; Nisbet, David R; Forsythe, John S; Meagher, Laurence

    2015-06-01

    Poly(oligo(ethylene glycol) methacrylate) (pOEGMA) brushes were grafted via surface-initiated atom transfer radical polymerization (SI-ATRP) from a poly(styrene-co-vinylbenzyl chloride) macroinitiator. While bromoisobutyryl initiator groups are most commonly used for this purpose, benzyl chloride initiators may be advantageous for some applications due to superior stability. Water-only graft solutions produced thicker brush coatings with superior low fouling properties (low protein adsorption and cell adhesion) versus mixed water/alcohol solutions. Coatings produced using 475 Da OEGMA (methyl ether terminated) further reduced non-specific interactions compared to 360 Da OEGMA (hydroxyl terminated). Initiator density had minimal effect on low fouling properties.

  3. Brassinosteroids in Arabidopsis thaliana.

    PubMed

    Fujioka, S; Noguchi, T; Yokota, T; Takatsuto, S; Yoshida, S

    1998-06-01

    From the seeds and siliques of Arabidopsis thaliana, six brassinosteroids, brassinolide, castasterone, typhasterol, 6-deoxocastasterone, 6-deoxotyphasterol and 6-deoxoteasterone, were identified by GC-mass spectrometry or GC-selected ion monitoring. As the occurrence of castasterone, typhasterol, 6-deoxocastasterone and 6-deoxotyphasterol in the shoots of A. thaliana has already been reported, this study provides evidence for the occurrence of the above four brassinosteroids in different organs, seeds and siliques, and the first evidence for the occurrence of brassinolide and 6-deoxoteasterone in A. thaliana. All brassinosteroids identified in this study belong to important components of both the early and late C-6 oxidation pathways, which were established in the cultured cells of Catharanthus roseus. This suggests that both pathways are operating in A. thaliana to produce the most biologically active brassinosteroid, brassinolide, which is responsible for growth and development of the plant.

  4. Spherical Oligo-Silicic Acid SOSA Disclosed as Possible Endogenous Digitalis-Like Factor.

    PubMed

    Kerek, Franz; Voicu, Victor A

    2014-01-01

    The Na(+)/K(+)-ATPase is a membrane ion-transporter protein, specifically inhibited by digitalis glycosides used in cardiac therapy. The existence in mammals of some endogenous digitalis-like factors (EDLFs) as presumed ATPase ligands is generally accepted. But the chemical structure of these factors remained elusive because no weighable amounts of pure EDLFs have been isolated. Recent high-resolution crystal structure data of Na(+)/K(+)-ATPase have located the hydrophobic binding pocket of the steroid glycoside ouabain. It remained uncertain if the EDLF are targeting this steroid-receptor or another specific binding site(s). Our recently disclosed spherical oligo-silicic acids (SOSA) fulfill the main criteria to be identified with the presumed EDL factors. SOSA was found as a very potent inhibitor of the Na(+)/K(+)-ATPase, Ca(2+)-ATPase, H(+)/K(+)-ATPase, and of K-dp-ATPase, with IC50 values between 0.2 and 0.5 μg/mL. These findings are even more astonishing while so far, neither monosilicic acid nor its poly-condensed forms have been remarked biologically active. With the diameter ϕ between 1 and 3 nm, SOSA still belong to molecular species definitely smaller than silica nano-particles with ϕ > 5 nm. In SOSA molecules, almost all Si-OH bonds are displayed on the external shell, which facilitates the binding to hydrophilic ATPase domains. SOSA is stable for long term in solution but is sensitive to freeze-drying, which could explain the failure of countless attempts to isolate pure EDLF. There is a strong resemblance between SOSA and vanadates, the previously known general inhibitors of P-type ATPases. SOSA may be generated endogenously by spherical oligomerization of the ubiquitously present monosilicic acid in animal fluids. The structure of SOSA is sensitive to the concentration of Na(+), K(+), Ca(2+), Mg(2+), and other ions suggesting a presumably archaic mechanism for the regulation of the ATPase pumps.

  5. Spherical Oligo-Silicic Acid SOSA Disclosed as Possible Endogenous Digitalis-Like Factor

    PubMed Central

    Kerek, Franz; Voicu, Victor A.

    2015-01-01

    The Na+/K+-ATPase is a membrane ion-transporter protein, specifically inhibited by digitalis glycosides used in cardiac therapy. The existence in mammals of some endogenous digitalis-like factors (EDLFs) as presumed ATPase ligands is generally accepted. But the chemical structure of these factors remained elusive because no weighable amounts of pure EDLFs have been isolated. Recent high-resolution crystal structure data of Na+/K+-ATPase have located the hydrophobic binding pocket of the steroid glycoside ouabain. It remained uncertain if the EDLF are targeting this steroid-receptor or another specific binding site(s). Our recently disclosed spherical oligo-silicic acids (SOSA) fulfill the main criteria to be identified with the presumed EDL factors. SOSA was found as a very potent inhibitor of the Na+/K+-ATPase, Ca2+-ATPase, H+/K+-ATPase, and of K-dp-ATPase, with IC50 values between 0.2 and 0.5 μg/mL. These findings are even more astonishing while so far, neither monosilicic acid nor its poly-condensed forms have been remarked biologically active. With the diameter ϕ between 1 and 3 nm, SOSA still belong to molecular species definitely smaller than silica nano-particles with ϕ > 5 nm. In SOSA molecules, almost all Si-OH bonds are displayed on the external shell, which facilitates the binding to hydrophilic ATPase domains. SOSA is stable for long term in solution but is sensitive to freeze-drying, which could explain the failure of countless attempts to isolate pure EDLF. There is a strong resemblance between SOSA and vanadates, the previously known general inhibitors of P-type ATPases. SOSA may be generated endogenously by spherical oligomerization of the ubiquitously present monosilicic acid in animal fluids. The structure of SOSA is sensitive to the concentration of Na+, K+, Ca2+, Mg2+, and other ions suggesting a presumably archaic mechanism for the regulation of the ATPase pumps. PMID:25667581

  6. Mixed DNA/Oligo(ethylene glycol) Functionalized Gold Surface Improve DNA Hybridization in Complex Media

    SciTech Connect

    Lee,C.; Gamble, L.; Grainger, D.; Castner, D.

    2006-01-01

    Reliable, direct 'sample-to-answer' capture of nucleic acid targets from complex media would greatly improve existing capabilities of DNA microarrays and biosensors. This goal has proven elusive for many current nucleic acid detection technologies attempting to produce assay results directly from complex real-world samples, including food, tissue, and environmental materials. In this study, we have investigated mixed self-assembled thiolated single-strand DNA (ssDNA) monolayers containing a short thiolated oligo(ethylene glycol) (OEG) surface diluent on gold surfaces to improve the specific capture of DNA targets from complex media. Both surface composition and orientation of these mixed DNA monolayers were characterized with x-ray photoelectron spectroscopy (XPS) and near-edge x-ray absorption fine structure (NEXAFS). XPS results from sequentially adsorbed ssDNA/OEG monolayers on gold indicate that thiolated OEG diluent molecules first incorporate into the thiolated ssDNA monolayer and, upon longer OEG exposures, competitively displace adsorbed ssDNA molecules from the gold surface. NEXAFS polarization dependence results (followed by monitoring the N 1s{yields}{pi}* transition) indicate that adsorbed thiolated ssDNA nucleotide base-ring structures in the mixed ssDNA monolayers are oriented more parallel to the gold surface compared to DNA bases in pure ssDNA monolayers. This supports ssDNA oligomer reorientation towards a more upright position upon OEG mixed adlayer incorporation. DNA target hybridization on mixed ssDNA probe/OEG monolayers was monitored by surface plasmon resonance (SPR). Improvements in specific target capture for these ssDNA probe surfaces due to incorporation of the OEG diluent were demonstrated using two model biosensing assays, DNA target capture from complete bovine serum and from salmon genomic DNA mixtures. SPR results demonstrate that OEG incorporation into the ssDNA adlayer improves surface resistance to both nonspecific DNA and protein

  7. Genetic and biochemical characterization of an oligo-α-1,6-glucosidase from Lactobacillus plantarum.

    PubMed

    Delgado, Susana; Flórez, Ana Belén; Guadamuro, Lucía; Mayo, Baltasar

    2017-04-04

    Although encoded in the genome of many Lactobacillus spp. strains, α-glucosidases have received little attention compared to other glycosyl hydrolases. In this study, a putative oligosaccharide(oligo)-α-1,6-glucosidase-encoding gene (malL) was identified in the genome of Lactobacillus plantarum LL441. malL coded for 572 amino acid residues with a calculated total molecular mass of 66.31kDa. No predicted signal peptide was observed, suggesting this enzyme to be localized within the cytoplasm of the cell. Homology studies of the deduced amino acid sequence in the area of its active sites classified the enzyme as a member of the α-amylase (AmyAC) superfamily of glycosyl hydrolases (GH), family 13 (GH13), subfamily 31 (GH13_31). malL was cloned in Escherichia coli and the coded enzyme overexpressed as a histidine-tagged protein (MalLHis). It was then purified and characterized. MalLHis protein showed strong hydrolytic activity towards 4-nitrophenyl-α-d-glucopyranoside (pNP-α-Glu) but not to other pNP-α-d- or pNP-β-d-derivatives. When using pNP-α-Glu as a substrate, MalLHis showed similar specific activities between pH5.0 and 6.0, and between 20 and 42°C (optimum 30°C). Among the natural carbohydrates assayed, MalLHis showed specificity towards isomaltose (Vmax and Km values of 40.64μmolmin(-1)mg(-1) and 6.22mM) and much less to isomaltulose (Vmax and Km values of 168.86μmolmin(-1)mg(-1) and 244.52mM). However, under the conditions of the assay, the enzyme showed no transglycosylation activity. Characterization of the entire complement of glycosidases in L. plantarum might reveal how strains of this species could be used in new biotechnological applications or in the development of functional foods.

  8. Si-C linked oligo(ethylene glycol) layers in silicon-based photonic crystals: optimization for implantable optical materials.

    PubMed

    Kilian, Kristopher A; Böcking, Till; Gaus, Katharina; Gal, Michael; Gooding, J Justin

    2007-07-01

    Porous silicon has shown potential for various applications in biology and medicine, which require that the material (1) remain stable for the length of the intended application and (2) resist non-specific adsorption of proteins. Here we explore the efficacy of short oligo(ethylene glycol) moieties incorporated into organic layers via two separate strategies in achieving these aims. In the first strategy the porous silicon structure was modified in a single step via hydrosilylation of alpha-oligo(ethylene glycol)-omega-alkenes containing three or six ethylene glycol units. The second strategy employs two steps: (1) hydrosilylation of succinimidyl-10-undecenoate and (2) coupling of an amino hexa(ethylene glycol) species. The porous silicon photonic crystals modified by the two-step strategy displayed greater stability relative to the single step procedure when exposed to conditions of physiological temperature and pH. Both strategies produced layers that resist non-specific adsorption of proteins as determined with fluorescently labelled bovine serum albumin. The antifouling behaviour and greater stability to physiological conditions provided by this chemistry enhances the suitability of porous silicon for biomaterials applications.

  9. Performance of the HSV OligoGen kit for the diagnosis of herpes simplex virus type 1 and 2.

    PubMed

    Parra-Sánchez, Manuel; Marcuello López, Ana; García-Rey, Silvia; Zakariya-Yousef Breval, Ismail; Bernal Martínez, Samuel; Pueyo Rodríguez, Isabel; Martín-Mazuelos, Estrella; Palomares Folía, José Carlos

    2016-07-01

    PCR methods are nowadays between the most rapid and sensitive methods for screening and diagnosing herpes simplex virus (HSV) type 1 and 2. The aim of this study was to analyze the reliability, accuracy, and usefulness of the new assay HSV OligoGen kit in comparison with the Roche LightCycler HSV ½ Qual Kit assay for the detection of HSV in clinical samples. For this analysis, a prospective study was designed for detection of HSV-1 and HSV-2 including 110 ulcer specimens, 48 urine, 48 endocervical, 43 cerebral spinal fluids, 4 urethral and 3 pharyngeal swabs that were sent from a regional STI clinic or an Intensive Clinical Unit, both in Seville, Spain. In comparison to the Roche LightCycler HSV ½ Qual Kit assay, sensitivity, specificity, positive and negative predicative values, and kappa value for HSV detection using the HSV OligoGen kit were 96.2%, 100%, 100%, 98.3%, and 0.97 for HSV-1, respectively. For HSV-2, the corresponding values were 98.3%, 100%, 100%, 99.5%, and 0.98, respectively. Statistical data obtained in this study confirms the usefulness and reliable results of this new assay.

  10. Variation in the pelvic and pectoral girdles of Australian Oligo-Miocene mekosuchine crocodiles with implications for locomotion and habitus.

    PubMed

    Stein, Michael D; Yates, Adam; Hand, Suzanne J; Archer, Michael

    2017-01-01

    Australian Oligo-Miocene mekosuchines (Crocodylia; Crocodyloidea) display wide diversity in cranial shape and inferred hunting strategies. Terrestrial habitus has been inferred for these distinctive predators. A direct morphological signal for locomotion can be expected in the postcrania, particularly the pelvic and pectoral girdles. Here we describe fossil materials of the girdles, which chart their morphological variation in the subfamily from Eocene through to Middle Miocene. Over this period, both girdles undergo significant morphological changes. Notably, an enclosed, ventrally orientated acetabulum in the ilium is developed in one lineage. This recapitulates the erect parasagittal configuration of the pelvic limb seen in many Mesozoic crocodylomorph lineages, suggesting consistent use of erect high-walking in these mekosuchines. Other pelves from the same Oligo-Miocene deposits display morphology closer to modern crocodilians, suggesting a partitioning of locomotory strategy among sympatric mekosuchines. Plesiomorphic and derived pelvic girdles are distinguishable by parsimony analysis, and the earliest examples of the mekosuchine pelvis more closely resemble gavialids and alligatorids while latter forms converge on crown group crocodylids in the morphology of the iliac crest. This suggests that a revaluation of the base relationship of Mekosuchinae within Eusuchia is necessary.

  11. Adapting biodegradable oligo(poly(ethylene glycol) fumarate) hydrogels for pigment epithelial cell encapsulation and lens regeneration.

    PubMed

    Zhang, Mimi W; Park, Hansoo; Guo, Xuan; Nakamura, Kenta; Raphael, Robert M; Kasper, F Kurtis; Mikos, Antonios G; Tsonis, Panagiotis A

    2010-04-01

    This study investigated the encapsulation of newt iris pigment epithelial cells (PECs), which have the ability to regenerate a lens by trans-differentiation in vivo, within a biodegradable hydrogel of oligo(poly(ethylene glycol) fumarate) crosslinked with poly(ethylene glycol)-diacrylate. Hydrogel beads of initial diameter of 1 mm were fabricated by a molding technique. The swelling ratio and degradation rate of the hydrogel beads decreased with increasing crosslinking ratios. Confocal microscopy confirmed the cytocompatibility of crosslinking hydrogel formulations as evidenced by the viability of an encapsulated model cell line within a crosslinked hydrogel bead. Hydrogel beads encapsulating iris PECs were also implanted into lentectomized newts in vivo; histological evaluation of explants after 30 days revealed a regenerated lens, thus demonstrating that the presence of degrading hydrogel did not adversely affect lens regeneration. The results of this study suggest the potential of a method for lens regeneration involving oligo(poly(ethylene glycol) fumarate) hydrogels for iris PEC encapsulation and transplantation.

  12. Fluorosilane compounds with oligo(ethylene oxide) substituent as safe electrolyte solvents for high-voltage lithium-ion batteries

    NASA Astrophysics Data System (ADS)

    Wang, Jinglun; Mai, Yongjin; Luo, Hao; Yan, Xiaodan; Zhang, Lingzhi

    2016-12-01

    Two fluorosilanes with oligo(ethylene oxide) unites were synthesized through hydrosilylation of chlorosilane with allyl substituted oligo(ethylene oxide) ether followed by fluorination with potassium fluoride. The synthesized fluorosilane compounds exhibited lower viscosity, higher dielectric constant and higher oxidation potential, compared with their non-fluorination counterparts. Difluoro(3-(2-(2-methoxyethoxy)ethoxy)propyl)methylsilane (DFSM2), one of the two compounds, was evaluated as high-voltage and thermal stable electrolyte co-solvent with the conventional carbonate-based electrolytes. Using an optimized electrolyte of 1M LiPF6 in EC/DFSM2/EMC (2/3/5 in vol.) with addition of 5 wt% fluoroethylene carbonate (FEC), high-voltage LiCoO2(LCO)/graphite full cell displayed outstanding cycling stability of 92.5% capacity retention after 135 cycles at 4.4 V upper cutoff voltage. Characterized by differential scanning calorimetry (DSC) analysis, the DFSM2-based electrolyte demonstrated higher thermal stability with lithiated graphite anode and delithiated LCO cathode, thus better safety feature compared with the conventional electrolyte.

  13. Adapting Biodegradable Oligo(Poly(Ethylene Glycol) Fumarate) Hydrogels for Pigment Epithelial Cell Encapsulation and Lens Regeneration

    PubMed Central

    Zhang, Mimi W.; Park, Hansoo; Guo, Xuan; Nakamura, Kenta; Raphael, Robert M.; Kasper, F. Kurtis

    2010-01-01

    This study investigated the encapsulation of newt iris pigment epithelial cells (PECs), which have the ability to regenerate a lens by trans-differentiation in vivo, within a biodegradable hydrogel of oligo(poly(ethylene glycol) fumarate) crosslinked with poly(ethylene glycol)-diacrylate. Hydrogel beads of initial diameter of 1 mm were fabricated by a molding technique. The swelling ratio and degradation rate of the hydrogel beads decreased with increasing crosslinking ratios. Confocal microscopy confirmed the cytocompatibility of crosslinking hydrogel formulations as evidenced by the viability of an encapsulated model cell line within a crosslinked hydrogel bead. Hydrogel beads encapsulating iris PECs were also implanted into lentectomized newts in vivo; histological evaluation of explants after 30 days revealed a regenerated lens, thus demonstrating that the presence of degrading hydrogel did not adversely affect lens regeneration. The results of this study suggest the potential of a method for lens regeneration involving oligo(poly(ethylene glycol) fumarate) hydrogels for iris PEC encapsulation and transplantation. PMID:19514850

  14. A predicted interactome for Arabidopsis.

    PubMed

    Geisler-Lee, Jane; O'Toole, Nicholas; Ammar, Ron; Provart, Nicholas J; Millar, A Harvey; Geisler, Matt

    2007-10-01

    The complex cellular functions of an organism frequently rely on physical interactions between proteins. A map of all protein-protein interactions, an interactome, is thus an invaluable tool. We present an interactome for Arabidopsis (Arabidopsis thaliana) predicted from interacting orthologs in yeast (Saccharomyces cerevisiae), nematode worm (Caenorhabditis elegans), fruitfly (Drosophila melanogaster), and human (Homo sapiens). As an internal quality control, a confidence value was generated based on the amount of supporting evidence for each interaction. A total of 1,159 high confidence, 5,913 medium confidence, and 12,907 low confidence interactions were identified for 3,617 conserved Arabidopsis proteins. There was significant coexpression of genes whose proteins were predicted to interact, even among low confidence interactions. Interacting proteins were also significantly more likely to be found within the same subcellular location, and significantly less likely to be found in conflicting localizations than randomly paired proteins. A notable exception was that proteins located in the Golgi were more likely to interact with Golgi, vacuolar, or endoplasmic reticulum sorted proteins, indicating possible docking or trafficking interactions. These predictions can aid researchers by extending known complexes and pathways with candidate proteins. In addition we have predicted interactions for many previously unknown proteins in known pathways and complexes. We present this interactome, and an online Web interface the Arabidopsis Interactions Viewer, as a first step toward understanding global signaling in Arabidopsis, and to whet the appetite for those who are awaiting results from high-throughput experimental approaches.

  15. Arabidopsis thaliana—Aphid Interaction

    PubMed Central

    Louis, Joe; Singh, Vijay; Shah, Jyoti

    2012-01-01

    Aphids are important pests of plants that use their stylets to tap into the sieve elements to consume phloem sap. Besides the removal of photosynthates, aphid infestation also alters source-sink patterns. Most aphids also vector viral diseases. In this chapter, we will summarize on recent significant findings in plant-aphid interaction, and how studies involving Arabidopsis thaliana and Myzus persicae (Sülzer), more commonly known as the green peach aphid (GPA), are beginning to provide important insights into the molecular basis of plant defense and susceptibility to aphids. The recent demonstration that expression of dsRNA in Arabidopsis can be used to silence expression of genes in GPA has further expanded the utility of Arabidopsis for evaluating the contribution of the aphid genome-encoded proteins to this interaction. PMID:22666177

  16. T Oligo-Primed Polymerase Chain Reaction (TOP-PCR): A Robust Method for the Amplification of Minute DNA Fragments in Body Fluids.

    PubMed

    Nai, Yu-Shin; Chen, Tzu-Han; Huang, Yu-Feng; Midha, Mohit K; Shiau, Hsin-Chieh; Shen, Chen-Yang; Chen, Chien-Jen; Yu, Alice L; Chiu, Kuo Ping

    2017-01-17

    Body fluid DNA sequencing is a powerful noninvasive approach for the diagnosis of genetic defects, infectious agents and diseases. The success relies on the quantity and quality of the DNA samples. However, numerous clinical samples are either at low quantity or of poor quality due to various reasons. To overcome these problems, we have developed T oligo-primed polymerase chain reaction (TOP-PCR) for full-length nonselective amplification of minute quantity of DNA fragments. TOP-PCR adopts homogeneous "half adaptor" (HA), generated by annealing P oligo (carrying a phosphate group at the 5' end) and T oligo (carrying a T-tail at the 3' end), for efficient ligation to target DNA and subsequent PCR amplification primed by the T oligo alone. Using DNA samples from body fluids, we demonstrate that TOP-PCR recovers minute DNA fragments and maintains the DNA size profile, while enhancing the major molecular populations. Our results also showed that TOP-PCR is a superior method for detecting apoptosis and outperforms the method adopted by Illumina for DNA amplification.

  17. T Oligo-Primed Polymerase Chain Reaction (TOP-PCR): A Robust Method for the Amplification of Minute DNA Fragments in Body Fluids

    PubMed Central

    Nai, Yu-Shin; Chen, Tzu-Han; Huang, Yu-Feng; Midha, Mohit K.; Shiau, Hsin-Chieh; Shen, Chen-Yang; Chen, Chien-Jen; Yu, Alice L.; Chiu, Kuo Ping

    2017-01-01

    Body fluid DNA sequencing is a powerful noninvasive approach for the diagnosis of genetic defects, infectious agents and diseases. The success relies on the quantity and quality of the DNA samples. However, numerous clinical samples are either at low quantity or of poor quality due to various reasons. To overcome these problems, we have developed T oligo-primed polymerase chain reaction (TOP-PCR) for full-length nonselective amplification of minute quantity of DNA fragments. TOP-PCR adopts homogeneous “half adaptor” (HA), generated by annealing P oligo (carrying a phosphate group at the 5′ end) and T oligo (carrying a T-tail at the 3′ end), for efficient ligation to target DNA and subsequent PCR amplification primed by the T oligo alone. Using DNA samples from body fluids, we demonstrate that TOP-PCR recovers minute DNA fragments and maintains the DNA size profile, while enhancing the major molecular populations. Our results also showed that TOP-PCR is a superior method for detecting apoptosis and outperforms the method adopted by Illumina for DNA amplification. PMID:28094343

  18. Synthesis of oligo(chloroorganoxy) chlorophosphazenes and investigation of these materials as combustion inhibitors in fiberglass-reinforced plastics based on epoxy and polyster resins

    SciTech Connect

    Fedorov, S.G.; Gol`din, G.S.; Nikitina, G.S.

    1992-03-10

    The authors have carried out the synthesis of linear oligo(chloroorganoxy)chlorophosphazenes (OCOCPs) by the interaction of linear oligochlorophosphazenes (LCPs) with ethylene oxide and a number of other expoxy compounds. Also, the authors have investigated the fire-retardant efficiency of the OCOCPs that the authors synthesized. 7 refs., 5 tabs.

  19. Calcium ion binding of three different types of oligo/polysialic acids as studied by equilibrium dialysis and circular dichroic methods.

    PubMed

    Shimoda, Y; Kitajima, K; Inoue, S; Inoue, Y

    1994-02-08

    Ca2+ binding properties of three different types of oligo/polysialic acid chains, i.e., oligo/poly(Neu5Ac), oligo/poly(Neu5Gc), and oligo/poly(KDN), were studied by equilibrium dialysis and circular dichroism. Colominic acid, high molecular weight polysialoglycoprotein (H-PSGP), low molecular weight polysialoglycoprotein (L-PSGP), and 3-deoxy-D-glycero-D-galacto-2-nonulosonic acid (KDN) glycoprotein were found to bind calcium ions with about 8-100 times the affinity of sialic acid monomer. Analysis by equilibrium dialysis of the binding of Ca2+ to colominic acid was biphasic, and the high-affinity interaction was shown to change with the degree of polymerization. Specific binding of Ca2+ to polysialic acid (polySia) caused characteristic effects in the circular dichroism spectrum. A pronounced decrease in the circular dichroism of polySia at 205 nm was observed upon addition of calcium. H-PSGP was found to bind calcium ions with 3-fold higher affinity than L-PSGP.

  20. Re-irradiation for oligo-recurrence from esophageal cancer with radiotherapy history: a multi-institutional study.

    PubMed

    Jingu, Keiichi; Niibe, Yuzuru; Yamashita, Hideomi; Katsui, Kuniaki; Matsumoto, Toshihiko; Nishina, Tomohiro; Terahara, Atsuro

    2017-09-05

    Neoadjuvant chemoradiotherapy following surgery has recently become a standard therapy. The purpose of the present study was to determine the effectiveness and toxicity of re-irradiation for oligo-recurrence in lymph nodes from esophageal cancer treated by definitive radiotherapy or by surgery with additional radiotherapy. We reviewed retrospectively 248 patients treated with (chemo)radiotherapy for oligo-recurrence in lymph nodes from esophageal cancer in five Japanese high-volume centers between 2000 and 2015. Thirty-three patients in whom re-irradiation was performed were enrolled in this study, and the results for patients in whom re-irradiation was performed were compared with the results for other patients. Median maximum lymph node diameter was 22 mm. Median total radiation dose was 60 Gy. The median calculated biological effective dose using the LQ model with α/β = 10 Gy (BED10) in patients in whom re-irradiation was performed was significantly lower than the median BED10 in others. There was no different factor except for BED10, histology and irradiation field between patients with a past irradiation history and patients without a past irradiation history. The median observation period in surviving patients in whom re-irradiation was performed was 21.7 months. The 3-year overall survival rate in the 33 patients with a past irradiation history was 17.9%, with a median survival period of 16.0 months. Overall survival rate and local control rate in patients with a past irradiation history were significantly worse than those in patients without a past irradiation history (log-rank test, p = 0.016 and p = 0.0007, respectively). One patient in whom re-irradiation was performed died from treatment-related gastric hemorrhage. Results in the present study suggested that re-irradiation for oligo-recurrence in lymph nodes from esophageal cancer treated by definitive radiotherapy or by surgery with additional radiotherapy might be acceptable but

  1. Urothelial cancer gene regulatory networks inferred from large-scale RNAseq, Bead and Oligo gene expression data.

    PubMed

    de Matos Simoes, Ricardo; Dalleau, Sabine; Williamson, Kate E; Emmert-Streib, Frank

    2015-05-14

    Urothelial pathogenesis is a complex process driven by an underlying network of interconnected genes. The identification of novel genomic target regions and gene targets that drive urothelial carcinogenesis is crucial in order to improve our current limited understanding of urothelial cancer (UC) on the molecular level. The inference of genome-wide gene regulatory networks (GRN) from large-scale gene expression data provides a promising approach for a detailed investigation of the underlying network structure associated to urothelial carcinogenesis. In our study we inferred and compared three GRNs by the application of the BC3Net inference algorithm to large-scale transitional cell carcinoma gene expression data sets from Illumina RNAseq (179 samples), Illumina Bead arrays (165 samples) and Affymetrix Oligo microarrays (188 samples). We investigated the structural and functional properties of GRNs for the identification of molecular targets associated to urothelial cancer. We found that the urothelial cancer (UC) GRNs show a significant enrichment of subnetworks that are associated with known cancer hallmarks including cell cycle, immune response, signaling, differentiation and translation. Interestingly, the most prominent subnetworks of co-located genes were found on chromosome regions 5q31.3 (RNAseq), 8q24.3 (Oligo) and 1q23.3 (Bead), which all represent known genomic regions frequently deregulated or aberated in urothelial cancer and other cancer types. Furthermore, the identified hub genes of the individual GRNs, e.g., HID1/DMC1 (tumor development), RNF17/TDRD4 (cancer antigen) and CYP4A11 (angiogenesis/ metastasis) are known cancer associated markers. The GRNs were highly dataset specific on the interaction level between individual genes, but showed large similarities on the biological function level represented by subnetworks. Remarkably, the RNAseq UC GRN showed twice the proportion of significant functional subnetworks. Based on our analysis of inferential

  2. Coplanar Oligo(p-phenylenedisilenylene)s as Si═Si Analogues of Oligo(p-phenylenevinylene)s: Evidence for Extended π-Conjugation through the Carbon and Silicon π-Frameworks.

    PubMed

    Li, Liangchun; Matsuo, Tsukasa; Hashizume, Daisuke; Fueno, Hiroyuki; Tanaka, Kazuyoshi; Tamao, Kohei

    2015-12-02

    A series of oligo(p-phenylenedisilenylene)s (Si-OPVs 1-4), silicon analogues of oligo(p-phenylenevinylene)s, up to the tetramer have been synthesized and isolated by the introduction of a newly developed protecting group [(HexO)MEind] for improving their solubility. The experimental and theoretical studies of the Si-OPVs 1-4 demonstrate the fully extended π-conjugation of the Si-OPV main chains. Single crystal X-ray analyses of the monomer 1 and the dimer 2 revealed the highly coplanar Si-OPV backbones facilitating the effective extension of the π-conjugation, which has further been validated by the significant increases in the absorption maxima from 465 nm for the monomer 1 to 610 nm for the tetramer 4. The absorption maxima exhibit an excellent fit to Meier's equation, leading to the estimation of an effective conjugation length (ECL) of 9 repeat units (nECL = 9) and the absorption maximum of 635 nm for the infinite chain (λ∞ = 635 nm). In sharp contrast to other nonemissive disilenes, the Si-OPVs 2-4 show an intense fluorescence from 613 to 668 nm at room temperature with the quantum yields up to 0.48. All the data presented here provide the first evidence for the efficient extended π-conjugation between the Si═Si double bonds and the carbon π-electron systems over the entire Si-OPV skeleton. This study reveals the possibility for developing the conjugated disilene π-systems, in which the Si═Si double bonds would be promising building blocks, significantly optimizing the intrinsic photophysical and electrochemical properties of the carbon-based π-conjugated materials.

  3. Leishmania OligoC-TesT as a Simple, Rapid, and Standardized Tool for Molecular Diagnosis of Cutaneous Leishmaniasis in Peru▿

    PubMed Central

    Espinosa, Diego; Boggild, Andrea K.; Deborggraeve, Stijn; Laurent, Thierry; Valencia, Cristian; Pacheco, Rosa; Miranda-Verástegui, César; Llanos-Cuentas, Alejandro; Leclipteux, Thierry; Dujardin, Jean-Claude; Büscher, Philippe; Arévalo, Jorge

    2009-01-01

    Molecular methods such as PCR have become attractive tools for diagnosis of cutaneous leishmaniasis (CL), both for their high sensitivity and for their specificity. However, their practical use in routine diagnosis is limited due to the infrastructural requirements and the lack of any standardization. Recently, a simplified and standardized PCR format for molecular detection of Leishmania was developed. The Leishmania OligoC-TesT is based on simple and rapid detection using a dipstick with PCR-amplified Leishmania DNA. In this study, we estimated the diagnostic accuracy of the Leishmania OligoC-TesT for 61 specimens from 44 CL-suspected patients presenting at the leishmaniasis clinic of the Instituto de Medicina Tropical Alexander von Humboldt, Peru. On the basis of parasitological detection and the leishmanin skin test (LST), patients were classified as (i) confirmed CL cases, (ii) LST-positive cases, and (iii) LST-negative cases. The sensitivities of the Leishmania OligoC-TesT was 74% (95% confidence interval (CI), 60.5% to 84.1%) for lesion aspirates and 92% (95% CI, 81.2% to 96.9%) for scrapings. A significantly higher sensitivity was observed with a conventional PCR targeting the kinetoplast DNA on the aspirates (94%) (P = 0.001), while there was no significant difference in sensitivity for the lesion scrapings (88%) (P = 0.317). In addition, the Leishmania OligoC-TesT was evaluated for 13 CL-suspected patients in two different peripheral health centers in the central jungle of Peru. Our findings clearly indicate the high accuracy of the Leishmania OligoC-TesT for lesion scrapings for simple and rapid molecular diagnosis of CL in Peru. PMID:19553579

  4. Leishmania OligoC-TesT as a simple, rapid, and standardized tool for molecular diagnosis of cutaneous leishmaniasis in Peru.

    PubMed

    Espinosa, Diego; Boggild, Andrea K; Deborggraeve, Stijn; Laurent, Thierry; Valencia, Cristian; Pacheco, Rosa; Miranda-Verástegui, César; Llanos-Cuentas, Alejandro; Leclipteux, Thierry; Dujardin, Jean-Claude; Büscher, Philippe; Arévalo, Jorge

    2009-08-01

    Molecular methods such as PCR have become attractive tools for diagnosis of cutaneous leishmaniasis (CL), both for their high sensitivity and for their specificity. However, their practical use in routine diagnosis is limited due to the infrastructural requirements and the lack of any standardization. Recently, a simplified and standardized PCR format for molecular detection of Leishmania was developed. The Leishmania OligoC-TesT is based on simple and rapid detection using a dipstick with PCR-amplified Leishmania DNA. In this study, we estimated the diagnostic accuracy of the Leishmania OligoC-TesT for 61 specimens from 44 CL-suspected patients presenting at the leishmaniasis clinic of the Instituto de Medicina Tropical Alexander von Humboldt, Peru. On the basis of parasitological detection and the leishmanin skin test (LST), patients were classified as (i) confirmed CL cases, (ii) LST-positive cases, and (iii) LST-negative cases. The sensitivities of the Leishmania OligoC-TesT was 74% (95% confidence interval (CI), 60.5% to 84.1%) for lesion aspirates and 92% (95% CI, 81.2% to 96.9%) for scrapings. A significantly higher sensitivity was observed with a conventional PCR targeting the kinetoplast DNA on the aspirates (94%) (P = 0.001), while there was no significant difference in sensitivity for the lesion scrapings (88%) (P = 0.317). In addition, the Leishmania OligoC-TesT was evaluated for 13 CL-suspected patients in two different peripheral health centers in the central jungle of Peru. Our findings clearly indicate the high accuracy of the Leishmania OligoC-TesT for lesion scrapings for simple and rapid molecular diagnosis of CL in Peru.

  5. Comparative Study on Surface-Initiated ATRP and SI-ARGET ATRP of Oligo(Ethylene Glycol) Methacrylate on Gold.

    PubMed

    Lee, Bong Soo; Kim, Ji Yup; Park, Ji Hun; Cho, Woo Kyung; Choi, Insung S

    2016-03-01

    Oligo(ethylene glycol) methacrylate (OEGMA) was polymerized from a polymerization initiator-presenting gold substrate by Activator ReGenerated by Electron Transfer Atom Transfer Radical Polymerization (ARGET ATRP) in water. Compared with the normal surface-initiated ATRP (SI-ATRP), SI-ARGET ATRP of OEGMA proceeded smoothly in the presence of air with L-ascorbic acid as a reducing agent and a CuBr2/2,2'-bipyridyl complex at the ppm level. In addition, SI-ARGET ATRP did not require the additional steps for removing a polymerization inhibitor from the OEGMA monomer and for deoxygenating the solvent. The ellipsometric measurements showed that the polymerized OEGMA (pOEGMA) films prepared by SI-ARGET ATRP were on average 10 times thicker than those prepared by normal SI-ATRP with the same monomer concentration and polymerization time.

  6. HTP-OligoDesigner: An Online Primer Design Tool for High-Throughput Gene Cloning and Site-Directed Mutagenesis.

    PubMed

    Camilo, Cesar M; Lima, Gustavo M A; Maluf, Fernando V; Guido, Rafael V C; Polikarpov, Igor

    2016-01-01

    Following burgeoning genomic and transcriptomic sequencing data, biochemical and molecular biology groups worldwide are implementing high-throughput cloning and mutagenesis facilities in order to obtain a large number of soluble proteins for structural and functional characterization. Since manual primer design can be a time-consuming and error-generating step, particularly when working with hundreds of targets, the automation of primer design process becomes highly desirable. HTP-OligoDesigner was created to provide the scientific community with a simple and intuitive online primer design tool for both laboratory-scale and high-throughput projects of sequence-independent gene cloning and site-directed mutagenesis and a Tm calculator for quick queries.

  7. Energy-transfer efficiency in stacked oligo(p-phenylene vinylene)s: pronounced effects of order.

    PubMed

    Hoeben, Freek J M; Schenning, Albertus P H J; Meijer, E W

    2005-11-11

    The supramolecular structure of two types of oligo(p-phenylene vinylene) (OPV) building blocks in dodecane solution is studied. Monofunctional chromophores (MOPV) form well-defined helical assemblies, whereas bifunctional molecules (BOPV) aggregate into so-called frustrated stacks, lacking any higher helical order. This difference in organization has a major influence on the transfer of excitation energy through the assemblies. Energy transfer to supramolecularly incorporated guests (MOPV with lower bandgap) is used to probe the intrinsic differences in exciton mobility in these two types of mixed aggregates. From the observed donor fluorescence quenching, it can be concluded that the helically ordered nature of the MOPV stacks facilitates the transfer of excitation energy, yielding evidence for higher exciton mobility in the well-ordered assemblies than in the frustrated stacks. Finally, the concept of energy transfer in supramolecular assemblies is extended to the solid state by the successful implementation in a light-emitting diode (LED).

  8. Oligo(p-phenylene ethynylene) with Cyanoacrylate Terminal Groups and Graphene Composite as Fluorescent Chemical Sensor for Cysteine.

    PubMed

    Adachi, Naoya; Yoshinari, Mariko; Suzuki, Eri; Okada, Mari

    2017-04-08

    A chemical sensor for cysteine (Cys) was fabricated based on a fluorescent oligo(p-phenylene ethynylene)s (OPEs) and OPE-graphene oxide (GO) composite. OPE with cyanoacrylate terminal groups were synthesized by a Pd-catalyzed Sonogashira coupling reaction and Knoevenagel condensation for use as a chemical sensor for Cys. The optical properties and Cys sensing capability of the cyanoacrylate modified OPE and OPE-GO composite were investigated. In addition of Cys, the fluorescence of OPE was blue-shifted and decreased (fluorescence turn-off), while the fluorescence of the OPE-GO composite was enhanced (fluorescence turn-on). Thus, OPE with cyanoacrylate terminal groups and OPE-GO composite acts a highly sensitive fluorescent chemical sensor for Cys.

  9. [Malabsorption of fermentable oligo-, di-, or monosaccharides and polyols (FODMAP) as a common cause of unclear abdominal discomfort].

    PubMed

    Goebel-Stengel, M; Mönnikes, H

    2014-06-01

    Carbohydrate malabsorption is a frequent but underestimated cause of unexplained gastrointestinal symptoms like meteorism, flatulence, pain and diarrhea. By means of hydrogen and/or methane breath test after ingestion of the respective carbohydrate it can be identified and diagnosed easily, fast and reliably by successful nutritional therapy. Besides the well known complaints caused by lactose and fructose malabsorption, other fermentable oligo-, di-, or monosaccharides and polyols (akronym: FODMAP) can cause abdominal discomfort and IBS-like symptoms. In addition to lactose (dairy products) and fructose (apples, pears, mango, watermelon), FODMAPs comprise galactans (legumes), fructans (wheat, onions, garlic, artichoke) and the artificial sweeteners sorbitol, mannitol, maltitol and xylitol (sugar free candy, light products). A general restriction of all FODMAP components can be beneficial in relieving symptoms and improving quality of life in patients with functional gastrointestinal complaints.

  10. Highly efficient synthesis of monodisperse poly(ethylene glycols) and derivatives through macrocyclization of oligo(ethylene glycols).

    PubMed

    Zhang, Hua; Li, Xuefei; Shi, Qiuyan; Li, Yu; Xia, Guiquan; Chen, Long; Yang, Zhigang; Jiang, Zhong-Xing

    2015-03-16

    A macrocyclic sulfate (MCS)-based approach to monodisperse poly(ethylene glycols) (M-PEGs) and their monofunctionalized derivatives has been developed. Macrocyclization of oligo(ethylene glycols) (OEGs) provides MCS (up to a 62-membered macrocycle) as versatile precursors for a range of monofunctionalized M-PEGs. Through iterative nucleophilic ring-opening reactions of MCS without performing group protection and activation, a series of M-PEGs, including the unprecedented 64-mer (2850 Da), can be readily prepared. Synthetic simplicity coupled with versatility of this new strategy may pave the way for broader applications of M-PEGs. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Construction and validation of a 45K rice oligonucleotide array

    USDA-ARS?s Scientific Manuscript database

    We have constructed and validated a 43,311 oligonucleotide (oligos, 50-70-mers) gene array (NSF 45K) based on 45,116 gene models from release 3 of The Institute for Genomic Research's rice pseudomolecules. To test the array, we generated expression profiles on light- and dark-grown rice leaf tissue...

  12. Oligo-Miocene reservoir sequence characterization and structuring in the Sisseb El Alem-Kalaa Kebira regions (Northeastern Tunisia)

    NASA Astrophysics Data System (ADS)

    Houatmia, Faten; Khomsi, Sami; Bédir, Mourad

    2015-11-01

    The Sisseb El Alem-Enfidha basin is located in the northeastern Tunisia, It is borded by Nadhour - Saouaf syncline to the north, Kairouan plain to the south, the Mediterranean Sea to the east and Tunisian Atlassic "dorsale" to the west. Oligocene and Miocene deltaic deposits present the main potential deep aquifers in this basin with high porosity (25%-30%). The interpretation of twenty seismic reflection profiles, calibrated by wire line logging data of twelve oil wells, hydraulic wells and geologic field sections highlighted the impact of tectonics on the structuring geometry of Oligo-Miocene sandstones reservoirs and their distribution in raised structures and subsurface depressions. Miocene seismostratigraphy analysis from Ain Ghrab Formation (Langhian) to the Segui Formation (Quaternary) showed five third-order seismic sequence deposits and nine extended lenticular sandy bodies reservoirs limited by toplap and downlap surfaces unconformities, Oligocene deposits presented also five third- order seismic sequences with five extended lenticular sandy bodies reservoirs. The Depth and the thickness maps of these sequence reservoir packages exhibited the structuring of this basin in sub-basins characterized by important lateral and vertical geometric and thichness variations. Petroleum wells wire line logging correlation with clay volume calculation showed an heterogeneous multilayer reservoirs of Oligocene and Miocene formed by the arrangement of fourteen sandstone bodies being able to be good reservoirs, separated by impermeable clay packages and affected by faults. Reservoirs levels correspond mainly to the lower system tract (LST) of sequences. Intensive fracturing by deep seated faults bounding the different sub-basins play a great role for water surface recharge and inter-layer circulations between affected reservoirs. The total pore volume of the Oligo-Miocene reservoir sandy bodies in the study area, is estimated to about 4 × 1012 m3 and equivalent to 4

  13. Development of an oligo DNA microarray for the European sea bass and its application to expression profiling of jaw deformity

    PubMed Central

    2010-01-01

    Background The European sea bass (Dicentrarchus labrax) is a marine fish of great importance for fisheries and aquaculture. Functional genomics offers the possibility to discover the molecular mechanisms underlying productive traits in farmed fish, and a step towards the application of marker assisted selection methods in this species. To this end, we report here on the development of an oligo DNA microarray for D. labrax. Results A database consisting of 19,048 unique transcripts was constructed, of which 12,008 (63%) could be annotated by similarity and 4,692 received a GO functional annotation. Two non-overlapping 60mer probes were designed for each unique transcript and in-situ synthesized on glass slides using Agilent SurePrint™ technology. Probe design was positively completed for 19,035 target clusters; the oligo microarray was then applied to profile gene expression in mandibles and whole-heads of fish affected by prognathism, a skeletal malformation that strongly affects sea bass production. Statistical analysis identified 242 transcripts that are significantly down-regulated in deformed individuals compared to normal fish, with a significant enrichment in genes related to nervous system development and functioning. A set of genes spanning a wide dynamic range in gene expression level were selected for quantitative RT-PCR validation. Fold change correlation between microarray and qPCR data was always significant. Conclusions The microarray platform developed for the European sea bass has a high level of flexibility, reliability, and reproducibility. Despite the well known limitations in achieving a proper functional annotation in non-model species, sufficient information was obtained to identify biological processes that are significantly enriched among differentially expressed genes. New insights were obtained on putative mechanisms involved on mandibular prognathism, suggesting that bone/nervous system development might play a role in this phenomenon

  14. Araport: the Arabidopsis information portal.

    PubMed

    Krishnakumar, Vivek; Hanlon, Matthew R; Contrino, Sergio; Ferlanti, Erik S; Karamycheva, Svetlana; Kim, Maria; Rosen, Benjamin D; Cheng, Chia-Yi; Moreira, Walter; Mock, Stephen A; Stubbs, Joseph; Sullivan, Julie M; Krampis, Konstantinos; Miller, Jason R; Micklem, Gos; Vaughn, Matthew; Town, Christopher D

    2015-01-01

    The Arabidopsis Information Portal (https://www.araport.org) is a new online resource for plant biology research. It houses the Arabidopsis thaliana genome sequence and associated annotation. It was conceived as a framework that allows the research community to develop and release 'modules' that integrate, analyze and visualize Arabidopsis data that may reside at remote sites. The current implementation provides an indexed database of core genomic information. These data are made available through feature-rich web applications that provide search, data mining, and genome browser functionality, and also by bulk download and web services. Araport uses software from the InterMine and JBrowse projects to expose curated data from TAIR, GO, BAR, EBI, UniProt, PubMed and EPIC CoGe. The site also hosts 'science apps,' developed as prototypes for community modules that use dynamic web pages to present data obtained on-demand from third-party servers via RESTful web services. Designed for sustainability, the Arabidopsis Information Portal strategy exploits existing scientific computing infrastructure, adopts a practical mixture of data integration technologies and encourages collaborative enhancement of the resource by its user community. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  15. Araport: the Arabidopsis Information Portal

    PubMed Central

    Krishnakumar, Vivek; Hanlon, Matthew R.; Contrino, Sergio; Ferlanti, Erik S.; Karamycheva, Svetlana; Kim, Maria; Rosen, Benjamin D.; Cheng, Chia-Yi; Moreira, Walter; Mock, Stephen A.; Stubbs, Joseph; Sullivan, Julie M.; Krampis, Konstantinos; Miller, Jason R.; Micklem, Gos; Vaughn, Matthew; Town, Christopher D.

    2015-01-01

    The Arabidopsis Information Portal (https://www.araport.org) is a new online resource for plant biology research. It houses the Arabidopsis thaliana genome sequence and associated annotation. It was conceived as a framework that allows the research community to develop and release ‘modules’ that integrate, analyze and visualize Arabidopsis data that may reside at remote sites. The current implementation provides an indexed database of core genomic information. These data are made available through feature-rich web applications that provide search, data mining, and genome browser functionality, and also by bulk download and web services. Araport uses software from the InterMine and JBrowse projects to expose curated data from TAIR, GO, BAR, EBI, UniProt, PubMed and EPIC CoGe. The site also hosts ‘science apps,’ developed as prototypes for community modules that use dynamic web pages to present data obtained on-demand from third-party servers via RESTful web services. Designed for sustainability, the Arabidopsis Information Portal strategy exploits existing scientific computing infrastructure, adopts a practical mixture of data integration technologies and encourages collaborative enhancement of the resource by its user community. PMID:25414324

  16. Systemic endopolyploidy in Arabidopsis thaliana

    SciTech Connect

    Galbraith, D.W.; Harkins, K.R. ); Knapp, S. )

    1991-07-01

    Microfluorometric analysis of the nuclear DNA contents of the somatic tissues of Arabidopsis thaliana has revealed extensive endoreduplication, resulting in tissues that comprise mixtures of polypoloid cells. Endoreduplication was found in all tissues except those of the inflorescences and was developmentally regulated according to the age of the tissues and their position within the plant.

  17. The salty tale of Arabidopsis.

    PubMed

    Sanders, D

    2000-06-29

    High concentrations of sodium chloride are toxic to most plant species. New insights into the mechanisms by which plants tolerate salt have emerged from the identification of genes in Arabidopsis thaliana that play a critical part in physiological resistance to salt.

  18. The Phenylpropanoid Pathway in Arabidopsis

    PubMed Central

    Fraser, Christopher M.; Chapple, Clint

    2011-01-01

    The phenylpropanoid pathway serves as a rich source of metabolites in plants, being required for the biosynthesis of lignin, and serving as a starting point for the production of many other important compounds, such as the flavonoids, coumarins, and lignans. In spite of the fact that the phenylpropanoids and their derivatives are sometimes classified as secondary metabolites, their relevance to plant survival has been made clear via the study of Arabidopsis and other plant species. As a model system, Arabidopsis has helped to elucidate many details of the phenylpropanoid pathway, its enzymes and intermediates, and the interconnectedness of the pathway with plant metabolism as a whole. These advances in our understanding have been made possible in large part by the relative ease with which mutations can be generated, identified, and studied in Arabidopsis. Herein, we provide an overview of the research progress that has been made in recent years, emphasizing both the genes (and gene families) associated with the phenylpropanoid pathway in Arabidopsis, and the end products that have contributed to the identification of many mutants deficient in the phenylpropanoid metabolism: the sinapate esters. PMID:22303276

  19. Identification, characterization, and developmental expression of a novel alpha 2-->8-KDN-transferase which terminates elongation of alpha 2-->8-linked oligo-polysialic acid chain synthesis in trout egg polysialoglycoproteins.

    PubMed

    Angata, T; Kitazume, S; Terada, T; Kitajima, K; Inoue, S; Troy, F A; Inoue, Y

    1994-10-01

    A novel glycosyltransferase which catalyses transfer of deaminated neuraminic acid, KDN (2-keto-3-deoxy-D-glycero-D-galacto-nononic acid) from CMP-KDN to the non-reducing termini of oligo-polysialyl chains of polysialoglycoprotein (PSGP), was discovered in the ovary of rainbow trout (Oncorhynchus mykiss). The KDN-transferase activity was optimal at neutral pH, and stimulated 2 to 2.5-fold by 2-5 mM Mg2+ or Mn2+. Expression of KDN-transferase was developmentally regulated in parallel with expression of the alpha 2-->8-polysialyltransferase, which catalyses synthesis of the oligo-polysialyl chains in PSGP. Incorporation of the KDN residues into the oligo-polysialyl chains prevented their further elongation, resulting in 'capping' of the oligo-polysialyl chains. This is the first example of a glycosyltransferase that catalyses termination of alpha 2-->8-polysialylation in glycoproteins.

  20. Assessing Gravitropic Responses in Arabidopsis.

    PubMed

    Barker, Richard; Cox, Benjamin; Silber, Logan; Sangari, Arash; Assadi, Amir; Masson, Patrick

    2016-01-01

    Arabidopsis thaliana was the first higher organism to have its genome sequenced and is now widely regarded as the model dicot. Like all plants, Arabidopsis develops distinct growth patterns in response to different environmental stimuli. This can be seen in the gravitropic response of roots. Methods to investigate this particular tropism are presented here. First, we describe a high-throughput time-lapse photographic analysis of root growth and curvature response to gravistimulation allowing the quantification of gravitropic kinetics and growth rate at high temporal resolution. Second, we present a protocol that allows a quantitative evaluation of gravitropic sensitivity using a homemade 2D clinostat. Together, these approaches allow an initial comparative analysis of the key phenomena associated with root gravitropism between different genotypes and/or accessions.

  1. Asparagine Metabolic Pathways in Arabidopsis.

    PubMed

    Gaufichon, Laure; Rothstein, Steven J; Suzuki, Akira

    2016-04-01

    Inorganic nitrogen in the form of ammonium is assimilated into asparagine via multiple steps involving glutamine synthetase (GS), glutamate synthase (GOGAT), aspartate aminotransferase (AspAT) and asparagine synthetase (AS) in Arabidopsis. The asparagine amide group is liberated by the reaction catalyzed by asparaginase (ASPG) and also the amino group of asparagine is released by asparagine aminotransferase (AsnAT) for use in the biosynthesis of amino acids. Asparagine plays a primary role in nitrogen recycling, storage and transport in developing and germinating seeds, as well as in vegetative and senescence organs. A small multigene family encodes isoenzymes of each step of asparagine metabolism in Arabidopsis, except for asparagine aminotransferase encoded by a single gene. The aim of this study is to highlight the structure of the genes and encoded enzyme proteins involved in asparagine metabolic pathways; the regulation and role of different isogenes; and kinetic and physiological properties of encoded enzymes in different tissues and developmental stages.

  2. Cold tolerance in Arabidopsis kamchatica.

    PubMed

    Armstrong, Jessica J; Takebayashi, Naoki; Sformo, Todd; Wolf, Diana E

    2015-03-01

    • Cold tolerance is a critically important factor determining how plants will be influenced by climate change, including changes in snowcover and extreme weather events. Although a great deal is known about cold tolerance in Arabidopsis thaliana, it is not highly cold tolerant. This study examined cold tolerance and its genetic diversity in an herbaceous subarctic relative, Arabidopsis kamchatica, which generally occurs in much colder climates.• Thermal analysis and electrolyte leakage were used to estimate supercooling points and lethal temperatures (LT50) in cold-acclimated and nonacclimated families from three populations of A. kamchatica.• Arabidopsis kamchatica was highly cold tolerant, with a mean LT50 of -10.8°C when actively growing, and -21.8°C when cold acclimated. It also was able to supercool to very low temperatures. Surprisingly, actively growing plants supercooled more than acclimated plants (-14.7 vs. -12.7°C). There was significant genetic variation for cold tolerance both within and among populations. However, both cold tolerance and genetic diversity were highest in the midlatitude population rather than in the far north, indicating that adaptations to climate change are most likely to arise in the center of the species range rather than at the edges.• Arabidopsis kamchatica is highly cold tolerant throughout its range. It is far more freeze tolerant than A. thaliana, and supercooled to lower temperatures, suggesting that A. kamchatica provides a valuable complement to A. thaliana for cold tolerance research. © 2015 Botanical Society of America, Inc.

  3. Extended monolayer of cyano-ended oligo(para-phenylenes) at the air/HOPG interface investigated by high-resolution AFM

    NASA Astrophysics Data System (ADS)

    Hourani, W.; Lamare, S.; Makoudi, Y.; Palmino, F.; Cherioux, F.

    2016-10-01

    The formation of functional networks on surfaces is one of the main challenges in the field of nanotechnologies. In this paper, we shall propose a very simple process which can be used to achieve the formation of extended monolayer of functional oligo(para-phenylenes) molecules at the air/graphite interface. By developing a convergent strategy, we successfully achieved the synthesis of oligo(para-phenylenes) molecules with a tuneable length. The photophysical properties of these new oligomers were characterized by UV-vis absorption and fluorescence spectroscopy. Deposition of these molecules by a simple spin-coating process on a highly oriented pyrolytic graphite (HOPG) surface leads to the formation of extended monolayered 2D networks. These networks were characterized by atomic force microscopy experiments under ambient conditions with submolecular resolution thus providing the adsorption model of these molecules on an HOPG surface.

  4. New deuterated oligo(ethylene glycol) building blocks and their use in the preparation of surface active lipids possessing labeled hydrophilic tethers.

    PubMed

    Faragher, Robert J; Schwan, Adrian L

    2008-02-15

    For the introduction of additional analysis protocols of tethered molecules, a method is presented to prepare functionalized, deuterated oligo(ethylene glycols) from ethylene glycol-d4. Partial oligomerization of ethylene glycol-d4 and conversion to ditosylates is accompanied by coupling reactions to prepare doubly benzyl protected oligo(ethylene glycols) with two to five repeating units. The tetramer bearing 16 deuteria was elaborated at both ends to eventually prepare 2,3-di-O-phytanyl-sn-glycerol-1-tetraethylene glycol-d,l-alpha-lipoic acid ester (DPTL), which bears a fully deuterated tetra(ethylene glycol) spacer group. Through linking of functionalized components, an analogue of DPTL possessing an octa(ethylene glycol) spacer group was prepared, both in deuterated and unlabeled form.

  5. BODIPY-based fluorescent thermometer as a lysosome-targetable probe: how the oligo(ethylene glycols) compete photoinduced electron transfer.

    PubMed

    Wang, Hua; Wu, Yongquan; Shi, Yanlin; Tao, Pan; Fan, Xing; Su, Xinyan; Kuang, Gui-Chao

    2015-02-16

    A novel BODIPY-based fluorescent thermometer, which shows a lysosome-targeting property, was successfully prepared. Due to the electron-donating ability of the oligo(ethylene glycols), the photoinduced electron-transfer pathway from morpholine to BODIPY dye is blocked. The fluorescence of the thermometer quenched by intramolecular rotation at room temperature was progressively enhanced during heating due to the increased microviscosity around the fluorophore.

  6. [Correlation of the spermatozoa morphological anomaly with the presence of aneuploidies in its nuclei in the patients with astheno-, oligo- and teratozoospermia].

    PubMed

    Fes'kov, A M; Zhilkova, E S; Bezpechnaia, I M; Somova, E V; Fes'kov, V A

    2013-01-01

    Examination of the numerous anomalies of the chromosomes 13, 18, 21, X, Y was carried out using FISH method before the IVF attempt in the patients with astheno-, oligo- and teratozoospermia. The percentage of aneuploid spermatozoa was magnificently higher (p < 0.05) in patients with oligozoospermia comparing with the ones with astheno- and teratozoospermia. There is a significant difference in content of spermatozoa with cytoplasmic drop depending on the FISH result.

  7. Oligo(ethylene glycol)-incorporated hybrid linear alkyl side chains for n-channel polymer semiconductors and their effect on the thin-film crystalline structure.

    PubMed

    Kim, Ran; Kang, Boseok; Sin, Dong Hun; Choi, Hyun Ho; Kwon, Soon-Ki; Kim, Yun-Hi; Cho, Kilwon

    2015-01-28

    Oligo(ethylene glycol)-incorporated hybrid linear alkyl side chains, serving as solubilizing groups, are designed and introduced into naphthalene-diimide-based n-channel copolymers. The synthesized polymers exhibit unipolar n-type operation with an electron mobility of up to 1.64 cm(2) V(-1) s(-1), which demonstrates the usefulness of the hybrid side chains in polymer electronics applications.

  8. An International Bioinformatics Infrastructure to Underpin the Arabidopsis Community

    USDA-ARS?s Scientific Manuscript database

    The future bioinformatics needs of the Arabidopsis community as well as those of other scientific communities that depend on Arabidopsis resources were discussed at a pair of recent meetings held by the Multinational Arabidopsis Steering Committee (MASC) and the North American Arabidopsis Steering C...

  9. Using "Arabidopsis" Genetic Sequences to Teach Bioinformatics

    ERIC Educational Resources Information Center

    Zhang, Xiaorong

    2009-01-01

    This article describes a new approach to teaching bioinformatics using "Arabidopsis" genetic sequences. Several open-ended and inquiry-based laboratory exercises have been designed to help students grasp key concepts and gain practical skills in bioinformatics, using "Arabidopsis" leucine-rich repeat receptor-like kinase (LRR…

  10. Using "Arabidopsis" Genetic Sequences to Teach Bioinformatics

    ERIC Educational Resources Information Center

    Zhang, Xiaorong

    2009-01-01

    This article describes a new approach to teaching bioinformatics using "Arabidopsis" genetic sequences. Several open-ended and inquiry-based laboratory exercises have been designed to help students grasp key concepts and gain practical skills in bioinformatics, using "Arabidopsis" leucine-rich repeat receptor-like kinase (LRR…

  11. The Human OligoGenome Resource: a database of oligonucleotide capture probes for resequencing target regions across the human genome.

    PubMed

    Newburger, Daniel E; Natsoulis, Georges; Grimes, Sue; Bell, John M; Davis, Ronald W; Batzoglou, Serafim; Ji, Hanlee P

    2012-01-01

    Recent exponential growth in the throughput of next-generation DNA sequencing platforms has dramatically spurred the use of accessible and scalable targeted resequencing approaches. This includes candidate region diagnostic resequencing and novel variant validation from whole genome or exome sequencing analysis. We have previously demonstrated that selective genomic circularization is a robust in-solution approach for capturing and resequencing thousands of target human genome loci such as exons and regulatory sequences. To facilitate the design and production of customized capture assays for any given region in the human genome, we developed the Human OligoGenome Resource (http://oligogenome.stanford.edu/). This online database contains over 21 million capture oligonucleotide sequences. It enables one to create customized and highly multiplexed resequencing assays of target regions across the human genome and is not restricted to coding regions. In total, this resource provides 92.1% in silico coverage of the human genome. The online server allows researchers to download a complete repository of oligonucleotide probes and design customized capture assays to target multiple regions throughout the human genome. The website has query tools for selecting and evaluating capture oligonucleotides from specified genomic regions.

  12. Synthesis of amphiphilic alternating polyesters with oligo(ethylene glycol) side chains and potential use for sustained release drug delivery.

    PubMed

    Wang, Wei; Ding, Jianxun; Xiao, Chunsheng; Tang, Zhaohui; Li, Di; Chen, Jie; Zhuang, Xiuli; Chen, Xuesi

    2011-07-11

    Novel amphiphilic alternating polyesters, poly((N-phthaloyl-l-glutamic anhydride)-co-(2-(2-(2-methoxyethoxy)ethoxy)methyl)oxirane) (P(PGA-co-ME(2)MO)), were synthesized by alternating copolymerization of PGA and ME(2)MO. The structures of the synthesized polyesters were characterized by (1)H NMR, (13)C NMR, FT-IR, and GPC analyses. Because of the presence of oligo(ethylene glycol) (OEG) side chains, the polyesters could self-assemble into thermosensitive micelles. Dynamic light scattering (DLS) showed that these micelles underwent thermoinduced size decrease without intermicellar aggregation. In vitro methyl thiazolyl tetrazolium (MTT) assay demonstrated that the polyesters were biocompatible to Henrietta Lacks (HeLa) cells, rendering their potential for drug delivery applications. Two hydrophobic drugs, rifampin and doxorubicin (DOX), were loaded into the polyester micelles and observed to be released in a zero-order sustained manner. The sustained release could be accelerated in lower pH or in the presence of proteinase K, due to the degradation of the polyester under these conditions. Remarkably, in vitro cell experiments showed that the polyester micelles accomplished fast release of DOX inside cells and higher anticancer efficacy as compared with the free DOX. With enhanced stability during circulation condition and accelerated drug release at the target sites (e.g., low pH or enzyme presence), these novel polyesters with amphiphilic structures are promising to be used in sustained release drug delivery systems.

  13. Incorporation of phosphate group modulates bone cell attachment and differentiation on oligo(polyethylene glycol) fumarate hydrogel

    PubMed Central

    Dadsetan, Mahrokh; Giuliani, Melissa; Wanivenhaus, Florian; Runge, M. Brett; Charlesworth, Jon E.; Yaszemski, Michael J.

    2014-01-01

    In this work, we have investigated the development of a synthetic hydrogel that contains a negatively charged phosphate group for use as a substrate for bone cell attachment and differentiation in culture. The photoreactive, phosphate-containing molecule, bis(2-(methacryloyloxy)ethyl)phosphate (BP), was incorporated into oligo(polyethylene glycol) fumarate hydrogel and the mechanical, rheological and thermal properties of the resulting hydrogels were characterized. Our results showed changes in hydrogel compression and storage moduli with incorporation of BP. The modification also resulted in decreased crystallinity as recorded by differential scanning calorimetry. Our data revealed that incorporation of BP improved attachment and differentiation of human fetal osteoblast (hFOB) cells in a dose-dependent manner. A change in surface chemistry and mineralization of the phosphate-containing surfaces verified by scanning electron microscopy and energy dispersive X-ray analysis was found to be important for hFOB cell attachment and differentiation. We also demonstrated that phosphate-containing hydrogels support attachment and differentiation of primary bone marrow stromal cells. These findings suggest that BP-modified hydrogels are capable of sustaining attachment and differentiation of both bone marrow stromal cells and osteoblasts that are critical for bone regeneration. PMID:22277774

  14. Ehealth monitoring in irritable bowel syndrome patients treated with low fermentable oligo-, di-, mono-saccharides and polyols diet.

    PubMed

    Pedersen, Natalia; Vegh, Zsuzsanna; Burisch, Johan; Jensen, Lisbeth; Ankersen, Dorit Vedel; Felding, Maria; Andersen, Nynne Nyboe; Munkholm, Pia

    2014-06-07

    In the present study we report on changes in irritable bowel syndrome-severity scoring system (IBS-SSS) and irritable bowel syndrome-quality of life (IBS-QoL) in 19 IBS patients, aged 18 to 74 years (F/M: 14/5), during 12 wk registering their symptoms on the web-application (www.ibs.constant-care.dk). During a control period of the first 6-wk patients were asked to register their IBS-SSS and IBS-QoL on the web-application weekly without receiving any intervention. Thereafter, low fermentable oligo-, di-, mono-saccharides and polyols (FODMAP) diet (LFD) was introduced for the next 6 wk while continuing the registration. Though a small sample size a significant improvement in disease activity (IBS-SSS) was observed during both the control period, median: 278 (range: 122-377), P = 0.02, and subsequently during the LFD period, median: 151 (range: 29-334), P < 0.01. The IBS-QoL solely changed significantly during the LFD period, median: 67 (37-120), P < 0.01. The significant reduction in disease activity during the control period shows a positive effect of the web-application on IBS symptoms when presented as a "traffic light". However adding the diet reduced IBS-SSS to < 150, inactive to mild symptoms. In the future results from larger scale trials are awaited.

  15. Poly(oligo(ethylene glycol) methyl ether methacrylate) Brushes on High-κ Metal Oxide Dielectric Surfaces for Bioelectrical Environments.

    PubMed

    Joh, Daniel Y; McGuire, Felicia; Abedini-Nassab, Roozbeh; Andrews, Joseph B; Achar, Rohan K; Zimmers, Zackary; Mozhdehi, Darush; Blair, Rebecca; Albarghouthi, Faris; Oles, William; Richter, Jacob; Fontes, Cassio M; Hucknall, Angus M; Yellen, Benjamin B; Franklin, Aaron D; Chilkoti, Ashutosh

    2017-02-15

    Advances in electronics and life sciences have generated interest in "lab-on-a-chip" systems utilizing complementary metal oxide semiconductor (CMOS) circuitry for low-power, portable, and cost-effective biosensing platforms. Here, we present a simple and reliable approach for coating "high-κ" metal oxide dielectric materials with "non-fouling" (protein- and cell-resistant) poly(oligo(ethylene glycol) methyl ether methacrylate (POEGMA) polymer brushes as biointerfacial coatings to improve their relevance for biosensing applications utilizing advanced electronic components. By using a surface-initiated "grafting from" strategy, POEGMA films were reliably grown on each material, as confirmed by ellipsometric measurements and X-ray photoelectron spectroscopy (XPS) analysis. The electrical behavior of these POEGMA films was also studied to determine the potential impact on surrounding electronic devices, yielding information on relative permittivity and breakdown field for POEGMA in both dry and hydrated states. We show that the incorporation of POEGMA coatings significantly reduced levels of nonspecific protein adsorption compared to uncoated high-κ dielectric oxide surfaces as shown by protein resistance assays. These attributes, combined with the robust dielectric properties of POEGMA brushes on high-κ surfaces open the way to incorporate this protein and cell resistant polymer interface into CMOS devices for biomolecular detection in a complex liquid milieu.

  16. Synthesis and application of monodisperse oligo(oxyethylene)-grafted polystyrene resins for solid-phase organic synthesis.

    PubMed

    Lumpi, Daniel; Braunshier, Christian; Horkel, Ernst; Hametner, Christian; Fröhlich, Johannes

    2014-07-14

    In a preliminary investigation by our group, we found that poly(styrene-oxyethylene) graft copolymers (PS-PEG), for example, TentaGel resins, are advantageous for gel-phase (13)C NMR spectroscopy. Because of the solution-like environment provided by the PS-PEG resins, good spectral quality of the attached moiety can be achieved, which is useful for nondestructive on-resin analysis. The general drawbacks of such resins are low loading capacities and the intense signal in the spectra resulting from the PEG linker (>50 units). Here, we describe the characterization of solvent-dependent swelling and reaction kinetics on a new type of resin for solid-phase organic synthesis (SPOS) that allows an accurate monitoring by gel-phase NMR without the above disadvantages. A series of polystyrene-oligo(oxyethylene) graft copolymers containing monodisperse PEG units (n = 2-12) was synthesized. A strong correlation between the linker (PEG) length and the line widths in the (13)C gel-phase spectra was observed, with a grafted PEG chain of 8 units giving similar results in terms of reactivity and gel-phase NMR monitoring to TentaGel resin. Multistep on-resin reaction sequences were performed to prove the applicability of the resins in solid-phase organic synthesis.

  17. An enhanced adsorption in puerarin retention on oligo-beta-cyclodextrin grafted poly(glycidyl methacrylate) media.

    PubMed

    Yang, Li; Tan, Tianwei

    2010-01-01

    The poly(glycidyl methacrylate) adsorbents P(GMA-EDMA) and P(GMA-DVB) were synthesized by the radical suspension-polymerization method and farther coupled by oligo-beta-cyclodextrin (CDP) to obtain P(GMA-EDMA)-CDP and P(GMA-DVB)-CDP. The synthesized polymeric media were characterized by Fourier transform infrared (FTIR) spectrometer, scanning electron microscopy, and BET surface area. The adsorption of puerarin from aqueous solution onto the four media, i.e., P(GMA-EDMA), P(GMA-DVB), P(GMA-EDMA)-CDP, and P(GMA-DVB)-CDP, was studied. An enhanced adsorption of puerarin apparently presented on grafted media. The interaction between the polymeric media and the puerarin was researched by FTIR. The result shows that the adsorption efficiency on P(GMA-DVB)-CDP driven by multiple weak interactions is much higher than that on P(GMA-EDMA) driven by hydrogen bonding interaction only and on P(GMA-DVB) or P(GMA-EDMA)-CDP driven by two interactions.

  18. Interfacial tension analysis of oligo(ethylene glycol)-terminated self-assembled monolayers and their resistance to bacterial attachment.

    PubMed

    Ista, Linnea K; López, Gabriel P

    2012-09-04

    The fouling resistance of oligo(ethylene glycol) (OEG)-terminated self-assembled monolayers (SAMs) of alkanethiolates on gold has been well established. Although hydration of the OEG chains seems key to OEG-SAM resistance to macromolecular adsorption and cellular attachment, the details of how hydration prevents biofouling have been inferred largely through computational methods. Because OEG-SAMs of different lengths exhibit differing degrees of fouling resistance, the interactions between water and OEG-SAMs leading to fouling resistance can be deduced by comparing the properties of fouling and nonfouling OEG-SAMs. While all OEG-SAMs had similar water contact angles, contact angles taken with glycerol were able to individuate between different OEG-SAMs and between fouling and nonfouling OEG-SAMs. Subsequent estimation of surface and interfacial tension using a colloidal model showed that nonfouling surfaces are associated with an increased negative interfacial tension between those OEG-SAMs that resisted attachment and water. Further analysis of this interfacial tension experimentally confirmed current mathematical models that cite OEG-water hydrogen-bond formation as a driving force behind short-term fouling resistance. Finally, we found a correlation between solid-water interfacial tension and packing density and molecular density of ethylene glycol.

  19. Incorporation of phosphate group modulates bone cell attachment and differentiation on oligo(polyethylene glycol) fumarate hydrogel.

    PubMed

    Dadsetan, Mahrokh; Giuliani, Melissa; Wanivenhaus, Florian; Brett Runge, M; Charlesworth, Jon E; Yaszemski, Michael J

    2012-04-01

    In this work, we have investigated the development of a synthetic hydrogel that contains a negatively charged phosphate group for use as a substrate for bone cell attachment and differentiation in culture. The photoreactive, phosphate-containing molecule, bis(2-(methacryloyloxy)ethyl)phosphate (BP), was incorporated into oligo(polyethylene glycol) fumarate hydrogel and the mechanical, rheological and thermal properties of the resulting hydrogels were characterized. Our results showed changes in hydrogel compression and storage moduli with incorporation of BP. The modification also resulted in decreased crystallinity as recorded by differential scanning calorimetry. Our data revealed that incorporation of BP improved attachment and differentiation of human fetal osteoblast (hFOB) cells in a dose-dependent manner. A change in surface chemistry and mineralization of the phosphate-containing surfaces verified by scanning electron microscopy and energy dispersive X-ray analysis was found to be important for hFOB cell attachment and differentiation. We also demonstrated that phosphate-containing hydrogels support attachment and differentiation of primary bone marrow stromal cells. These findings suggest that BP-modified hydrogels are capable of sustaining attachment and differentiation of both bone marrow stromal cells and osteoblasts that are critical for bone regeneration. Copyright © 2012. Published by Elsevier Ltd.

  20. Modification of fluorous substrates with oligo(ethylene glycol) via "click" chemistry for long-term resistance of cell adhesion.

    PubMed

    Contreras-Caceres, Rafael; Santos, Catherine M; Li, Siheng; Kumar, Amit; Zhu, Zhiling; Kolar, Satya S; Casado-Rodriguez, Miguel A; Huang, Yongkai; McDermott, Alison; Lopez-Romero, Juan Manuel; Cai, Chengzhi

    2015-11-15

    In this work perfluorinated substrates fabricated from SiO2 glass slides are modified with oligo(ethylene glycol) (OEG) units for long-term resistance of cell adhesion purposes, based on fluorous interactions and click chemistry. Specifically, fluorous substrates, prepared by treatment of glass slides with 1H, 1H, 2H, 2H-perfluorodecyltrimethoxysilane (FAS17), were coated with ethynyl-OEG-C8F17, followed by covalent attachment of an azido-OEG via copper-catalyzed azide-alkyne cycloaddition (CuAAC) "click" reaction. We demonstrate that the resultant surface avoid fibrinogen adsorption and resisted cell adhesion for over 14days. X-ray photoemission spectroscopy (XPS) analysis and contact angle goniometry measurements confirm the presence of the OEG molecules on the fluorous substrates. Bright field optical images show total absence of 3T3 fibroblast cells on the OEG modified fluorinated substrate for 1 and 5days, and a remarkably decrease of cell adhesion at 14days.

  1. Sugar-coated proteins: the importance of degree of polymerisation of oligo-galacturonic acid on protein binding and aggregation.

    PubMed

    Xu, Amy Y; Melton, Laurence D; Ryan, Timothy M; Mata, Jitendra P; Jameson, Geoffrey B; Rekas, Agata; Williams, Martin A K; McGillivray, Duncan J

    2017-04-05

    We have simplified the structural heterogeneity of protein-polysaccharide binding by investigating protein binding to oligosaccharides. The interactions between bovine beta-lactoglobulin A (βLgA) and oligo-galacturonic acids (OGAs) with various numbers of sugar residues have been investigated with a range of biophysical techniques. We show that the βLgA-OGA interaction is critically dependent on the length of the oligosaccharide. Isothermal titration calorimetry results suggest that a minimum length of 7 or 8 sugar residues is required in order to exhibit appreciable exothermic interactions with βLgA - shorter oligosaccharides show no enthalpic interactions at any concentration ratio. When titrating βLgA into OGAs with more than 7-8 sugar residues the sample solution also became turbid with increasing amounts of βLgA, indicating the formation of macroscopic assemblies. Circular dichroism, thioflavin T fluorescence and small angle X-ray/neutron scattering experiments revealed two structural regimes during the titration. When OGAs were in excess, βLgA formed discrete assemblies upon OGA binding, and no subsequent aggregation was observed. However, when βLgA was present in excess, multi-scale structures were formed and this eventually led to the separation of the solution into two liquid-phases.

  2. Biodegradable pH/temperature-sensitive oligo(β-amino ester urethane) hydrogels for controlled release of doxorubicin.

    PubMed

    Huynh, Cong Truc; Nguyen, Minh Khanh; Lee, Doo Sung

    2011-08-01

    An injectable biodegradable pH/temperature-sensitive oligo(β-amino ester urethane) (OAEU) was synthesized. The OAEU was synthesized by addition polymerization between the isocyanate groups of 1,6-diisocyanato hexamethylene and the hydroxyl groups of a synthesized monomer piperazine dihydroxyl amino ester (monomer PDE) in chloroform in the presence of dibutyltin dilaurate as a catalyst. The synthesized OAEU was characterized by (1)H NMR spectroscopy, Fourier transform infrared spectroscopy and gel permeation chromatography. The aqueous solutions of OAEU showed a sol-to-gel-to-sol phase transition as a function of temperature and pH. The gel window covered the physiological conditions (37°C, pH 7.4) and could be controlled by changing the OAEU concentration. After a subcutaneous injection of the OAEU solution into Sprague-Dawley rats, a gel formed rapidly in situ and remained in the body for more than 2 weeks. The in vitro cytotoxicity test and in vitro degradation showed that the OAEU hydrogel was non-cytotoxic and biodegradable. The in vitro release of doxorubicin from this OAEU hydrogel was sustained for more than 10 days. This injectable biodegradable pH/temperature-sensitive OAEU hydrogel is a potential candidate as a drug/protein carrier and in biomedical applications.

  3. Poorly differentiated and anaplastic thyroid carcinomas: chromosomal and oligo-array profile of five new cell lines.

    PubMed

    Rodrigues, R F; Roque, L; Krug, T; Leite, V

    2007-04-23

    Information on gene alterations associated to poorly differentiated (PDTC) and anaplastic thyroid carcinomas (ATC) is scarce. Using human cancer cell lines as a tool for gene discovery, we performed a cytogenetic and oligo-array analysis in five new cell lines derived from two PDTC and three ATC. In PDTC we evidenced, as important, the involvement of the MAPK/ERK kinase pathway, and downregulation of a group of suppressor genes that include E-cadherin. In ATC, downregulation of a specific group of oncosuppressor genes was also observed. Our ATC cell lines presented chromosomal markers of gene amplification, and we were able to identify for the first time the nature of the involved amplicon target genes. We found that the main molecular differences between the two cell line types were related to signal transduction pathways, cell adhesion and motility process. TaqMan experiments performed for five amplicon target genes and for two genes, which allowed a clear distinction between ATC and PDTC: CDH13 and PLAU corroborated array results, not only in the cell lines, but also in an additional set of primary 14 PDTC and three ATC. We suggest that our findings may represent new tools for the development of more effective therapies to the hitherto untreatable ATC.

  4. Ehealth monitoring in irritable bowel syndrome patients treated with low fermentable oligo-, di-, mono-saccharides and polyols diet

    PubMed Central

    Pedersen, Natalia; Vegh, Zsuzsanna; Burisch, Johan; Jensen, Lisbeth; Ankersen, Dorit Vedel; Felding, Maria; Andersen, Nynne Nyboe; Munkholm, Pia

    2014-01-01

    In the present study we report on changes in irritable bowel syndrome-severity scoring system (IBS-SSS) and irritable bowel syndrome-quality of life (IBS-QoL) in 19 IBS patients, aged 18 to 74 years (F/M: 14/5), during 12 wk registering their symptoms on the web-application (www.ibs.constant-care.dk). During a control period of the first 6-wk patients were asked to register their IBS-SSS and IBS-QoL on the web-application weekly without receiving any intervention. Thereafter, low fermentable oligo-, di-, mono-saccharides and polyols (FODMAP) diet (LFD) was introduced for the next 6 wk while continuing the registration. Though a small sample size a significant improvement in disease activity (IBS-SSS) was observed during both the control period, median: 278 (range: 122-377), P = 0.02, and subsequently during the LFD period, median: 151 (range: 29-334), P < 0.01. The IBS-QoL solely changed significantly during the LFD period, median: 67 (37-120), P < 0.01. The significant reduction in disease activity during the control period shows a positive effect of the web-application on IBS symptoms when presented as a “traffic light”. However adding the diet reduced IBS-SSS to < 150, inactive to mild symptoms. In the future results from larger scale trials are awaited. PMID:24914395

  5. Electronic transport in oligo-para-phenylene junctions attached to carbon nanotube electrodes: Transition-voltage spectroscopy and chirality

    SciTech Connect

    Brito Silva, C. A. Jr.; Silva, S. J. S. da; Leal, J. F. P.; Pinheiro, F. A.; Del Nero, J.

    2011-06-15

    We have investigated, by means of a nonequilibrium Green's function method coupled to density functional theory, the electronic transport properties of molecular junctions composed of oligo-para-phenylene (with two, three, four, and five phenyl rings) covalently bridging the gap between metallic carbon nanotubes electrodes. We have found that the current is strongly correlated to a purely geometrical chiral parameter, both on-resonance and off-resonance. The Fowler-Nordheim plot exhibits minima, V{sub min}, that occur whenever the tail of a resonant transmission peak enters in the bias window. This result corroborates the scenario in which the coherent transport model gives the correct interpretation to transition voltage spectroscopy (TVS). We have shown that V{sub min} corresponds to voltages where a negative differential resistance (NDR) occurs. The finding that V{sub min} corresponds to voltages that exhibit NDR, which can be explained only in single-molecule junctions within the coherent transport model, further confirms the applicability of such models to adequately interpret TVS. The fact that the electrodes are organic is at the origin of differences in the behavior of V{sub min} if compared to the case of molecular junctions with nonorganic contacts treated so far.

  6. Synthesis, characterization, conformation and self-assembly behavior of polypeptide-based brush with oligo (ethylene glycol) side chains

    NASA Astrophysics Data System (ADS)

    Huang, Yugang; Luo, Weiang; Ye, Guodong

    2015-02-01

    A new polypeptide-based copolymer brush composed of poly (γ-propargyl-L-glutamate)-block-poly (propylene oxide)-block-poly (γ-propargyl-L-glutamate) backbone (PPLG-b-PPO-b-PPLG) and oligo (ethylene glycol) (PEG) side-chain was synthesized by combination of N-carboxyanhydride ring-opening polymerization and click chemistry. Nearly 100% grafting efficiency was achieved by copper-catalyzed azide-alkyne Huisgen 1,3-dipolar cycloaddition (CuAAc) reaction. The α-helical conformation adopted by the grafted polypeptide blocks in water was relatively stable and showed a reversible change in a heating-cooling circle from 5 to 70 °C. It displayed weak stability against elevated temperature but still reversible changes in the presence of 0.47 M NaCl. The brushes were amphiphilic and could self-assemble into thermo-sensitive micelles in water. Big micelles could break into small micelles upon heating due to the improved solubility.

  7. Charge separation in a covalently-linked phthalocyanine-oligo(p-phenylenevinylene)-C60 system. Influence of the solvent polarity.

    PubMed

    Cid, Juan-José; Kahnt, Axel; Vázquez, Purificación; Guldi, Dirk M; Torres, Tomás

    2012-03-01

    A photo- and redoxactive system ZnPc-oPPV-C(60)2, in which the photoexcited state electron donor - zinc phthalocyanine - and the ground state electron acceptor - C(60) - are connected by a oligo(p-phenylenevinylene) (oPPV) spacer, has been synthesized in a multi-step synthesis by means of two consecutive Wadsworth-Horner-Emmons and a dipolar 1,3-cycloaddition reactions as key steps. The simpler system ZnPc-C(60)1 has also been prepared as a reference model for photophysical studies. In this regards, the photophysical investigations by means of fluorescence, flash photolysis, and transient-absorption spectroscopy have manifested a clear dependence between charge transfer kinetics and spatial arrangement. In both systems, intramolecular charge separation evolves from the photoexcited ZnPc and yields the ZnPc(·+)/C(60)(·-) radical ion pairs. Interestingly, the ZnPc(·+)/C(60)(·-) radical ion pair lifetimes and quantum yields are strongly impacted by the solvent polarity and the distance. To this end, maximum radical ion pair lifetimes of 2900 and 5530 ps were found in anisol for 1 and 2, respectively.

  8. Reversible protein adsorption and bioadhesion on monolayers terminated with mixtures of oligo(ethylene glycol) and methyl groups.

    PubMed

    Balamurugan, Subramanian; Ista, Linnea K; Yan, Juchao; López, Gabriel P; Fick, Jörg; Himmelhaus, Michael; Grunze, Michael

    2005-10-26

    Surface-grafted, environmentally responsive polymers have shown great promise for controlling adsorption and desorption of macromolecules and cells on solid surfaces. In the paper, we demonstrate that certain mixed self-assembled monolayers (SAMs) of oligo(ethylene glycol) (OEG) and methyl-terminated alkanethiolates on gold form surfaces with switchable hydrophobicity and tendency for protein adsorption and cellular attachment. At temperatures above 32 degrees C, SAMs with a surface density of approximately 50% OEG adsorbed significant amounts of pyruvate kinase and lysozyme, whereas below this temperature, these same SAMs were resistant to the adsorption of these proteins. Furthermore, protein layers adsorbed to these SAMs above 32 degrees C were removed upon rinsing with water below this temperature. Similar results were seen for attachment and release of the marine bacterium, Cobetia marina. The change from nonresistance to adsorptive state of the SAMs was concomitant with a change in advancing water contact angle. Vibrational sum frequency generation spectroscopy suggests that the temperature-induced changes coincide with a disorder-to-partial order transition of the hydrated methylene chains of the OEG moieties within the SAMs. Mixed OEG-methyl SAMs represent both a convenient means of controlling macromolecular and cellular adsorption within the laboratory and a useful tool for relating adsorption properties to molecular structures within the SAMs.

  9. Protein-resistant polyurethane via surface-initiated atom transfer radical polymerization of oligo(ethylene glycol) methacrylate.

    PubMed

    Jin, Zhilin; Feng, Wei; Zhu, Shiping; Sheardown, Heather; Brash, John L

    2009-12-15

    Protein-resistant polyurethane (PU) surfaces were prepared by surface-initiated simultaneous normal and reverse atom transfer radical polymerization (s-ATRP) of poly(oligo(ethylene glycol) methacrylate) (poly (OEGMA)). Oxygen plasma treatment was employed for initial activation of the PU surface. The grafted polymer chain length was adjusted by varying the molar ratio of monomer to sacrificial initiator in solution from 5:1 to 200:1. The modified PU surfaces were characterized by water contact angle, X-ray photoelectron spectroscopy (XPS), and atomic force microscopy (AFM). Protein adsorption experiments from tris-buffered saline (TBS) and plasma were carried out to evaluate the protein-resistance of the surfaces. Adsorption from single and binary protein solutions as well as from plasma was significantly reduced after modification. Adsorption decreased with increasing poly(OEGMA) chain length. Fibrinogen (Fg) adsorption on the 200:1 monomer/initiator surface was in the range of 3-33 ng/cm(2) representing 96-99% reduction compared with the unmodified PU. Fg adsorption from 0.01-10% plasma was as low as 1-5 ng/cm(2). Moreover, binary protein adsorption experiments using Fg and lysozyme (Lys) showed that protein size is a factor in the protein resistance of these surfaces.

  10. Coexistence of macroprolactinaemia and hyperprolactinaemia in women with oligo-/amenorrhoea is associated with high risk of pituitary adenomas.

    PubMed

    Lewandowski, Krzysztof C; Gasior-Perczak, Danuta; Kowalska, Aldona; Lewinski, Andrzej

    2014-05-01

    Macroprolactin may cause elevation of prolactin (PRL) concentrations measured by standard assays. In our study, we assessed the prevalence of pituitary lesions in women with macroprolactinaemia and either oligomenorrhoea or secondary amenorrhoea. Pituitary MRI scans were performed in 61 women aged 31.0  ±  6.7 years (mean  ±  SD), with raised PRL concentrations due to macroprolactinaemia, detected by 25% polyethylene glycol (PEG) precipitation method (PRL recovery <40%). After PEG precipitation of macroprolactin, free PRL concentrations were still raised in 36 (59%) women. Microadenomas were detected in 10 patients out of 61 (16.4%), with raised free PRL in 9 of these cases, while macroadenomas were detected in 4 out of 61 (6.6%) women, all of whom also had raised free PRL. In case of coexistence of macroprolactinaemia and raised free PRL after PEG precipitation of macroprolactin, the chance of finding of either a micro- or a macroadenoma was 36% (13 cases out of 36). We conclude that hyperprolactinaemia and macroprolactinaemia may coexist in the same patient. Furthermore, if free PRL is raised after PEG precipitation of macroprolactin, then the chance of finding either a pituitary micro- or macroadenoma in women with oligo-/amenorrhoea is over 30%. Therefore pituitary magnetic resonance imaging is mandatory in all such cases.

  11. Carbon-bridged oligo(p-phenylenevinylene)s for photostable and broadly tunable, solution-processable thin film organic lasers

    PubMed Central

    Morales-Vidal, Marta; Boj, Pedro G.; Villalvilla, José M.; Quintana, José A.; Yan, Qifan; Lin, Nai-Ti; Zhu, Xiaozhang; Ruangsupapichat, Nopporn; Casado, Juan; Tsuji, Hayato; Nakamura, Eiichi; Díaz-García, María A.

    2015-01-01

    Thin film organic lasers represent a new generation of inexpensive, mechanically flexible devices for spectroscopy, optical communications and sensing. For this purpose, it is desired to develop highly efficient, stable, wavelength-tunable and solution-processable organic laser materials. Here we report that carbon-bridged oligo(p-phenylenevinylene)s serve as optimal materials combining all these properties simultaneously at the level required for applications by demonstrating amplified spontaneous emission and distributed feedback laser devices. A series of six compounds, with the repeating unit from 1 to 6, doped into polystyrene films undergo amplified spontaneous emission from 385 to 585 nm with remarkably low threshold and high net gain coefficients, as well as high photostability. The fabricated lasers show narrow linewidth (<0.13 nm) single mode emission at very low thresholds (0.7 kW cm−2), long operational lifetimes (>105 pump pulses for oligomers with three to six repeating units) and wavelength tunability across the visible spectrum (408–591 nm). PMID:26416643

  12. Cytokine induction by a linear 1,3-glucan, curdlan-oligo, in mouse leukocytes in vitro.

    PubMed

    Hida, T H; Ishibashi, K; Miura, N N; Adachi, Y; Shirasu, Y; Ohno, N

    2009-01-01

    Curdlan, an extracellular bacterial polysaccharide, is a linear beta-1,3-glucan. Previously, we developed Curdlan-oligo (CRDO). We investigated its effect on the production of cytokines in leukocytes from mice, and compared its activity with that of SCG, a 6-branched 1,3-beta-glucan. Splenocytes from DBA/2 mice were cultured with CRDO or SCG (0, 1, 10 or 100 microg/ml) in vitro, and then the supernatants were collected to measure cytokines. Bone marrow-derived dendritic cells (BMDCs) were cultured with CRDO (0, 1, 10 or 100 ng/ml) in vitro, and then the supernatant was collected to measure cytokines. SCG stimulated splenocytes in DBA/2 mice to produce GM-CSF, IFN-gamma and TNF-alpha. CRDO induced production of GM-CSF and IFN-gamma, but not TNF-alpha. The amounts of GM-CSF and IFN-gamma were small compared with those produced in response to SCG. The effect of SCG on TNF-alpha production was partially inhibited by CRDO. In bone marrow-derived dendritic cells, CRDO induced production of TNF-alpha and IL-6. Taken together, these results suggest that CRDO stimulated mouse leukocytes to induce the production of cytokines, and the mechanism of the effect of CRDO on leukocytes is different from that of SCG.

  13. Carbon-bridged oligo(p-phenylenevinylene)s for photostable and broadly tunable, solution-processable thin film organic lasers

    NASA Astrophysics Data System (ADS)

    Morales-Vidal, Marta; Boj, Pedro G.; Villalvilla, José M.; Quintana, José A.; Yan, Qifan; Lin, Nai-Ti; Zhu, Xiaozhang; Ruangsupapichat, Nopporn; Casado, Juan; Tsuji, Hayato; Nakamura, Eiichi; Díaz-García, María A.

    2015-09-01

    Thin film organic lasers represent a new generation of inexpensive, mechanically flexible devices for spectroscopy, optical communications and sensing. For this purpose, it is desired to develop highly efficient, stable, wavelength-tunable and solution-processable organic laser materials. Here we report that carbon-bridged oligo(p-phenylenevinylene)s serve as optimal materials combining all these properties simultaneously at the level required for applications by demonstrating amplified spontaneous emission and distributed feedback laser devices. A series of six compounds, with the repeating unit from 1 to 6, doped into polystyrene films undergo amplified spontaneous emission from 385 to 585 nm with remarkably low threshold and high net gain coefficients, as well as high photostability. The fabricated lasers show narrow linewidth (<0.13 nm) single mode emission at very low thresholds (0.7 kW cm-2), long operational lifetimes (>105 pump pulses for oligomers with three to six repeating units) and wavelength tunability across the visible spectrum (408-591 nm).

  14. Langmuir-Blodgett films incorporating molecular wire candidates of ester-substituted oligo(phenylene-ethynylene) derivatives

    NASA Astrophysics Data System (ADS)

    Villares, Ana; Lydon, Donocadh P.; Robinson, Benjamin J.; Ashwell, Geoffrey J.; Royo, Félix M.; Low, Paul J.; Cea, Pilar

    2008-12-01

    Langmuir and Langmuir-Blodgett (LB) films of two "wire-like" oligo(phenylene-ethynylene) methyl ester derivatives, namely methyl-4-[(4″-(nonyloxyphenylethynyl)-4'-(phenylethynyl)]-benzoate and methyl-4-[(4″-hexadecyloxyphenylethynyl)-4'-(phenylethynyl]-benzoate (abbreviated as C9BPEB and C16BPEB), have been prepared and characterized. Surface pressure isotherms for both materials have been obtained, with C9BPEB showing more expanded monolayers. An analysis of the reflection spectra of monolayer films at the air-water interface suggests the formation of H-aggregates, and supports an organizational model in which tilt angles of C16BPEB and C9BPEB molecules with respect to the water surface are approximately 70° and 60°, respectively. The sequential transfer of monolayers of these BPEB ester derivatives onto solid substrates results in a Z-type deposition in the case of C9BPEB and Y-type for C16BPEB. The current-voltage ( I- V) characteristics of LB monolayers are relatively symmetrical for both films, with the asymmetric contacts more evident in the I- V C16BPEB characteristics.

  15. Suicide gene therapy using reducible poly (oligo-D-arginine) for the treatment of spinal cord tumors.

    PubMed

    Won, Young-Wook; Kim, Kyung-Min; An, Sung Su; Lee, Minhyung; Ha, Yoon; Kim, Yong-Hee

    2011-12-01

    Suicide gene therapy based on a combination of herpes simplex virus-thymidine kinase (HSV-tk) and ganciclovir (GCV) has obstacles to achieving a success in clinical use for the treatment of cancer due to inadequate thymidine kinase (TK) expression. The primary concern for improving anticancer efficacy of the suicide gene therapy is to develop an appropriate carrier that highly expresses TK in vivo. Despite great advances in the development of non-viral vectors, none has been used in cancer suicide gene therapy, not even in experimental challenge. Reducible poly (oligo-D-arginine) (rPOA), one of the effective non-viral carriers working in vivo, was chosen to deliver HSV-tk to spinal cord tumors which are appropriate targets for suicide gene therapy. Since the system exerts toxicity only in dividing cells, cells in the central nervous system, which are non-proliferative, are not sensitive to the toxic metabolites. In the present study, we demonstrated that the locomotor function of the model rat was maintained through the tumor suppression resulting from the tumor-selective suicide activity by co-administration of rPOA/HSV-tk and GCV. Thus, rPOA plays a crucial role in suicide gene therapy for cancer, and an rPOA/HSV-tk and GCV system could help promote in vivo trials of suicide gene therapy.

  16. Photochemistry of "end-only" oligo-p-phenylene ethynylenes: complexation with sodium dodecyl sulfate reduces solvent accessibility.

    PubMed

    Hill, Eric H; Evans, Deborah G; Whitten, David G

    2013-08-06

    Cationic oligo-p-phenylene ethynylenes are very effective light-activated biocides and biosensors but degrade upon exposure to light. In this study, we explore the photochemistry of a class of "end-only" compounds from this series, which have cationic moieties on the ends of the backbone. Product characterization by mass spectrometry reveals that the photoreactivity of these molecules is higher than that of a previously studied oligomer and that the primary products of photolysis result from the addition of water or oxygen across the triple bond. In addition, a product suggesting the addition of peroxide or other reactive oxygen species across the triple bond was observed. To explore avenues by which the photodegradation of these compounds can be mitigated, the effects of complexation with sodium dodecyl sulfate micelles on their photochemistry was explored. Classical molecular dynamics simulations revealed that compounds that were protected from photolysis by SDS buried their phenylene ethynylene backbones into the interior of the micelle, protecting it from contact with water. This work has revealed a molecular basis for the protection of a novel class of light-activated biocides from irradiation that is consistent with the proposed photochemistry of these compounds. This information can be useful for developing photodegradation-resistant biocidal materials and applications for current compounds and leads to new molecular design.

  17. Efficient synthesis of diverse heterobifunctionalized clickable oligo(ethylene glycol) linkers: potential applications in bioconjugation and targeted drug delivery.

    PubMed

    Goswami, Lalit N; Houston, Zachary H; Sarma, Saurav J; Jalisatgi, Satish S; Hawthorne, M Frederick

    2013-02-21

    Herein we describe the sequential synthesis of a variety of azide-alkyne click chemistry-compatible heterobifunctional oligo(ethylene glycol) (OEG) linkers for bioconjugation chemistry applications. Synthesis of these bioorthogonal linkers was accomplished through desymmetrization of OEGs by conversion of one of the hydroxyl groups to either an alkyne or azido functionality. The remaining distal hydroxyl group on the OEGs was activated by either a 4-nitrophenyl carbonate or a mesylate (-OMs) group. The -OMs functional group served as a useful precursor to form a variety of heterobifunctionalized OEG linkers containing different highly reactive end groups, e.g., iodo, -NH(2), -SH and maleimido, that were orthogonal to the alkyne or azido functional group. Also, the alkyne- and azide-terminated OEGs are useful for generating larger discrete poly(ethylene glycol) (PEG) linkers (e.g., PEG(16) and PEG(24)) by employing a Cu(I)-catalyzed 1,3-dipolar cycloaddition click reaction. The utility of these clickable heterobifunctional OEGs in bioconjugation chemistry was demonstrated by attachment of the integrin (α(v)β(3)) receptor targeting peptide, cyclo-(Arg-Gly-Asp-D-Phe-Lys) (cRGfKD) and to the fluorescent probe sulfo-rhodamine B. The synthetic methodology presented herein is suitable for the large scale production of several novel heterobifunctionalized OEGs from readily available and inexpensive starting materials.

  18. Dynamique des faciès détritiques oligo-miocènes de Tunisie

    NASA Astrophysics Data System (ADS)

    Yaich, C.

    1992-07-01

    The Oligo-Miocene outcrops spread over a large part of Central and Northern Tunisia; from South to North, one can find: 1) the deltaic complex of Fortuna Formation: It consists of a deltaic complex which is basically formed by clayey sandstones with some marine intercalations. This complex progrades from W and S-W to N-E. Vertically it appears as a regressive megasequence which is divided in two large regressive sequences each one having its own deltaic system, the upper one shows a clear progression of the fluvial channels on the sediments of the deltaic plain, all of which progrades on the prodeltaic beds; 2) the Numidian flysch: occurring as a relatively regressive megasequence, the Numidian flysch shows in most of surveyed sections the superposition of a proximal material (inner fan) with undersea channels, grain flow, slumps, flux and proximal turbidites (Ta-e) on a relatively deeper and lobed material with distal turbidites (middle fan). The drifts go to N150-N200 and have a tendency to move from the North southwards; 3) The micaceous sandstones and marly limestones of Galite Island: on this island, the sedimentary series shows a fine sandstone, sometimes coarse with quartz pebbles, very rich in muscovite and feldspath, intercalated within a clayey and carbonate series. From the dynamic point of view it consists of a proximal part of deep sea fan (Inner fan) joined by gritty and carbonate proximal turbidites almost exclusively slump of very changeable sizes.

  19. OligoHeatMap (OHM): an online tool to estimate and display hybridizations of oligonucleotides onto DNA sequences.

    PubMed

    Croce, Olivier; Chevenet, François; Christen, Richard

    2008-07-01

    The efficiency of molecular methods involving DNA/DNA hybridizations depends on the accurate prediction of the melting temperature (T(m)) of the duplex. Many softwares are available for T(m) calculations, but difficulties arise when one wishes to check if a given oligomer (PCR primer or probe) hybridizes well or not on more than a single sequence. Moreover, the presence of mismatches within the duplex is not sufficient to estimate specificity as it does not always significantly decrease the T(m). OHM (OligoHeatMap) is an online tool able to provide estimates of T(m) for a set of oligomers and a set of aligned sequences, not only as text files of complete results but also in a graphical way: T(m) values are translated into colors and displayed as a heat map image, either stand alone or to be used by softwares such as TreeDyn to be included in a phylogenetic tree. OHM is freely available at http://bioinfo.unice.fr/ohm/, with links to the full source code and online help.

  20. Sustained Delivery of Dibutyryl Cyclic Adenosine Monophosphate to the Transected Spinal Cord Via Oligo [(Polyethylene Glycol) Fumarate] Hydrogels

    PubMed Central

    Rooney, Gemma E.; Knight, Andrew M.; Madigan, Nicolas N.; Gross, LouAnn; Chen, BingKun; Giraldo, Catalina Vallejo; Seo, Seungmae; Nesbitt, Jarred J.; Dadsetan, Mahrokh; Yaszemski, Michael J.

    2011-01-01

    This study describes the use of oligo [(polyethylene glycol) fumarate] (OPF) hydrogel scaffolds as vehicles for sustained delivery of dibutyryl cyclic adenosine monophosphate (dbcAMP) to the transected spinal cord. dbcAMP was encapsulated in poly(lactic-co-glycolic acid) (PLGA) microspheres, which were embedded within the scaffolds architecture. Functionality of the released dbcAMP was assessed using neurite outgrowth assays in PC12 cells and by delivery to the transected spinal cord within OPF seven channel scaffolds, which had been loaded with Schwann cells or mesenchymal stem cells (MSCs). Our results showed that encapsulation of dbcAMP in microspheres lead to prolonged release and continued functionality in vitro. These microspheres were then successfully incorporated into OPF scaffolds and implanted in the transected thoracic spinal cord. Sustained delivery of dbcAMP inhibited axonal regeneration in the presence of Schwann cells but rescued MSC-induced inhibition of axonal regeneration. dbcAMP was also shown to reduce capillary formation in the presence of MSCs, which was coupled with significant functional improvements. Our findings demonstrate the feasibility of incorporating PLGA microsphere technology for spinal cord transection studies. It represents a novel sustained delivery mechanism within the transected spinal cord and provides a platform for potential delivery of other therapeutic agents. PMID:21198413

  1. Functional studies of cochleate assemblies of an oligo-acyl-lysyl with lipid mixtures for combating bacterial multidrug resistance.

    PubMed

    Sarig, Hadar; Ohana, Dafna; Epand, Raquel F; Mor, Amram; Epand, Richard M

    2011-10-01

    The cationic antimicrobial oligo-acyl-lysyls (OAKs) interact with lipid mixtures mimicking the composition of bacterial cytoplasmic membranes. We have reported the ability of one such OAK, C(12)K-7α(8), to cluster anionic lipids and to promote a structural change with lipid bilayers to form rolled cylindrical structures or cochleates, without requiring divalent cations for their assembly. These assemblies can be exploited for drug delivery, permitting their synergistic use with antibiotics in systemic therapy to increase efficacy and reduce toxicity. Our previous studies of the biophysical properties of these systems led us to select mixtures with the goal of optimizing their potential for enhancing effectiveness in combating bacterial multidrug resistance. Here, we further investigate the properties of such mixtures that result in enhanced in vivo activity. The role of erythromycin in the assembly of cochleates with OAK in the gel and the liquid crystalline states were assessed, as well as the encapsulation efficiency of the systems chosen. In addition, we found that erythromycin did not undermine the ability of OAKs to induce fusion of vesicles, fusion being an essential component of cochleate formation. The in vivo activity of the new assemblies tested resulted in higher survival rates of animals infected with multidrug resistant bacteria.

  2. Radiation-grafting of 2-hydroxyethylmethacrylate and oligo (ethylene glycol) methyl ether methacrylate onto polypropylene films by one step method

    NASA Astrophysics Data System (ADS)

    Ramírez-Jiménez, Alejandro; Alvarez-Lorenzo, Carmen; Concheiro, Angel; Bucio, Emilio

    2012-01-01

    Polypropylene films were modified with 2-hydroxyethylmethacrylate (HEMA) and oligo (ethylene glycol) methyl ether methacrylate (OEGMA) using the pre-irradiation method with gamma-rays (one step method). The effect of absorbed dose from 10 to 100 kGy, temperature (50, 60, and 70 °C), monomer concentration between 12.5% and 62.5%, monomers ratio from 10% to 90% and reaction time from 5 to 50 h; on the degree of grafting was determined. The grafted samples were analyzed by FTIR-ATR, TGA, DSC, swelling, and contact angle. Grafts onto polymeric films between 3% and 109% were obtained at doses from 10 to 100 kGy and a dose rate around 7.4 kGy/h. The graft percent increased with the content in HEMA in the HEMA:OEGMA feed mixture, which indicates a lower reactivity of OEGMA compared to HEMA. The hydrogel layer grafted on the polypropylene substrate increases the hydrophilicity of the surface and also provides certain temperature-responsiveness, which may be of interest for biomedical applications.

  3. Reconciling structural and thermodynamic predictions using all-atom and coarse-grain force fields: the case of charged oligo-arginine translocation into DMPC bilayers.

    PubMed

    Hu, Yuan; Sinha, Sudipta Kumar; Patel, Sandeep

    2014-10-16

    Using the translocation of short, charged cationic oligo-arginine peptides (mono-, di-, and triarginine) from bulk aqueous solution into model DMPC bilayers, we explore the question of the similarity of thermodynamic and structural predictions obtained from molecular dynamics simulations using all-atom and Martini coarse-grain force fields. Specifically, we estimate potentials of mean force associated with translocation using standard all-atom (CHARMM36 lipid) and polarizable and nonpolarizable Martini force fields, as well as a series of modified Martini-based parameter sets. We find that we are able to reproduce qualitative features of potentials of mean force of single amino acid side chain analogues into model bilayers. In particular, modifications of peptide-water and peptide-membrane interactions allow prediction of free energy minima at the bilayer-water interface as obtained with all-atom force fields. In the case of oligo-arginine peptides, the modified parameter sets predict interfacial free energy minima as well as free energy barriers in almost quantitative agreement with all-atom force field based simulations. Interfacial free energy minima predicted by a modified coarse-grained parameter set are -2.51, -4.28, and -5.42 for mono-, di-, and triarginine; corresponding values from all-atom simulations are -0.83, -3.33, and -3.29, respectively, all in units of kcal/mol. We found that a stronger interaction between oligo-arginine and the membrane components and a weaker interaction between oligo-arginine and water are crucial for producing such minima in PMFs using the polarizable CG model. The difference between bulk aqueous and bilayer center states predicted by the modified coarse-grain force field are 11.71, 14.14, and 16.53 kcal/mol, and those by the all-atom model are 6.94, 8.64, and 12.80 kcal/mol; those are of almost the same order of magnitude. Our simulations also demonstrate a remarkable similarity in the structural aspects of the ensemble of

  4. Reconciling Structural and Thermodynamic Predictions Using All-Atom and Coarse-Grain Force Fields: The Case of Charged Oligo-Arginine Translocation into DMPC Bilayers

    PubMed Central

    2015-01-01

    Using the translocation of short, charged cationic oligo-arginine peptides (mono-, di-, and triarginine) from bulk aqueous solution into model DMPC bilayers, we explore the question of the similarity of thermodynamic and structural predictions obtained from molecular dynamics simulations using all-atom and Martini coarse-grain force fields. Specifically, we estimate potentials of mean force associated with translocation using standard all-atom (CHARMM36 lipid) and polarizable and nonpolarizable Martini force fields, as well as a series of modified Martini-based parameter sets. We find that we are able to reproduce qualitative features of potentials of mean force of single amino acid side chain analogues into model bilayers. In particular, modifications of peptide–water and peptide–membrane interactions allow prediction of free energy minima at the bilayer–water interface as obtained with all-atom force fields. In the case of oligo-arginine peptides, the modified parameter sets predict interfacial free energy minima as well as free energy barriers in almost quantitative agreement with all-atom force field based simulations. Interfacial free energy minima predicted by a modified coarse-grained parameter set are −2.51, −4.28, and −5.42 for mono-, di-, and triarginine; corresponding values from all-atom simulations are −0.83, −3.33, and −3.29, respectively, all in units of kcal/mol. We found that a stronger interaction between oligo-arginine and the membrane components and a weaker interaction between oligo-arginine and water are crucial for producing such minima in PMFs using the polarizable CG model. The difference between bulk aqueous and bilayer center states predicted by the modified coarse-grain force field are 11.71, 14.14, and 16.53 kcal/mol, and those by the all-atom model are 6.94, 8.64, and 12.80 kcal/mol; those are of almost the same order of magnitude. Our simulations also demonstrate a remarkable similarity in the structural aspects of

  5. Efficient use of artificial micro-RNA to downregulate the expression of genes at the post-transcriptional level in Arabidopsis thaliana.

    PubMed

    Ud-Din, A; Rauf, M; Ghafoor, S; Khattak, M N K; Hameed, M W; Shah, H; Jan, S; Muhammad, K; Rehman, A; Inamullah

    2016-04-07

    Micro-RNAs are cellular components regulating gene expression at the post-transcription level. In the present study, artificial micro-RNAs were used to decrease the transcript level of two genes, AtExpA8 (encoding an expansin) and AHL25 (encoding an AT-hook motif nuclear localized protein) in Arabidopsis thaliana. The backbone of the Arabidopsis endogenous MIR319a micro-RNA was used in a site-directed mutagenesis approach for the generation of artificial micro-RNAs targeting two genes. The recombinant cassettes were expressed under the control of the CaMV 35S promoter in individual A. thaliana plants. Transgenic lines of the third generation were tested by isolating total RNA and by subsequent cDNA synthesis using oligo-dT18 primers and mRNAs as templates. The expression of the two target genes was checked through quantitative real-time polymerase chain reaction to confirm reduced transcript levels for AtExpA8 and AHL25. Downregulation of AtExpA8 resulted in the formation of short hypocotyls compared with those of the wild-type control in response to low pH and high salt concentration. This technology could be used to prevent the expression of exogenous and invading genes posing a threat to the normal cellular physiology of the host plant.

  6. Taxonomy and Phylogeny of Arabidopsis (Brassicaceae)

    PubMed Central

    Al-Shehbaz, Ihsan A.; O'Kane, Steve L.

    2002-01-01

    Detailed taxonomic, cytological, and phylogenetic accounts of Arabidopsis are presented. As currently delimited, the genus consists of nine species all of which are indigenous to Europe, with the ranges of two species extending into northern and eastern Asia and North American into central United States. A survey of chromosome numbers in the genus is presented, and the country of origin for each count is given. Detailed descriptions of all species and subspecies and keys to all taxa are provided. Generic assignments are updated for the 50 species previously included in Arabidopsis. A cladogram of the species of Arabidopsis based on molecular phylogenetic studies by the authors is given. PMID:22303187

  7. Evaluation of the Speed-oligo Direct Mycobacterium tuberculosis Assay for Molecular Detection of Mycobacteria in Clinical Respiratory Specimens

    PubMed Central

    Lara-Oya, Ana; Mendoza-Lopez, Pablo; Rodriguez-Granger, Javier; Fernández-Sánchez, Ana María; Bermúdez-Ruiz, María Pilar; Toro-Peinado, Inmaculada; Palop-Borrás, Begoña; Navarro-Marí, Jose María

    2013-01-01

    We present the first evaluation of a novel molecular assay, the Speed-oligo Direct Mycobacterium tuberculosis (SO-DMT) assay, which is based on PCR combined with a dipstick for the detection of mycobacteria and the specific identification of M. tuberculosis complex (MTC) in respiratory specimens. A blind evaluation was carried out in two stages: first, under experimental conditions on convenience samples comprising 20 negative specimens, 44 smear- and culture-positive respiratory specimens, and 11 sputa inoculated with various mycobacterium-related organisms; and second, in the routine workflow of 566 fresh respiratory specimens (4.9% acid-fast bacillus [AFB] smear positives, 7.6% MTC positives, and 1.8% nontuberculous mycobacteria [NTM] culture positives) from two Mycobacterium laboratories. SO-DMT assay showed no reactivity in any of the mycobacterium-free specimens or in those with mycobacterium-related organisms. Compared to culture, the sensitivity in the selected smear-positive specimens was 0.91 (0.92 for MTC and 0.90 for NTM), and there was no molecular detection of NTM in a tuberculosis case or vice versa. With respect to culture and clinical data, the sensitivity, specificity, and positive and negative predictive values for the SO-DMT system in routine specimens were 0.76 (0.93 in smear positives [1.0 for MTC and 0.5 for NTM] and 0.56 in smear negatives [0.68 for MTC and 0.16 for NTM]), 0.99, 0.85 (1.00 in smear positives and 0.68 in smear negatives), and 0.97, respectively. Molecular misidentification of NTM cases occurred when testing 2 gastric aspirates from two children with clinically but not microbiologically confirmed lung tuberculosis. The SO-DMT assay appears to be a fast and easy alternative for detecting mycobacteria and differentiating MTC from NTM in smear-positive respiratory specimens. PMID:23100355

  8. Hexactinellid sponges reported from shallow waters in the Oligo-Miocene Pirabas Formation (N Brazil) are in fact cheilostome bryozoans

    NASA Astrophysics Data System (ADS)

    Muricy, Guilherme; Domingos, Celso; Távora, Vladimir A.; Ramalho, Laís V.; Pisera, Andrzej; Taylor, Paul

    2016-12-01

    Although hexactinellid sponges occur exclusively in deep and/or cold waters, three species of hexactinellids have been reported from shallow and warm waters in Oligo-Miocene deposits of the Pirabas Formation in northern Brazil: Aphrocallistes estevoui, A. lobata and Manzonia aprutina. Here we re-examine these fossils and show that they are not hexactinellid sponges but instead comprise three species of cheilostome bryozoans of the genus Celleporaria (Family Lepraliellidae). Two of these are new to science, viz., Celleporaria pirabasensis sp. nov. and Celleporaria triangulavicularis sp. nov., and the third could not be identified to species level due to poor preservation. Colonies of all three species are massive and multilaminar, with irregular layers of zooids produced by frontal budding. Autozooids have marginal areolar pores and a rounded, asinuate primary orifice. All colonies also have suboral adventitious avicularia and interzooidal avicularia, although of different shapes and sizes. Celleporaria triangulavicularis sp. nov. has distinctive triangular interzooidal avicularia. The underside of the frontal shield was seen only in Celleporaria pirabasensis sp. nov. and Celleporaria sp., in which it is umbonuloid. Ovicells were only seen in Celleporaria pirabasensis sp. nov. and are cap-shaped. The three species differ among themselves mainly in the shape and position of the adventitious and interzooidal avicularia. The presence of several typical bryozoan traits and the absence of spicule traces or any other sponge features clearly demonstrate that these fossils are bryozoans, not sponges. The change in the classification of these fossils from hexactinellids to bryozoans of the genus Celleporaria eliminates the incongruence of the occurrence of deep-water species in the warm shallow water depositional environment of the Pirabas Formation.

  9. In vivo release of plasmid DNA from composites of oligo(poly(ethylene glycol)fumarate) and cationized gelatin microspheres.

    PubMed

    Kasper, F Kurtis; Kushibiki, Toshihiro; Kimura, Yu; Mikos, Antonios G; Tabata, Yasuhiko

    2005-10-20

    Composites of cationized gelatin microspheres (CGMS), crosslinked with either 3 mM or 6 mM glutaraldehyde solution, and a novel hydrogel material, oligo(poly(ethylene glycol)fumarate) (OPF) were fabricated and investigated toward prolonging the release of plasmid DNA in vivo relative to the constituent materials. The composites and constituent materials were investigated in a subcutaneous murine model to assess the release of 125I-labeled plasmid DNA and 125I-labeled cationized gelatin in vivo. The time profiles of the radioactivity remaining were employed to compare the profiles of DNA release and cationized gelatin degradation. Both composite formulations (incorporating either 3 mM or 6 mM CGMS) prolonged the bioavailability of plasmid DNA relative to both injected plasmid DNA solution and the respective non-embedded cationized gelatin microspheres. Injected plasmid DNA solution persisted in the subject for only 7-10 days, whereas the persistence of DNA from composites of OPF and either 3 mM or 6 mM CGMS extended to at least day 42. The 3 mM and 6 mM CGMS each increased the persistence of DNA slightly, relative to injection of DNA solution, to between 28 and 35 days. Interestingly, the release profile of plasmid DNA from composites was not significantly different from the release of DNA from OPF alone. The release of plasmid DNA from the composites was in accord with the degradation of the microspheres within the OPF. These results show that composites of OPF and cationized gelatin microspheres are able to prolong the availability of plasmid DNA in vivo relative to cationized gelatin microspheres alone and provide a promising candidate material for the sustained, controlled release of plasmid DNA.

  10. Oligo-carrageenans enhance growth and contents of cellulose, essential oils and polyphenolic compounds in Eucalyptus globulus trees.

    PubMed

    González, Alberto; Contreras, Rodrigo A; Moenne, Alejandra

    2013-07-24

    Eucalyptus globulus (Myrtaceae) originated in Australia and has been introduced in countries with temperate weather in order to obtain wood for cellulose extraction and building purposes. In this work, we analyzed the potential stimulation of growth in height and trunk diameter as well as the content of holo-cellulose, α-cellulose (long cellulose chains), essential oils and polyphenolic compounds (PPCs) in E. globulus trees treated with oligo-carrageenans (OCs) kappa, lambda and iota, at 1 mg mL⁻¹, once a week, four times in total and then cultivated for three additional years without further treatment. Eucalyptus treated with OCs kappa, lambda and iota showed an increase in height, mainly with OCs kappa and iota by 58% and 47%, respectively, and in trunk diameter by 44% and 40%, respectively. In addition, OCs induced an increase in the contents of holo-cellulose and α-cellulose, mainly OCs kappa and iota which increased holo-cellulose by 8% and 5%, respectively, and α-cellulose by 16 and 13%, respectively. Moreover, OCs increased the content of essential oils, mainly OCs kappa and iota by 67% and 39%, respectively. Furthermore, OCs decreased the concentration of total phenolic compounds but differentially changed the concentration of several PPCs such as genistein, rutin, ellagic acid, morin, luteolin and quercetin with potential antimicrobial activities. Thus, marine algae OCs kappa, lambda and iota stimulate growth of E. globulus trees by enhancing height and trunk diameter as well as the content of α-cellulose, total essential oils, and some PPCs with potential antimicrobial activities.

  11. In vivo bone and soft tissue response to injectable, biodegradable oligo(poly(ethylene glycol) fumarate) hydrogels.

    PubMed

    Shin, Heungsoo; Quinten Ruhé, P; Mikos, Antonios G; Jansen, John A

    2003-08-01

    This study was designed to assess in vivo bone and soft tissue behavior of novel oligo(poly(ethylene glycol) fumarate) (OPF) hydrogels using a rabbit model. In vitro degradation of the OPF hydrogels was also investigated in order to compare with in vivo characteristics. Four groups of OPF hydrogel implants were synthesized by alternation of crosslinking density, poly(ethylene glycol) (PEG) block length of OPF, and cell-binding peptide content. The in vitro degradation rate of OPF hydrogels increased with decreasing crosslinking density of hydrogels, which was characterized by measuring weight loss and swelling ratio of hydrogels and medium pH change. Examination of histological sections of the subcutaneous and cranial implants showed that an uniform thin circumferential fibrous capsule was formed around the OPF hydrogel implants. Quantitative evaluation of the tissue response revealed that no statistical difference existed in capsule quality or thickness between implant groups, implantation sites or implantation times. At 4 weeks, there was a very limited number of inflammatory and multinuclear cells at the implant-fibrous capsule interface for all implants. However, at 12 weeks, OPF hydrogels with PEG block length of number average molecular weight 6090+/-90 showed extensive surface erosion and superficial fragmentation that was surrounded by a number of inflammatory cells, while OPF hydrogels with PEG block length of number average molecular weight 930+/-10 elicited minimal degradation. Constant fibrous capsule layers and number of inflammatory cells were observed regardless of the incorporation of cell-binding peptide and crosslinking density of OPF hydrogels with PEG block length of number average molecular weight 930+/-90. These results confirm that the degradation of implants can be controlled by tailoring the macromolecular structure of OPF hydrogels. Additionally, histological evaluation of implants proved that the OPF hydrogel is a promising material for

  12. Oligo-Miocene thinning of the Beni Bousera peridotites and their Variscan crustal host rocks, Internal Rif, Morocco

    NASA Astrophysics Data System (ADS)

    Gueydan, Frédéric; Pitra, Pavel; Afiri, Abdelkhaleq; Poujol, Marc; Essaifi, Abderrahim; Paquette, Jean-Louis

    2015-06-01

    Deciphering Variscan versus Alpine history in the Internal Rif system is a key to constrain the tectonic evolution of the Alboran domain and hence the geodynamics of the western Mediterranean system during the Cenozoic. This study focuses on the evolution of the metamorphic envelope of the Beni Bousera massif and its relation to the underlying peridotites. Combining structural geology, metamorphic petrology, and laser ablation inductively coupled plasma mass spectrometry U-Th-Pb dating of monazite, this study contributes to the understanding of the tectonic history of the western Internal Rif. The regional foliation (S2) is characterized by low pressure-high temperature (LP-HT) mineral assemblages and obliterates a former foliation (S1) developed along a Barrovian (medium pressure-medium temperature, MP-MT) metamorphic gradient. The dating of some metamorphic monazite grains from a micaschist and a migmatitic gneiss demonstrates that the crustal envelope of the peridotite recorded two distinct tectonometamorphic episodes. Data from monazite inclusions in S1 garnet suggest that the first event, D1, is older than 250-170 Ma and likely related to the Variscan collision, in agreement with the Barrovian type of the metamorphic gradient. The second event, D2, is Alpine in age (at circa 21 Ma) and corresponds to a strong lithosphere thinning allowing subsequent subcontinental mantle exhumation. Such a tectonic context provides an explanation for the LP-HT metamorphic gradient that is recorded in the regional foliation of the western Betic-Rif system. This extension is probably related to a subduction slab rollback in the western end of the Mediterranean realm during the Oligo-Miocene times. No evidence for a Tertiary high pressure/low temperature metamorphism has been identified in the studied area.

  13. Oligo(ethylene glycol)-modified β-cyclodextrin-based polyrotaxanes for simultaneously modulating solubility and cellular internalization efficiency.

    PubMed

    Tamura, Atsushi; Ohashi, Moe; Yui, Nobuhiko

    We developed stimuli-labile polyrotaxanes (PRXs) composed of β-cyclodextrin (β-CD), Pluronic as an axle polymer, and acid-cleavable N-triphenylmethyl groups as bulky stopper molecules, and found that the PRXs are potent therapeutics for Niemann-Pick type C disease, because the PRX can effectively reduce intracellular cholesterol through the intracellular release of threaded β-CDs. In general, the PRXs need to be chemically modified with hydrophilic functional groups because PRXs are not soluble in aqueous media. Herein, four series of oligo(ethylene glycol)s (OEGs) with different ethylene glycol repeating unit (2 or 3) and chemical structure of OEG terminal (hydroxy or methoxy) were modified onto the threaded β-CDs in PRX. The effects of the structure of OEG on the aqueous solubility, toxicity, and cellular internalization efficiency of OEG-modified PRXs were investigated to optimize the chemical structure of OEG. The hydroxy-terminated OEG-modified PRXs showed excellent solubility in aqueous media and no toxicity, regardless of the number of ethylene glycol repeating units. In the case of the methoxy-terminated OEG-modified PRXs, sufficient solubility in aqueous media and negligible toxicity were observed when the number of ethylene glycol repeating units was 3, while low solubility and toxicity were observed when the ethylene glycol repeating unit was 2. Additionally, cellular uptake levels of methoxy-terminated OEG-modified PRXs in RAW264.7 cells were higher than those of hydroxy-terminated OEG-modified PRXs. Consequently, the chemical structure of the OEG strongly affects the chemical and biological properties of the PRXs, and that a methoxy-terminated OEG with 3 ethylene glycol repeating units is the most preferable modification of PRXs, since the resultant PRX is sufficiently soluble in aqueous media, non-toxic, and possesses high cellular internalization efficiency.

  14. Gold nanoparticles decorated with oligo(ethylene glycol) thiols: surface charges and interactions with proteins in solution.

    PubMed

    Schollbach, Moritz; Zhang, Fajun; Roosen-Runge, Felix; Skoda, Maximilian W A; Jacobs, Robert M J; Schreiber, Frank

    2014-07-15

    We have studied oligo(ethylene glycol) (OEG) thiol self-assembled monolayer (SAM) coated gold nanoparticles (AuOEG) and their interactions with proteins in solutions using electrophoretic and dynamic light scattering (ELS and DLS). The results are compared with poly(ethylene glycol) (PEG) thiol coated AuNPs (AuPEG). We show that both AuOEG and AuPEG particles carry a low net negative charge and are very stable (remaining so for more than one year), but long-term aging or dialysis can reduce the stability. If the decorated AuNPs are mixed with bovine serum albumin (BSA), both effective size and zeta-potential of the AuNPs remain unchanged, indicating no adsorption of BSA to the colloid surface. However, when mixed with lysozyme, zeta-potential values increase with protein concentrations and lead to a charge inversion, indicating adsorption of lysozyme to the colloid surface. The colloidal solutions of AuOEG become unstable near zero charge, indicated by a cluster peak in the DLS measurements. The AuPEG solutions show similar charge inversion upon addition of lysozyme, but the solutions are stable under all experimental conditions, presumably because of the strong steric effect of PEG. Washing the protein bound colloids by centrifugation can remove only part of the adsorbed lysozyme molecules indicating that a few proteins adsorb strongly to the colloids. The effective charge inversion and rather strongly bound lysozyme on the colloid surface may suggest that in addition to the charges formed at the SAM-water interface, there are defects on the surface of the colloid, which are accessible to the proteins. The results of this study of surface charge, and stability shed light on the interaction with proteins of SAM coated AuNPs and their applications. Copyright © 2014 Elsevier Inc. All rights reserved.

  15. Sulfenome mining in Arabidopsis thaliana

    PubMed Central

    Waszczak, Cezary; Akter, Salma; Eeckhout, Dominique; Persiau, Geert; Wahni, Khadija; Bodra, Nandita; Van Molle, Inge; De Smet, Barbara; Vertommen, Didier; Gevaert, Kris; De Jaeger, Geert; Van Montagu, Marc; Messens, Joris; Van Breusegem, Frank

    2014-01-01

    Reactive oxygen species (ROS) have been shown to be potent signaling molecules. Today, oxidation of cysteine residues is a well-recognized posttranslational protein modification, but the signaling processes steered by such oxidations are poorly understood. To gain insight into the cysteine thiol-dependent ROS signaling in Arabidopsis thaliana, we identified the hydrogen peroxide (H2O2)-dependent sulfenome: that is, proteins with at least one cysteine thiol oxidized to a sulfenic acid. By means of a genetic construct consisting of a fusion between the C-terminal domain of the yeast (Saccharomyces cerevisiae) AP-1–like (YAP1) transcription factor and a tandem affinity purification tag, we detected ∼100 sulfenylated proteins in Arabidopsis cell suspensions exposed to H2O2 stress. The in vivo YAP1-based trapping of sulfenylated proteins was validated by a targeted in vitro analysis of DEHYDROASCORBATE REDUCTASE2 (DHAR2). In DHAR2, the active site nucleophilic cysteine is regulated through a sulfenic acid-dependent switch, leading to S-glutathionylation, a protein modification that protects the protein against oxidative damage. PMID:25049418

  16. Arabidopsis thaliana life without phytochromes

    PubMed Central

    Strasser, Bárbara; Sánchez-Lamas, Maximiliano; Yanovsky, Marcelo J.; Casal, Jorge J.; Cerdán, Pablo D.

    2010-01-01

    Plants use light as a source of energy for photosynthesis and as a source of environmental information perceived by photoreceptors. Testing whether plants can complete their cycle if light provides energy but no information about the environment requires a plant devoid of phytochromes because all photosynthetically active wavelengths activate phytochromes. Producing such a quintuple mutant of Arabidopsis thaliana has been challenging, but we were able to obtain it in the flowering locus T (ft) mutant background. The quintuple phytochrome mutant does not germinate in the FT background, but it germinates to some extent in the ft background. If germination problems are bypassed by the addition of gibberellins, the seedlings of the quintuple phytochrome mutant exposed to red light produce chlorophyll, indicating that phytochromes are not the sole red-light photoreceptors, but they become developmentally arrested shortly after the cotyledon stage. Blue light bypasses this blockage, rejecting the long-standing idea that the blue-light receptors cryptochromes cannot operate without phytochromes. After growth under white light, returning the quintuple phytochrome mutant to red light resulted in rapid senescence of already expanded leaves and severely impaired expansion of new leaves. We conclude that Arabidopsis development is stalled at several points in the presence of light suitable for photosynthesis but providing no photomorphogenic signal. PMID:20176939

  17. Separation of oligo/polymers of 5-N-acetylneuraminic acid, 5-N-glycolylneuraminic acid, and 2-keto-3-deoxy-D-glycero-D-galacto-nononic acid by high-performance anion-exchange chromatography with pulsed amperometric detector.

    PubMed

    Zhang, Y; Inoue, Y; Inoue, S; Lee, Y C

    1997-08-01

    A sensitive and efficient method to analyze oligo/ poly-sialic acids containing alpha2-8-linked 5-N-acetylneuraminic acid (Neu5Ac), 5-N-glycolylneuraminic acid (Neu5Gc), and deaminated neuraminic acid (KDN) using high-performance anion-exchange chromatography (HPAEC) with a pulsed amperometric detector (PAD-2) has been developed. Using a CarboPac PA-100 column and sodium nitrate as the pushing agent, polymers in colominic acid with degree of polymerization (DP) up to 80 were separated in 68 min. A similar DP-based resolution was also obtained on a CarboPac PA-1 column. The elution ladders of the Neu5Ac, Neu5Gc, and KDN series were sufficiently different to be used as diagnostic indices. This technique was applied to identification of the sialic acid components in a polysialoglycoprotein (PSGP) sample as well as monitoring the oligo/poly-KDN-containing fractions during the purification of KDN-containing glycoprotein (KDN-gp). The maximum DPs of oligo-Neu5Gc and oligo-KDN that can be detected in PSGP and KDN-gp hydrolysates were 11 and 8, respectively. The high sensitivity of this method was demonstrated by the quantification of Neu5Ac oligomers. Distributions of the monomer and oligo/polymers in the acid and enzymatic hydrolysates of colominic acid and PSGP under different conditions were also studied.

  18. PAIR: the predicted Arabidopsis interactome resource.

    PubMed

    Lin, Mingzhi; Shen, Xueling; Chen, Xin

    2011-01-01

    The predicted Arabidopsis interactome resource (PAIR, http://www.cls.zju.edu.cn/pair/), comprised of 5990 experimentally reported molecular interactions in Arabidopsis thaliana together with 145,494 predicted interactions, is currently the most comprehensive data set of the Arabidopsis interactome with high reliability. PAIR predicts interactions by a fine-tuned support vector machine model that integrates indirect evidences for interaction, such as gene co-expressions, domain interactions, shared GO annotations, co-localizations, phylogenetic profile similarities and homologous interactions in other organisms (interologs). These predictions were expected to cover 24% of the entire Arabidopsis interactome, and their reliability was estimated to be 44%. Two independent example data sets were used to rigorously validate the prediction accuracy. PAIR features a user-friendly query interface, providing rich annotation on the relationships between two proteins. A graphical interaction network browser has also been integrated into the PAIR web interface to facilitate mining of specific pathways.

  19. The fifth international conference on Arabidopsis research

    SciTech Connect

    Hangarter, R.; Scholl, R.; Davis, K.; Feldmann, K.

    1993-12-31

    This volume contains abstracts of oral and poster presentations made in conjunction with the Fifth International Conference on Arabidopsis Research held August 19--22, 1993 at the Ohio State University, Columbus, Ohio.

  20. Synthesis of a strained acetylenic macrocycle incorporating a para-oligo[2]cruciform bridge bent over nanoscopic dimensions: structural, electronic, spectroscopic, and ion-sensing properties.

    PubMed

    Baxter, Paul N W; Gisselbrecht, Jean-Paul; Karmazin-Brelot, Lydia; Varnek, Alexandre; Allouche, Lionel

    2013-09-09

    An Eglinton-Galbraith diethyne cyclization preferentially yielded a structurally unusual macrocycle, comprising a strained conjugated oligo[2]cruciform wire, forced into a 2.2 nm bow-shape by a terpyridine rein or tether, and stabilized towards light and heat by four insulating triisopropylsilylacetylene (TIPSA) substituents. Spectroscopic ion-binding studies revealed the macrocycle to exhibit a particularly high UV/Vis selectivity for Pd(II) in dilute solution, and one of its precursors to afford a variety of luminescence quenching and color responses to particular metals, suggestive of promising ion-sensor applications. Under more concentrated conditions, the new macrocycle is able to bind specific metals (e.g., Au(I)) within its cavity despite the steric constraints. Intriguingly, variable-temperature (VT) UV/Vis/(1)H NMR investigations showed the TIPSA substituents to undergo restricted intramolecular motions along with reversible changes in the spectroscopic bandgap of the compound with temperature. In line with the theoretical calculations, the VT UV/Vis observations are consistent with a thermal modulation of the electronic conjugation through the strained oligo[2]cruciform bridge, which is coupled with redistributions within a mixture of conformational isomers of the macrocycle with differing relative twisting between the TIPSA-substituted phenyl rings. Overall, the generation of a para-oligo[2]cruciform, bent and flexed over nanoscopic dimensions through conformational tethering within the macrocyclic ring is noteworthy, and suggests a general approach to nanosized, curved, and strained, yet heat- and light-stable, para-phenyleneethynylene oligomers with unique physicochemical properties and challenging theoretical possibilities. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Effect of the Novel Biodegradable N, O-Carboxymethylchitosan and Oligo-Chitosan on the Platelet Thrombogenicity Cascade in von Willebrand Disease.

    PubMed

    Periayah, Mercy Halleluyah; Halim, Ahmad Sukari; Mat Saad, Arman Zaharil; Yaacob, Nik Soriani; Hussein, Abdul Rahim; Abdul Karim, Faraizah; Abdul Rashid, Ahmad Hazri; Ujang, Zanariah

    2015-09-01

    Von Willebrand disease (vWD) is the second least common hemostatic disorder in Malaysia, and it has a low prevalence. This study examined the underlying platelet thrombogenicity cascades in the presence of different formulations of chitosan-derivatives in vWD patients. This paper aimed to determine the significant influence of chitosan biomaterial in stimulating the platelet thrombogenicity cascades that involve the von Willebrand factor, Factor 8, Thromboxane A2, P2Y12 and Glycoprotein IIb/IIIa in vWD. Variable chitosan formulations of N,O-Carboxymethylchitosan (NO-CMC) and Oligo-Chitosan (O-C) were tested. Fourteen vWD subjects voluntarily participated in this study after signing informed consent forms. The patient's demographic profiles, family history, type of vWD, clinical symptoms and laboratory profiles were recorded and analyzed. Enzyme-linked immunosorbent assay, flow cytometry and Western blot tests were used to determine the level of the chitosan-adhered-platelet-mechanisms. The study revealed that most patients were predominantly affected by vWD type I. The O-C group of chitosan's scaffold pores is sufficient to allow for nutrients and cells. The O-C-stimulated-mediators are capable of initiating the platelet actions and were detected to expedite the blood coagulation processes. The oligo-group of chitosans was capable of amplifying and triggering more platelet activator's pathways via the studied mediators. The present findings suggest that the ability of each type of chitosan to coagulate blood varies depending on its chemical composition. The oligo group of chitosans is potentially capable of triggering platelet thrombogenicity cascades by activating platelets in vWD patients to form a platelet plug for hemostasis process. Copyright © 2015 Elsevier Ltd. All rights reserved.

  2. Viral agents causing lower respiratory tract infections in hospitalized children: evaluation of the Speed-Oligo® RSV assay for the detection of respiratory syncytial virus.

    PubMed

    Sánchez-Yebra, W; Ávila-Carrillo, J A; Giménez-Sánchez, F; Reyes-Bertos, A; Sánchez-Forte, M; Morales-Torres, M; Rojas, A; Mendoza, J

    2012-03-01

    Respiratory syncytial virus (RSV) is the viral agent which is more frequently involved in lower respiratory tract infections (LRTIs) in infants under 1 year of age in developed countries. A new oligochromatographic assay, Speed-Oligo® RSV, was designed and optimized for the specific detection and identification of RSV subtypes A and B. The test was evaluated in 289 clinical samples from 169 hospitalized children using an immunochromatography (IC) test, virus isolation by culture, and an in-house real-time polymerase chain reaction (RT-PCR). Other viruses causing LRTIs were investigated by cell culture or PCR-based tests. Sixty-two patients were infected by RSV (36.7%). In addition, adenovirus, influenza B, parainfluenza 2, and human metapneumovirus were detected in rates ranging from 5 to 8%. A proportion of 10.1% of the patients had mixed infections. The sensitivity, specificity, and positive and negative predictive values were, respectively, 94.9, 99.4, 98.9, and 97.4% for Speed-Oligo® RSV, 92.9, 96.3, 92.9, and 96.3% for RT-PCR/RSV, and 58.4, 98.1, 93.3, and 82.6% for IC. Our rates of viral detection and co-infection were similar to those of previously reported series. Finally, we find that Speed-Oligo® RSV is a rapid and easy-to-perform technique for the detection of RSV and the identification of subtypes A and B.

  3. Oligo-Miocene foraminiferal record (Miogypsinidae, Lepidocyclinidae and Nummulitidae) from the Western Taurides (SW Turkey): Biometry and implications for the regional geology

    NASA Astrophysics Data System (ADS)

    Özcan, Ercan; Less, György; Báldi-Beke, Mária; Kollányi, Katalin; Acar, Ferhat

    2009-05-01

    The marine Oligo-Miocene units of western Taurides, deposited under different tectonic regimes (in Bey Dağları platform in foreland and coeval sequences in hinterland), were studied to establish a high-resolution biostratigraphic framework. Biometric study of the full spectrum of larger foraminifera in a regional scale allowed us correlating them with the shallow benthic zonation (SBZ) system introduced by [Cahuzac, B., Poignant, A., 1997. Essai de biozonation de l'Oligo-Miocène dans les bassins européens à l'aide des grands foraminifères néritiques. Bulletin de la Société géologique de France 168, 155-169], and to determine the ages of these sites on zonal precision for the first time. In correlating these assemblages to standard shallow benthic zones, planktonic data were also used whenever possible. Taxa, classified under the genera Nummulites, Miogypsina, Miolepidocyclina, Nephrolepidina, Eulepidina, Heterostegina, Operculina and Cycloclypeus (?) and their assemblages, closely resemble to the fauna described from European basins. These groups characterize the SBZ 22B to 25 zones referring to a time interval from early Chattian to Burdigalian. However, a main gap in late Chattian (SBZ 23) and in early part of the Aquitanian (SBZ 24) is also recorded in the platform succession. In the meantime, rare Eulepidina in the Burdigalian levels suggest a clear Indo-Pacific influence. Based on the discovery of early Chattian (SBZ 22B) deposits (previously mapped under Eocene/Miocene units), the Oligo-Miocene stratigraphy of the Bey Dağları platform is also revised. A more precise chronology for regional Miocene transgression is presented based on the miogypsinid evolutionary scale.

  4. The impact of self-reported oligo-amenorrhea and hirsutism on fertility and lifetime reproductive success: results from the Northern Finland Birth Cohort 1966.

    PubMed

    West, S; Vähäsarja, M; Bloigu, A; Pouta, A; Franks, S; Hartikainen, A-L; Järvelin, M-R; Corbett, S; Vääräsmäki, M; Morin-Papunen, L

    2014-03-01

    To what extent do self-reported oligo-amenorrhea and hirsutism affect reproductive performance (childlessness, age at first delivery, family size and miscarriage rates)? At the age of 44, among women with both self-reported oligo-amenorrhea and hirsutism the prevalence of childlessness was not significantly different from non-symptomatic women but they had a smaller family size than non-symptomatic women. Polycystic ovary syndrome (PCOS) is a common endocrine disorder characterized by oligo-amenorrhea or amenorrhea, hyperandrogenism and hirsutism and it is the most frequent cause of anovulatory infertility, but there are few studies on the reproductive capacity of women with PCOS. In our previous population-based cohort study the women with self-reported oligo-amenorrhea and hirsutism were found to have more infertility problems and smaller family size than non-symptomatic women at the age of 31. A prospective population-based cohort study. The population of the study is derived from the prospective Northern Finland Birth Cohort 1966 (NFBC1966), comprising all expected births from the year 1966 in the two northernmost provinces of Finland (n = 12 058). Of them, 5889 were females. Enrollment in this database begun at the 24th gestational week and so far data have been collected from the subjects at the ages of 1, 14 and 31 years. A postal questionnaire including questions about oligo-amenorrhea and hirsutism was sent to all women at the age of 31 (n = 5608, response rate 81%, n = 4535) and a clinical examination was performed (attendance rate 76.5%). Those who reported both hirsutism and oligo-amenorrhea were defined as women with both symptoms (n = 153). Data on pregnancies/deliveries were obtained from the Finnish Medical Birth Register (FMBR) in 2010 when the women were 44 years old. Women with both symptoms had delivered at least one child as often as non-symptomatic women [75.2 versus 79.0%, adjusted odds ratio (OR) 0.86, 95% confidence intervals (CI) 0

  5. Cell Polarity Signaling in Arabidopsis

    PubMed Central

    Yang, Zhenbiao

    2009-01-01

    Cell polarization is intimately linked to plant development, growth, and responses to the environment. Major advances have been made in our understanding of the signaling pathways and networks that regulate cell polarity in plants owing to recent studies on several model systems, e.g., tip growth in pollen tubes, cell morphogenesis in the leaf epidermis, and polar localization of PINs. From these studies we have learned that plant cells use conserved mechanisms such as Rho family GTPases to integrate both plant-specific and conserved polarity cues and to coordinate the cytoskeketon dynamics/reorganization and vesicular trafficking required for polarity establishment and maintenance. This review focuses upon signaling mechanisms for cell polarity formation in Arabidopsis, with an emphasis on Rho GTPase signaling in polarized cell growth and how these mechanisms compare with those for cell polarity signaling in yeast and animal systems. PMID:18837672

  6. Apoplastic Diffusion Barriers in Arabidopsis

    PubMed Central

    Schreiber, Lukas; Franke, Rochus Benni; Geldner, Niko; Reina-Pinto, José J.; Kunst, Ljerka

    2013-01-01

    During the development of Arabidopsis and other land plants, diffusion barriers are formed in the apoplast of specialized tissues within a variety of plant organs. While the cuticle of the epidermis is the primary diffusion barrier in the shoot, the Casparian strips and suberin lamellae of the endodermis and the periderm represent the diffusion barriers in the root. Different classes of molecules contribute to the formation of extracellular diffusion barriers in an organ- and tissue-specific manner. Cutin and wax are the major components of the cuticle, lignin forms the early Casparian strip, and suberin is deposited in the stage II endodermis and the periderm. The current status of our understanding of the relationships between the chemical structure, ultrastructure and physiological functions of plant diffusion barriers is discussed. Specific aspects of the synthesis of diffusion barrier components and protocols that can be used for the assessment of barrier function and important barrier properties are also presented. PMID:24465172

  7. Tetrapyrrole Metabolism in Arabidopsis thaliana

    PubMed Central

    Tanaka, Ryouichi; Kobayashi, Koichi; Masuda, Tatsuru

    2011-01-01

    Higher plants produce four classes of tetrapyrroles, namely, chlorophyll (Chl), heme, siroheme, and phytochromobilin. In plants, tetrapyrroles play essential roles in a wide range of biological activities including photosynthesis, respiration and the assimilation of nitrogen/sulfur. All four classes of tetrapyrroles are derived from a common biosynthetic pathway that resides in the plastid. In this article, we present an overview of tetrapyrrole metabolism in Arabidopsis and other higher plants, and we describe all identified enzymatic steps involved in this metabolism. We also summarize recent findings on Chl biosynthesis and Chl breakdown. Recent advances in this field, in particular those on the genetic and biochemical analyses of novel enzymes, prompted us to redraw the tetrapyrrole metabolic pathways. In addition, we also summarize our current understanding on the regulatory mechanisms governing tetrapyrrole metabolism. The interactions of tetrapyrrole biosynthesis and other cellular processes including the plastid-to-nucleus signal transduction are discussed. PMID:22303270

  8. Protein resistant surfaces: comparison of acrylate graft polymers bearing oligo-ethylene oxide and phosphorylcholine side chains.

    PubMed

    Feng, Wei; Zhu, Shiping; Ishihara, Kazuhiko; Brash, John L

    2006-03-01

    The objective of this work was to compare poly(ethylene glycol) (PEG) and phosphorylcholine (PC) moieties as surface modifiers with respect to their ability to inhibit protein adsorption. Surfaces were prepared by graft polymerization of the methacrylate monomers oligo(ethylene glycol) methyl ether methacrylate (OEGMA, MW 300, PEG side chains of length n=4.5) and 2-methacryloyloxyethyl phosphorylcholine (MPC, MW 295). The grafted polymers thus contained short PEG chains and PC, respectively, as side groups. Grafting on silicon was carried out using surface-initiated atom transfer radical polymerization (ATRP). Graft density was controlled via the surface density of the ATRP initiator, and chain length of the grafts was controlled via the ratio of monomer to sacrificial initiator. The grafted surfaces were characterized by water contact angle, x-ray photoelectron spectroscopy, and atomic force microscopy. The effect of graft density and chain length on fibrinogen adsorption from buffer was investigated using radio labeling methods. Adsorption to both MPC- and OEGMA-grafted surfaces was found to decrease with increasing graft density and chain length. Adsorption on the MPC and OEGMA surfaces for a given chain length and density was essentially the same. Very low adsorption levels of the order of 7 ngcm(2) were seen on the most resistant surfaces. The effect of protein size on resistance to adsorption was studied using binary solutions of lysozyme (MW 14 600) and fibrinogen (MW 340 000). Adsorption levels in these experiments were also greatly reduced on the grafted surfaces compared to the control surfaces. It was concluded that at the lowest graft density, both proteins had unrestricted access to the substrate, and the relative affinities of the proteins for the substrate (higher affinity of fibrinogen) determined the composition of the layer. At the highest graft density also, where the adsorption of both proteins was very low, no preference for one or the other

  9. Petrogenesis of the post-collisional Oligo-Miocene Volcanism in NW Anatolia (Turkey): Balıkesir Volcanites

    NASA Astrophysics Data System (ADS)

    Ünal, Alp; Altunkaynak, Şafak; Benowitz, Jeff A.

    2016-04-01

    In this study, we present whole-rock chemical and Sr-Nd-Pb-O isotopic compositions as well as 40Ar/39Ar ages of Balıkesir volcanites to evaluate the nature, genesis and timing of the post-collisional Oligo-Miocene magmatism in NW Anatolia. Three main volcano-stratigraphic groups distinguished in the Balıkesir volcanites on the basis of field observations and petrographical investigations; 1) andesitic lavas and related pyroclastic units representing the lower part of the volcanic sequence; 2) Trachyandesite- basaltic trachyandesite lavas and 3) dacitic lavas and associated pyroclastic units corresponding to the upper part of the volcanic sequence. Both andesitic and dacitic pyroclastic units are represented with ash fall, ash block flow and flow breccia units. Geochemically, Balıkesir volcanites are ranging in composition from basaltic trachy-andesite to dacite. They are sub-alkaline in character and show enrichment in large ion lithophile elements (LILE) and light rare earth elements (LREE) relative to the high field strength elements (HFSE). Balıkesir volcanites display depletion in P, Ta, Nb and Ti. All these trace element characteristics and inter-element ratios suggest that magma forming the Balıkesir volcanites show similar patterns to those of subduction-related arc magmas and/or post collisional lavas. They have high initial 87Sr/86Sr ratios (0.707109-0.708620), low 143Nd/144Nd (0.512322- 0.512493). 206Pb/204Pb and 207Pb/204Pb values vary from 18.703 to 18.867 and 15.681 to 15.714, respectively and ɛNd values range between -5.61 and -2.27. 18O isotopic ratios range between 8.3 and 11.8. All these isotopic characteristics and major-trace element compositions of Balıkesir volcanites suggest that the lavas are co-genetic and originated from a hybrid magma derived from enriched mantle (EM II) source. 40Ar/39Ar dating yielded isochron ages of 22.9±0.2 - 21.0±0.2 which is consistent with other volcanic and plutonic associations of western Anatolia (eg

  10. An oligo-based microarray offers novel transcriptomic approaches for the analysis of pathogen resistance and fruit quality traits in melon (Cucumis melo L.)

    PubMed Central

    Mascarell-Creus, Albert; Cañizares, Joaquin; Vilarrasa-Blasi, Josep; Mora-García, Santiago; Blanca, José; Gonzalez-Ibeas, Daniel; Saladié, Montserrat; Roig, Cristina; Deleu, Wim; Picó-Silvent, Belén; López-Bigas, Nuria; Aranda, Miguel A; Garcia-Mas, Jordi; Nuez, Fernando; Puigdomènech, Pere; Caño-Delgado, Ana I

    2009-01-01

    Background Melon (Cucumis melo) is a horticultural specie of significant nutritional value, which belongs to the Cucurbitaceae family, whose economic importance is second only to the Solanaceae. Its small genome of approx. 450 Mb coupled to the high genetic diversity has prompted the development of genetic tools in the last decade. However, the unprecedented existence of a transcriptomic approaches in melon, highlight the importance of designing new tools for high-throughput analysis of gene expression. Results We report the construction of an oligo-based microarray using a total of 17,510 unigenes derived from 33,418 high-quality melon ESTs. This chip is particularly enriched with genes that are expressed in fruit and during interaction with pathogens. Hybridizations for three independent experiments allowed the characterization of global gene expression profiles during fruit ripening, as well as in response to viral and fungal infections in plant cotyledons and roots, respectively. Microarray construction, statistical analyses and validation together with functional-enrichment analysis are presented in this study. Conclusion The platform validation and enrichment analyses shown in our study indicate that this oligo-based microarray is amenable for future genetic and functional genomic studies of a wide range of experimental conditions in melon. PMID:19821986

  11. RoboOligo: software for mass spectrometry data to support manual and de novo sequencing of post-transcriptionally modified ribonucleic acids.

    PubMed

    Sample, Paul J; Gaston, Kirk W; Alfonzo, Juan D; Limbach, Patrick A

    2015-05-26

    Ribosomal ribonucleic acid (RNA), transfer RNA and other biological or synthetic RNA polymers can contain nucleotides that have been modified by the addition of chemical groups. Traditional Sanger sequencing methods cannot establish the chemical nature and sequence of these modified-nucleotide containing oligomers. Mass spectrometry (MS) has become the conventional approach for determining the nucleotide composition, modification status and sequence of modified RNAs. Modified RNAs are analyzed by MS using collision-induced dissociation tandem mass spectrometry (CID MS/MS), which produces a complex dataset of oligomeric fragments that must be interpreted to identify and place modified nucleosides within the RNA sequence. Here we report the development of RoboOligo, an interactive software program for the robust analysis of data generated by CID MS/MS of RNA oligomers. There are three main functions of RoboOligo: (i) automated de novo sequencing via the local search paradigm. (ii) Manual sequencing with real-time spectrum labeling and cumulative intensity scoring. (iii) A hybrid approach, coined 'variable sequencing', which combines the user intuition of manual sequencing with the high-throughput sampling of automated de novo sequencing.

  12. Body Composition, Hemodynamic and Biochemical Parameters in Young Female Normal-Weight Oligo-amenorrheic and Eumenorrheic Athletes and Non-athletes

    PubMed Central

    Singhal, Vibha; de Lourdes Eguiguren, Maria; Eysenbach, Lindsey; Clarke, Hannah; Slattery, Meghan; Eddy, Kamryn; Ackerman, Kathryn E.; Misra, Madhusmita

    2014-01-01

    Aims Low-weight hypogonadal conditions such as anorexia nervosa are associated with marked changes in body composition, hemodynamic and hematological parameters, and liver enzymes. The impact of athletic activity in normal-weight adolescents with/without amenorrhea on these parameters has not been assessed. Our aim was to examine these parameters in normal-weight athletes and non-athletes and determine any associations of body composition, oligo-amenorrhea and exercise intensity. Methods We assessed vital signs, complete blood counts, liver enzymes, and regional body composition in 43 oligo-amenorrheic athletes (OAA), 24 eumenorrheic athletes (EA) and 23 non-athletes 14-21 years of age. Results BMI was lower in OAA than EA. Systolic and pulse pressure, and temperature were lowest in OAA. Blood counts did not differ among groups. AST was higher in both groups of athletes, while ALT was higher in OAA than EA and non-athletes. Total and regional fat was lower in OAA than other groups, positively associated with heart rate and inversely with liver enzymes. Conclusions Athletic activity is associated with higher AST, whereas menstrual dysfunction is associated with lower total and regional fat and higher ALT. Higher liver enzymes are associated with reductions in total and regional fat. PMID:25376841

  13. Purification of compounds from Lignum Dalbergia Odorifera using two-dimensional preparative chromatography with Click oligo (ethylene glycol) and C18 column.

    PubMed

    Feng, Jiatao; Xiao, Yuansheng; Guo, Zhimou; Yu, Danhua; Jin, Yu; Liang, Xinmiao

    2011-02-01

    Purification of compounds from traditional Chinese medicines (TCMs) is an important task for understanding the chemical composition of TCMs. However, it is difficult to obtain compounds with high enough purity for identification by NMR due to the complexity of TCMs in chemical composition. In this study, a two-dimensional purification method based on a Click oligo (ethylene glycol) column and a C18 column was developed to realize an orthogonal separation in preparative level for purifying compounds efficiently. The first dimensional preparation was performed on a Click oligo (ethylene glycol) column to simplify the sample into the fractions with good separation repeatability. On the first dimension, 7.2 g sample was separated into 11 fractions with a recovery of 86% within 6 h. A C18 column was taken as the second dimension to realize the high-performance separation and rapid preparation from the fractions collected from the first dimension. Eight compounds in fraction 6 and 2 compounds in fraction 8 were isolated and identified after optimizing the separation and collection parameters. This method is a high-efficient and orthogonal preparation method to improve the separation of a complex sample and increase the purity of the compounds, which benefits from the application of novel materials in the preparation and purification.

  14. Oligo-1,6-glucosidase and neopullulanase enzyme subfamilies from the alpha-amylase family defined by the fifth conserved sequence region.

    PubMed

    Oslancová, A; Janecek, S

    2002-11-01

    The alpha-amylase enzyme family is the largest family of glycoside hydrolases. It contains almost 30 different enzyme specificities covering hydrolases, transferases and isomerases. Some of the enzyme specificities from the family are closely related, others less so. This study, based on the analysis of 79 amino acid sequences, postulates two subfamilies in the framework of the aamylase family: the oligo-1,6-glucosidase subfamily and the neopullulanase subfamily. The specific sequence in the fifth conserved sequence region of the family served as the basis for defining the subfamilies: QpDln for the oligo-1,6-glucosidase subfamily and MPKln for the neopullulanase subfamily. This conserved sequence region is proposed to be the selection marker that enables one to distinguish between the two subfamilies. The 'intermediary' sequence MPDLN can be characteristic of the so-called intermediary group with a mixed enzyme specificity of alpha-amylase, cyclomaltodextrinase and neopullulanase. The evolutionary trees clearly supported the proposed definition of the two subfamilies.

  15. Engineering calcium oxalate crystal formation in Arabidopsis.

    PubMed

    Nakata, Paul A

    2012-07-01

    Many plants accumulate crystals of calcium oxalate. Just how these crystals form remains unknown. To gain insight into the mechanisms regulating calcium oxalate crystal formation, a crystal engineering approach was initiated utilizing the non-crystal-accumulating plant, Arabidopsis. The success of this approach hinged on the ability to transform Arabidopsis genetically into a calcium oxalate crystal-accumulating plant. To accomplish this transformation, two oxalic acid biosynthetic genes, obcA and obcB, from the oxalate-secreting phytopathogen, Burkholderia glumae were inserted into the Arabidopsis genome. The co-expression of these two bacterial genes in Arabidopsis conferred the ability not only to produce a measurable amount of oxalate but also to form crystals of calcium oxalate. Biochemical and cellular studies of crystal accumulation in Arabidopsis revealed features that are similar to those observed in the cells of crystal-forming plants. Thus, it appears that at least some of the basic components that comprise the calcium oxalate crystal formation machinery are conserved even in non-crystal-accumulating plants.

  16. Terpene Specialized Metabolism in Arabidopsis thaliana

    PubMed Central

    Tholl, Dorothea; Lee, Sungbeom

    2011-01-01

    Terpenes constitute the largest class of plant secondary (or specialized) metabolites, which are compounds of ecological function in plant defense or the attraction of beneficial organisms. Using biochemical and genetic approaches, nearly all Arabidopsis thaliana (Arabidopsis) enzymes of the core biosynthetic pathways producing the 5-carbon building blocks of terpenes have been characterized and closer insight has been gained into the transcriptional and posttranscriptional/translational mechanisms regulating these pathways. The biochemical function of most prenyltransferases, the downstream enzymes that condense the C5-precursors into central 10-, 15-, and 20-carbon prenyldiphosphate intermediates, has been described, although the function of several isoforms of C20-prenyltranferases is not well understood. Prenyl diphosphates are converted to a variety of C10-, C15-, and C20-terpene products by enzymes of the terpene synthase (TPS) family. Genomic organization of the 32 Arabidopsis TPS genes indicates a species-specific divergence of terpene synthases with tissue- and cell-type specific expression profiles that may have emerged under selection pressures by different organisms. Pseudogenization, differential expression, and subcellular segregation of TPS genes and enzymes contribute to the natural variation of terpene biosynthesis among Arabidopsis accessions (ecotypes) and species. Arabidopsis will remain an important model to investigate the metabolic organization and molecular regulatory networks of terpene specialized metabolism in relation to the biological activities of terpenes. PMID:22303268

  17. Nitric oxide reduces seed dormancy in Arabidopsis.

    PubMed

    Bethke, Paul C; Libourel, Igor G L; Jones, Russell L

    2006-01-01

    Dormancy is a property of many mature seeds, and experimentation over the past century has identified numerous chemical treatments that will reduce seed dormancy. Nitrogen-containing compounds including nitrate, nitrite, and cyanide break seed dormancy in a range of species. Experiments are described here that were carried out to further our understanding of the mechanism whereby these and other compounds, such as the nitric oxide (NO) donor sodium nitroprusside (SNP), bring about a reduction in seed dormancy of Arabidopsis thaliana. A simple method was devised for applying the products of SNP photolysis through the gas phase. Using this approach it was shown that SNP, as well as potassium ferricyanide (Fe(III)CN) and potassium ferrocyanide (Fe(II)CN), reduced dormancy of Arabidopsis seeds by generating cyanide (CN). The effects of potassium cyanide (KCN) on dormant seeds were tested and it was confirmed that cyanide vapours were sufficient to break Arabidopsis seed dormancy. Nitrate and nitrite also reduced Arabidopsis seed dormancy and resulted in substantial rates of germination. The effects of CN, nitrite, and nitrate on dormancy were prevented by the NO scavenger c-PTIO. It was confirmed that NO plays a role in reducing seed dormancy by using purified NO gas, and a model to explain how nitrogen-containing compounds may break dormancy in Arabidopsis is presented.

  18. Identifying essential genes in Arabidopsis thaliana.

    PubMed

    Meinke, David; Muralla, Rosanna; Sweeney, Colleen; Dickerman, Allan

    2008-09-01

    Eight years after publication of the Arabidopsis genome sequence and two years before completing the first phase of an international effort to characterize the function of every Arabidopsis gene, plant biologists remain unable to provide a definitive answer to the following basic question: what is the minimal gene set required for normal growth and development? The purpose of this review is to summarize different strategies employed to identify essential genes in Arabidopsis, an important component of the minimal gene set in plants, to present an overview of the datasets and specific genes identified to date, and to discuss the prospects for future saturation of this important class of genes. The long-term goal of this collaborative effort is to facilitate basic research in plant biology and complement ongoing research with other model organisms.

  19. Mineral chemistry, crystallization conditions and geodynamic implications of the Oligo-Miocene granitoids in the Biga Peninsula, Northwest Turkey

    NASA Astrophysics Data System (ADS)

    Aysal, Namık

    2015-06-01

    6.79% (mean = 4.15%). Meanwhile, the biotites, which display consistent oxygen fugacity values (-10.65 to -13.22), suggest their reliability with the typical values of calc-alkaline magma crystallization. These values suggest a relatively higher oxidation state during crystallization and are related to arc magmatism. All of the calculated values indicate that all of the plutons were emplaced at shallow crustal levels. It can be inferred that the Oligo-Miocene magmatism in NW Turkey may be linked to crustal thinning that resulted from slab roll-back and a back-arc extensional regime after the collision between the Sakarya Zone and Anatolide-Tauride Platform.

  20. Differentiation of programmed Arabidopsis cells

    PubMed Central

    Xie, De-Yu; Shi, Ming-Zhu

    2012-01-01

    Plants express genes that encode enzymes that catalyse reactions to form plant secondary metabolites in specific cell types. However, the mechanisms of how plants decide their cellular metabolic fate and how cells diversify and specialise their specific secondary metabolites remains largely unknown. Additionally, whether and how an established metabolic program impacts genome-wide reprogramming of plant gene expression is unclear. We recently isolated PAP1-programmed anthocyanin-producing (red) and -free (white) cells from Arabidopsis thaliana; our previous studies have indicated that the PAP1 expression level is similar between these two different cell types. Transcriptional analysis showed that the red cells contain the TTG1-GL3/TT8-PAP1 regulatory complex, which controls anthocyanin biosynthesis; in contrast, the white cells and the wild-type cells lack this entire complex. These data indicate that different regulatory programming underlies the different metabolic states of these cells. In addition, our previous transcriptomic comparison indicated that there is a clear difference in the gene expression profiles of the red and wild-type cells, which is probably a consequence of cell-specific reprogramming. Based on these observations, in this report we discuss the potential mechanisms that underlie the programming and reprogramming of gene expression involved in anthocyanin biosynthesis. PMID:22126737

  1. The selective isolation of the uterine oestradiol-receptor complex by binding to oligo(dT)-cellulose. The mediation of an essential activator in the transformation of cytosol receptor.

    PubMed Central

    Thrower, S; Hall, C; Lim, L; Davison, A N

    1976-01-01

    The [3H]oestradiol-receptor complex was selectively isolated from rat uterus cytosol by column chromatography on oligo(dT)-cellulose. Optimal conditions are described for the binding of the complex to oligo(dT)-cellulose, which is shown to be similar to its binding to DNA-cellulose. The cytosol complex has an apparent mol. wt. of 50,000-60,000 in high salt concentrations, as determined by Sephadex G-100 chromatography. This corresponds to the 4S cytoplasmic oestradiol receptor. In binding to oligo(dT)-cellulose the receptor is transformed into a form with an apparent mol.wt. of 100,000-120,000, corresponding to the 5S nuclear receptor complex. This transformation mimics the conversion in vivo of the cytoplasmic oestradiol receptor into the nuclear form. The binding of the complex to oligo(dT)-cellulose as a 5S nuclear form is unequivocally demonstrated to require the mediation of an activating present in the cytosol. The requirement for an activating factor is discussed in relation to reports that nuclear binding of the oestradiol-receptor complex is not dictated solely by the availability of the cytoplasmic oestradiol receptor. PMID:1008856

  2. Oligo-DNA Custom Macroarray for Monitoring Major Pathogenic and Non-Pathogenic Fungi and Bacteria in the Phyllosphere of Apple Trees

    PubMed Central

    He, Ying-Hong; Isono, Sayaka; Shibuya, Makoto; Tsuji, Masaharu; Adkar Purushothama, Charith-Raj; Tanaka, Kazuaki; Sano, Teruo

    2012-01-01

    Background To monitor the richness in microbial inhabitants in the phyllosphere of apple trees cultivated under various cultural and environmental conditions, we developed an oligo-DNA macroarray for major pathogenic and non-pathogenic fungi and bacteria inhabiting the phyllosphere of apple trees. Methods and Findings First, we isolated culturable fungi and bacteria from apple orchards by an agar-plate culture method, and detected 32 fungal and 34 bacterial species. Alternaria, Aureobasidium, Cladosporium, Rhodotorula, Cystofilobasidium, and Epicoccum genera were predominant among the fungi, and Bacillus, Pseudomonas, Sphingomonas, Methylobacterium, and Pantoea genera were predominant among the bacteria. Based on the data, we selected 29 major non-pathogenic and 12 phytopathogenic fungi and bacteria as the targets of macroarray. Forty-one species-specific 40-base pair long oligo-DNA sequences were selected from the nucleotide sequences of rDNA-internal transcribed spacer region for fungi and 16S rDNA for bacteria. The oligo-DNAs were fixed on nylon membrane and hybridized with digoxigenin-labeled cRNA probes prepared for each species. All arrays except those for Alternaria, Bacillus, and their related species, were specifically hybridized. The array was sensitive enough to detect 103 CFU for Aureobasidium pullulans and Bacillus cereus. Nucleotide sequencing of 100 each of independent fungal rDNA-ITS and bacterial 16S-rDNA sequences from apple tree was in agreement with the macroarray data obtained using the same sample. Finally, we analyzed the richness in the microbial inhabitants in the samples collected from apple trees in four orchards. Major apple pathogens that cause scab, Alternaria blotch, and Marssonina blotch were detected along with several non-phytopathogenic fungal and bacterial inhabitants. Conclusions The macroarray technique presented here is a strong tool to monitor the major microbial species and the community structures in the phyllosphere of

  3. Analysis of Unfolded Protein Response in Arabidopsis

    PubMed Central

    Chen, Yani; Brandizzi, Federica

    2014-01-01

    The unfolded protein response (UPR) is fundamental for development and adaption in eukaryotic cells. Arabidopsis has become one of the best model systems to uncover conserved mechanisms of the UPR in multicellular eukaryotes as well as organism-specific regulation of the UPR in plants. Monitoring the UPR in planta is an elemental approach to identifying regulatory components and to revealing molecular mechanisms of the plant UPR. In this chapter, we provide protocols for the induction and analyses of plant UPR at a molecular level in Arabidopsis. Three kinds of ER stress treatment methods and quantitation of the plant UPR activation are described here. PMID:23913037

  4. Oligo-recurrence predicts favorable prognosis of brain-only oligometastases in patients with non-small cell lung cancer treated with stereotactic radiosurgery or stereotactic radiotherapy: a multi-institutional study of 61 subjects.

    PubMed

    Niibe, Yuzuru; Nishimura, Tetsuo; Inoue, Tetsuya; Karasawa, Katsuyuki; Shioyama, Yoshiyuki; Jingu, Keiichi; Shirato, Hiroki

    2016-08-19

    To investigate the prognostic value of oligo-recurrence in patients with brain-only oligometastases of non-small cell lung cancer (NSCLC) treated with stereotactic radiosurgery (SRS) or stereotactic radiotherapy (SRT). Patients treated with SRS or SRT for brain-only NSCLC oligometastases in 6 high-volume institutions in Japan between 1996 and 2008 were reviewed. Eligible patients met 1), 2), and 4) or 1), 3), and 4) of the following: 1) NSCLC with 1 to 4 brain metastases on magnetic resonance imaging (MRI) treated with SRS or SRT; 2) control of the primary lesions (thorax) at the time of SRS or SRT for brain metastases (patients meeting this criterion formed the oligo-recurrence group); 3) with SRS or SRT for brain metastases, concomitant treatment for active primary lesions (thorax) with curative surgery or curative stereotactic body radiotherapy (SBRT), or curative chemoradiotherapy (sync-oligometastases group); and 4) Karnofsky performance status (KPS) ≥70. The median overall survival (OS) of all 61 patients was 26 months (95 % CI: 17.5-34.5 months). The 2-year and 5-year overall survival rates were 60.7 and 15.7 %, respectively. Stratified by oligostatus, the sync-oligometastases group achieved a median OS of 18 months (95 % CI: 14.8-21.1 months) and a 5-year OS of 0 %, while the oligo-recurrence group achieved a median OS of 41 months (95 % CI: 27.8-54.2 months) and a 5-year OS of 18.6 %. On multivariate analysis, oligo-recurrence was the only significant independent factor related to a favorable prognosis (hazard ratio: 0.253 (95 % CI: 0.082-0.043) (p = 0.025). The presence of oligo-recurrence can predict a favorable prognosis of brain-only oligometastases in patients with NSCLC treated with SRS or SRT.

  5. The combination of oligo- and polysaccharides and reticulated protein for the control of symptoms in patients with irritable bowel syndrome: Results of a randomised, placebo-controlled, double-blind, parallel group, multicentre clinical trial

    PubMed Central

    Alexea, Octavian; Bacarea, Vlad

    2015-01-01

    Background A medical device containing the film-forming agent reticulated protein and a prebiotic mixture of vegetable oligo- and polysaccharides has been developed, recently receiving European approval as MED class III for the treatment of chronic/functional or recidivant diarrhoea due to different causes including irritable bowel syndrome (IBS). In the present paper, we evaluate a protein preparation containing these components in comparison with placebo in adult patients with diarrhoea-predominant IBS. Methods In a randomised, placebo-controlled, double-blind, parallel group, multicentre clinical trial, patients were randomly assigned to receive the combination of oligo- and polysaccharides and reticulated protein and placebo (four oral tablets/day for 56 days). Demographic, clinical and quality of life characteristics and presence and intensity of abdominal pain and flatulence (seven-point Likert scale) were assessed at three study visits (baseline and at 28 and 56 days). Stool emissions were recorded on the diary card using the seven-point Bristol Stool Scale. Results A total of 128 patients were randomised to receive either tablets containing the combination (n = 63) or placebo (n = 65). Treatment with oligo- and polysaccharides and reticulated protein was safe and well tolerated. A significant improvement in symptoms across the study was observed in patients treated with oligo- and polysaccharides and reticulated protein between visit 2 and visit 3 in abdominal pain (p = 0.0167) and flatulence (p = 0.0373). We also detected a statistically significant increase in the quality of life of patients receiving the active treatment from baseline to visit 3 (p < 0.0001). Conclusions Treatment with oligo- and polysaccharides and reticulated protein is safe, improving IBS symptoms and quality of life of patients with diarrhoea-predominant IBS. PMID:27403313

  6. A broader role for AmyR in Aspergillus niger: regulation of the utilisation of D-glucose or D-galactose containing oligo- and polysaccharides.

    PubMed

    vanKuyk, Patricia A; Benen, Jaques A E; Wösten, Han A B; Visser, Jaap; de Vries, Ronald P

    2012-01-01

    AmyR is commonly considered a regulator of starch degradation whose activity is induced by the presence of maltose, the disaccharide building block of starch. In this study, we demonstrate that the role of AmyR extends beyond starch degradation. Enzyme activity assays, genes expression analysis and growth profiling on D-glucose- and D-galactose-containing oligo- and polysaccharides showed that AmyR regulates the expression of some of the Aspergillus niger genes encoding α- and β-glucosidases, α- and β- galactosidases, as well as genes encoding α-amlyases and glucoamylases. In addition, we provide evidence that D-glucose or a metabolic product thereof may be the inducer of the AmyR system in A. niger and not maltose, as is commonly assumed.

  7. Oligo-aspartic acid conjugates with benzo[c][2,6]naphthyridine-8-carboxylic acid scaffold as picomolar inhibitors of CK2.

    PubMed

    Vahter, Jürgen; Viht, Kaido; Uri, Asko; Enkvist, Erki

    2017-02-28

    Structurally diverse inhibitors of the protein kinase CK2 are required for regulation of this ubiquitous protein to establish biological roles of the enzyme which catalyzes the phosphorylation of a vast number of substrate proteins. In this article we disclose a series of new bisubstrate inhibitors of CK2 that are structurally represented by the oligo(l-Asp) peptide conjugates of benzo[c][2,6]naphthyridine-8-carboxylic acid. This fragment originated from CX-4945, the first in class inhibitor taken to clinical trials. The most potent conjugates possessed two-digit picomolar affinity and clear selectivity for CK2α in a panel of 140 protein kinases. Labeling of the inhibitors with a fluorescent dye yielded probes for a fluorescence anisotropy-based binding/displacement assay which can be used for analysis of CK2 and precise determination of affinity of the highly potent (tight-binding) CK2-targeting inhibitors.

  8. Prevailing Photocurrent Generation of D-π-A Type Oligo(phenyleneethynylene) in Contact with Gold over Dexter-Type Energy-Transfer Quenching.

    PubMed

    Uji, Hirotaka; Ito, Taichi; Matsumoto, Mitsuaki; Kimura, Shunsaku

    2016-03-03

    Photocurrent generation is observed with D-π-A type oligo(phenyleneethynylene) (OPE) physically contacting gold substrate. The OPE is conjugated with helical peptides, which helps the OPE moiety orient vertically on gold surface. This configuration makes the Dexter energy transfer difficult to occur even though one end of the D-π-A type OPE physically contacts gold. The anodic photocurrent continuously increases with increment of applying bias voltage from -0.3 to 0.5 V. The first principle calculations reveal that the increase in photocurrent generation is attributed partly to the change in the electron distributions of HOMO and LUMO of the D-π-A type OPE to be more localized with applying the positive potential.

  9. Presence of Potential Toxin-Producing Cyanobacteria in an Oligo-Mesotrophic Lake in Baltic Lake District, Germany: An Ecological, Genetic and Toxicological Survey

    PubMed Central

    Dadheech, Pawan K.; Selmeczy, Géza B.; Vasas, Gábor; Padisák, Judit; Arp, Wolfgang; Tapolczai, Kálmán; Casper, Peter; Krienitz, Lothar

    2014-01-01

    Massive developments of potentially toxic cyanobacteria in Lake Stechlin, an oligo-mesotrophic lake in the Baltic Lake District of Germany raised concerns about toxic contamination of these important ecosystems. Field samples in the phase of mass developments of cyanobacteria were used for genetic and toxicological analyses. Microcystins and microcystin genes were detected in field samples of the lake for the first time. However, the toxins were not produced by the dominant taxa (Dolichospermum circinale and Aphanizomenon flos-aquae) but by taxa, which were present only in low biomass in the samples (Microcystis cf. aeruginosa and Planktothrix rubescens). The phytoplankton successions during the study period revealed an increase of cyanobacterial populations. The findings contribute to the changes that have been investigated in Lake Stechlin since the mid-1990s. The possible reasons behind these developments may be climate change, special weather conditions and an increased nutrient pool. PMID:25268981

  10. Presence of potential toxin-producing cyanobacteria in an oligo-mesotrophic lake in Baltic Lake District, Germany: an ecological, genetic and toxicological survey.

    PubMed

    Dadheech, Pawan K; Selmeczy, Géza B; Vasas, Gábor; Padisák, Judit; Arp, Wolfgang; Tapolczai, Kálmán; Casper, Peter; Krienitz, Lothar

    2014-09-29

    Massive developments of potentially toxic cyanobacteria in Lake Stechlin, an oligo-mesotrophic lake in the Baltic Lake District of Germany raised concerns about toxic contamination of these important ecosystems. Field samples in the phase of mass developments of cyanobacteria were used for genetic and toxicological analyses. Microcystins and microcystin genes were detected in field samples of the lake for the first time. However, the toxins were not produced by the dominant taxa (Dolichospermum circinale and Aphanizomenon flos-aquae) but by taxa, which were present only in low biomass in the samples (Microcystis cf. aeruginosa and Planktothrix rubescens). The phytoplankton successions during the study period revealed an increase of cyanobacterial populations. The findings contribute to the changes that have been investigated in Lake Stechlin since the mid-1990s. The possible reasons behind these developments may be climate change, special weather conditions and an increased nutrient pool.

  11. Novel glyoxalases from Arabidopsis thaliana.

    PubMed

    Kwon, Kyu; Choi, Dongwook; Hyun, Jae Kyung; Jung, Hyun Suk; Baek, Kwanghee; Park, Chankyu

    2013-07-01

    We examined six Arabidopsis thaliana genes from the DJ-1/PfpI superfamily for similarity to the recently characterized bacterial and animal glyoxalases. Based on their sequence similarities, the six genes were classified into two sub-groups consisting of homologs of the human DJ-1 gene and the PH1704 gene of Pyrococcus horikoshii. Unlike the homologs from other species, all the A. thaliana genes have two tandem domains, which may have been created by gene duplication. The six AtDJ-1 proteins (a-f) were expressed in Escherichia coli for enzymatic assays with glyoxals. The DJ-1d protein, which belongs to the PH1704 sub-group, exhibits the highest activity against methylglyoxal and glyoxal, and K(m) values of 0.10 and 0.27 mm were measured for these two substrates, respectively, while the corresponding k(cat) values were 1700 and 2200 min(-1), respectively. The DJ-1a and DJ-1b glyoxalases exhibited higher specificity towards glyoxal. The other three proteins have either no or extremely low activity for glyoxals. For the DJ-1d enzyme, the residues, Cys120/313 and Glu19/212 at the active site and His121/314 and Glu94/287 at the oligomeric interface were mutated to alanines. As in other enzymes characterized to date, mutation of either the Cys or the Glu residues of the active site completely abolished enzyme activity, whereas mutation of the interface residues produced a variable decrease in activity. DJ-1d differs from its animal and bacterial homologs with respect to the configuration of its catalytic residues and the oligomeric property of the enzyme. When the wild-type DJ-1d enzyme was expressed in E. coli, the bacteria became resistant to glyoxals. © 2013 FEBS.

  12. Prognostic Value of MR Imaging Texture Analysis in Brain Non-Small Cell Lung Cancer Oligo-Metastases Undergoing Stereotactic Irradiation

    PubMed Central

    Tini, Paolo; Biondi, Michelangelo; Sebaste, Lucio; Vanzi, Eleonora; De Otto, Gianmarco; Rubino, Giovanni; Carfagno, Tommaso; Battaglia, Giuseppe; Pastina, Pierpaolo; Cerase, Alfonso; Mazzoni, Lorenzo Nicola; Banci Buonamici, Fabrizio; Pirtoli, Luigi

    2016-01-01

    Background  Stereotactic irradiation is widely used in brain oligo-metastases treatment. The aim of this study is to evaluate the prognostic value of magnetic resonance imaging (MRI) texture analysis (TA) of brain metastases (BM) of non-small cell lung cancer (NSCLC). Materials and methods  This study included thirty-eight consecutive patients undergoing stereotactic irradiation, that is, stereotactic fractionated radiotherapy (SRT) or radiosurgery (SRS), from January 2011 to December 2014 for 1-2 brain BM from NSCLC. Whole-brain radiotherapy (WBRT) was not delivered. The diagnostic MRI DICOM (Digital Imaging and Communications in Medicine) images were collected and analyzed with a homemade ImageJ macro, and typical TA parameters (mean, standard deviation, skewness, kurtosis, entropy, and uniformity) were evaluated for: brain progression-free survival; modality of brain metastatic progression (local progression or/and new metastases); and overall survival, after SRT/SRS. Results After SRT/SRS 14 patients (36.8%) experienced recurrence in the brain, with a recurrence in the irradiated site (five patients, 13.2%), new metastases (11 patients, 28.9%), local recurrence and new metastases (two patients, 5.25%). Nineteen patients (50%) died of tumor progression or other causes. Entropy and uniformity were significantly associated with local progression, whereas kurtosis was significantly associated with both local progression and new brain metastases. Conclusions  These results appear promising, since the knowledge of factors correlated with the modality of brain progression after stereotactic irradiation of brain oligo-metastatic foci of NSCLC might help in driving the best treatment in these patients (association of SRT/SRS with WBRT? Increase of SRT/SRS dose?). Our preliminary data needs confirmation in large patient series. PMID:27226944

  13. Prognostic Value of MR Imaging Texture Analysis in Brain Non-Small Cell Lung Cancer Oligo-Metastases Undergoing Stereotactic Irradiation.

    PubMed

    Nardone, Valerio; Tini, Paolo; Biondi, Michelangelo; Sebaste, Lucio; Vanzi, Eleonora; De Otto, Gianmarco; Rubino, Giovanni; Carfagno, Tommaso; Battaglia, Giuseppe; Pastina, Pierpaolo; Cerase, Alfonso; Mazzoni, Lorenzo Nicola; Banci Buonamici, Fabrizio; Pirtoli, Luigi

    2016-04-25

    BACKGROUND : Stereotactic irradiation is widely used in brain oligo-metastases treatment. The aim of this study is to evaluate the prognostic value of magnetic resonance imaging (MRI) texture analysis (TA) of brain metastases (BM) of non-small cell lung cancer (NSCLC). MATERIALS AND METHODS : This study included thirty-eight consecutive patients undergoing stereotactic irradiation, that is, stereotactic fractionated radiotherapy (SRT) or radiosurgery (SRS), from January 2011 to December 2014 for 1-2 brain BM from NSCLC. Whole-brain radiotherapy (WBRT) was not delivered. The diagnostic MRI DICOM (Digital Imaging and Communications in Medicine) images were collected and analyzed with a homemade ImageJ macro, and typical TA parameters (mean, standard deviation, skewness, kurtosis, entropy, and uniformity) were evaluated for: brain progression-free survival; modality of brain metastatic progression (local progression or/and new metastases); and overall survival, after SRT/SRS. After SRT/SRS 14 patients (36.8%) experienced recurrence in the brain, with a recurrence in the irradiated site (five patients, 13.2%), new metastases (11 patients, 28.9%), local recurrence and new metastases (two patients, 5.25%). Nineteen patients (50%) died of tumor progression or other causes. Entropy and uniformity were significantly associated with local progression, whereas kurtosis was significantly associated with both local progression and new brain metastases. CONCLUSIONS : These results appear promising, since the knowledge of factors correlated with the modality of brain progression after stereotactic irradiation of brain oligo-metastatic foci of NSCLC might help in driving the best treatment in these patients (association of SRT/SRS with WBRT? Increase of SRT/SRS dose?). Our preliminary data needs confirmation in large patient series.

  14. Provenance of Oligo-Miocene Strata from the Adriatic Foredeep of the Alps-Apennines System Determined through Detrital-Zircon U-Pb Geochronology

    NASA Astrophysics Data System (ADS)

    Dafov, L. N.; Anfinson, O. A.; Malusa', M. G.; Stockli, D. F.

    2014-12-01

    U-Pb geochronology of detrital zircon is an effective method for evaluating exhumation history, provenance, and depositional age constraints of sedimentary deposits. Over 1400 grains evaluated from thirteen samples collected from distal and proximal Oligo-Miocene strata of Adriatic turbidites are consistent with modern characterization of the proposed source region. Studies indicate that the principal source area of Oligo-Miocene strata from Adriatic deposits is the Lepontine Dome of the Central Alps. Our data reveals a significant shift in detrital zircon U-Pb age populations during the Oligocene-Miocene boundary which, when compared with data from modern sands, closely correlates to the westward shift of the erosional foci within the Lepontine Dome, from the Ticino to the Toce subdome, due to progressive indentation of Adria. This is coeval with progressive unroofing of Periadriatic magmatic rocks of Tertiary age along the Insubric Fault. The lowermost Upper Oligocene proximal samples collected from the Como and Villa Olmo Conglomerates are dominated by Caledonian and Cadomian detrital zircon U-Pb age populations. The uppermost Oligocene and lower Miocene proximal samples collected from the Como Conglomerate are dominated instead by Periadriatic detrital zircon. Distal samples collected from the Lower Oligocene Aveto Formation have a dominant Periadriatic age peak with lesser amounts of late Cretaceous, Variscan, Caledonian and Cadomian detrital zircon. The lowermost Upper Oligocene distal samples collected from the Macigno Formation contain populations of Periadriatic, Variscan, Caledonian, and Cadomian detrital zircon, with major shifts in relative abundance from the lower to upper strata. The most dramatic shift in provenance in the distal units is between two samples located relatively proximally to one another in the Modino unit: Upper Oligocene marls contains primarily Variscan and Caledonian zircon grains with no individuals yielding Periadriatic ages

  15. Characterization of Recombinant UDP- and ADP-Glucose Pyrophosphorylases and Glycogen Synthase To Elucidate Glucose-1-Phosphate Partitioning into Oligo- and Polysaccharides in Streptomyces coelicolor

    PubMed Central

    Asención Diez, Matías D.; Peirú, Salvador; Demonte, Ana M.; Gramajo, Hugo

    2012-01-01

    Streptomyces coelicolor exhibits a major secondary metabolism, deriving important amounts of glucose to synthesize pigmented antibiotics. Understanding the pathways occurring in the bacterium with respect to synthesis of oligo- and polysaccharides is of relevance to determine a plausible scenario for the partitioning of glucose-1-phosphate into different metabolic fates. We report the molecular cloning of the genes coding for UDP- and ADP-glucose pyrophosphorylases as well as for glycogen synthase from genomic DNA of S. coelicolor A3(2). Each gene was heterologously expressed in Escherichia coli cells to produce and purify to electrophoretic homogeneity the respective enzymes. UDP-glucose pyrophosphorylase (UDP-Glc PPase) was characterized as a dimer exhibiting a relatively high Vmax in catalyzing UDP-glucose synthesis (270 units/mg) and with respect to dTDP-glucose (94 units/mg). ADP-glucose pyrophosphorylase (ADP-Glc PPase) was found to be tetrameric in structure and specific in utilizing ATP as a substrate, reaching similar activities in the directions of ADP-glucose synthesis or pyrophosphorolysis (Vmax of 0.15 and 0.27 units/mg, respectively). Glycogen synthase was arranged as a dimer and exhibited specificity in the use of ADP-glucose to elongate α-1,4-glucan chains in the polysaccharide. ADP-Glc PPase was the only of the three enzymes exhibiting sensitivity to allosteric regulation by different metabolites. Mannose-6-phosphate, phosphoenolpyruvate, fructose-6-phosphate, and glucose-6-phosphate behaved as major activators, whereas NADPH was a main inhibitor of ADP-Glc PPase. The results support a metabolic picture where glycogen synthesis occurs via ADP-glucose in S. coelicolor, with the pathway being strictly regulated in connection with other routes involved with oligo- and polysaccharides, as well as with antibiotic synthesis in the bacterium. PMID:22210767

  16. An International Bioinformatics Infrastructure to Underpin the Arabidopsis Community

    PubMed Central

    2010-01-01

    The future bioinformatics needs of the Arabidopsis community as well as those of other scientific communities that depend on Arabidopsis resources were discussed at a pair of recent meetings held by the Multinational Arabidopsis Steering Committee and the North American Arabidopsis Steering Committee. There are extensive tools and resources for information storage, curation, and retrieval of Arabidopsis data that have been developed over recent years primarily through the activities of The Arabidopsis Information Resource, the Nottingham Arabidopsis Stock Centre, and the Arabidopsis Biological Resource Center, among others. However, the rapid expansion in many data types, the international basis of the Arabidopsis community, and changing priorities of the funding agencies all suggest the need for changes in the way informatics infrastructure is developed and maintained. We propose that there is a need for a single core resource that is integrated into a larger international consortium of investigators. We envision this to consist of a distributed system of data, tools, and resources, accessed via a single information portal and funded by a variety of sources, under shared international management of an International Arabidopsis Informatics Consortium (IAIC). This article outlines the proposal for the development, management, operations, and continued funding for the IAIC. PMID:20807877

  17. Engineering calcium oxalate crystal formation in Arabidopsis

    USDA-ARS?s Scientific Manuscript database

    Many plants accumulate crystals of calcium oxalate. Just how these crystals form remains unknown. To gain insight into the mechanisms regulating calcium oxalate crystal formation, a crystal engineering approach was initiated utilizing the non-crystal accumulating plant, Arabidopsis. The success of t...

  18. Shotgun Proteomic Analysis of Arabidopsis thaliana Leaves

    USDA-ARS?s Scientific Manuscript database

    Two shotgun tandem mass spectrometry proteomics approaches, Multidimensional Protein Identification Technology (MudPIT) and 1D-Gel-LC-MS/MS, were used to identify Arabidopsis thaliana leaf proteins. These methods utilize different protein/peptide separation strategies. Detergents not compatible wit...

  19. Biosynthetic Pathways of Brassinolide in Arabidopsis1

    PubMed Central

    Noguchi, Takahiro; Fujioka, Shozo; Choe, Sunghwa; Takatsuto, Suguru; Tax, Frans E.; Yoshida, Shigeo; Feldmann, Kenneth A.

    2000-01-01

    Our previous studies on the endogenous brassinosteroids (BRs) in Arabidopsis have provided suggestive evidence for the operation of the early C6-oxidation and the late C6-oxidation pathways, leading to brassinolide (BL) in Arabidopsis. However, to date the in vivo operation of these pathways has not been fully confirmed in this species. This paper describes metabolic studies using deuterium-labeled BRs in wild-type and BR-insensitive mutant (bri1) seedlings to establish the intermediates of the biosynthetic pathway of BL in Arabidopsis. The first evidence for the conversion of campestanol to 6-deoxocathasterone and the conversion of 6-deoxocathasterone to 6-deoxoteasterone is provided. The later biosynthetic steps (6-deoxoteasterone → 3-dehydro-6-deoxoteasterone → 6-deoxotyphasterol → 6-deoxocastasterone → 6α-hydroxycastasterone → castasterone → BL) were demonstrated by stepwise metabolic experiments. Therefore, these studies complete the documentation of the late C6-oxidation pathway. The biosynthetic sequence involved in the early C6-oxidation pathway (teasterone → 3-dehydroteasterone → typhasterol → castasterone → BL) was also demonstrated. These results show that both the early and late C6-oxidation pathways are functional in Arabidopsis. In addition we report two new observations: the presence of a new branch in the pathway, C6 oxidation of 6-deoxotyphasterol to typhasterol, and increased metabolic flow in BR-insensitive mutants. PMID:10982435

  20. Biosynthetic pathways of brassinolide in Arabidopsis.

    PubMed

    Noguchi, T; Fujioka, S; Choe, S; Takatsuto, S; Tax, F E; Yoshida, S; Feldmann, K A

    2000-09-01

    Our previous studies on the endogenous brassinosteroids (BRs) in Arabidopsis have provided suggestive evidence for the operation of the early C6-oxidation and the late C6-oxidation pathways, leading to brassinolide (BL) in Arabidopsis. However, to date the in vivo operation of these pathways has not been fully confirmed in this species. This paper describes metabolic studies using deuterium-labeled BRs in wild-type and BR-insensitive mutant (bri1) seedlings to establish the intermediates of the biosynthetic pathway of BL in Arabidopsis. The first evidence for the conversion of campestanol to 6-deoxocathasterone and the conversion of 6-deoxocathasterone to 6-deoxoteasterone is provided. The later biosynthetic steps (6-deoxoteasterone --> 3-dehydro-6-deoxoteasterone --> 6-deoxotyphasterol --> 6-deoxocastasterone --> 6alpha-hydroxycastasterone --> castasterone --> BL) were demonstrated by stepwise metabolic experiments. Therefore, these studies complete the documentation of the late C6-oxidation pathway. The biosynthetic sequence involved in the early C6-oxidation pathway (teasterone --> 3-dehydroteasterone --> typhasterol --> castasterone --> BL) was also demonstrated. These results show that both the early and late C6-oxidation pathways are functional in Arabidopsis. In addition we report two new observations: the presence of a new branch in the pathway, C6 oxidation of 6-deoxotyphasterol to typhasterol, and increased metabolic flow in BR-insensitive mutants.

  1. Arabidopsis, the Rosetta stone of flowering time?

    PubMed

    Simpson, Gordon G; Dean, Caroline

    2002-04-12

    Multiple environmental and endogenous inputs regulate when plants flower. The molecular genetic dissection of flowering time control in Arabidopsis has identified an integrated network of pathways that quantitatively control the timing of this developmental switch. This framework provides the basis to understand the evolution of different reproductive strategies and how floral pathways interact through seasonal progression.

  2. Imaging lipid droplets in Arabidopsis mutants

    USDA-ARS?s Scientific Manuscript database

    Confocal fluorescence microscopy was adapted for the imaging of neutral lipids in plant leaves with defects in normal lipid metabolism using two different fluorescent dyes. Disruptions in a gene locus, At4g24160, yielded Arabidopsis thaliana plants with a preponderance of oil bodies in their leaves ...

  3. Arabidopsis gene expression patterns during spaceflight

    NASA Astrophysics Data System (ADS)

    Paul, A.-L.; Ferl, R. J.

    The exposure of Arabidopsis thaliana (Arabidopsis) plants to spaceflight environments resulted in the differential expression of hundreds of genes. A 5 day mission on orbiter Columbia in 1999 (STS-93) carried transgenic Arabidopsis plants engineered with a transgene composed of the alcohol dehydrogenase (Adh) gene promoter linked to the β -Glucuronidase (GUS) reporter gene. The plants were used to evaluate the effects of spaceflight on two fronts. First, expression patterns visualized with the Adh/GUS transgene were used to address specifically the possibility that spaceflight induces a hypoxic stress response, and to assess whether any spaceflight response was similar to control terrestrial hypoxia-induced gene expression patterns. (Paul et al., Plant Physiol. 2001, 126:613). Second, genome-wide patterns of native gene expression were evaluated utilizing the Affymetrix ATH1 GeneChip? array of 8,000 Arabidopsis genes. As a control for the veracity of the array analyses, a selection of genes identified with the arrays was further characterized with quantitative Real-Time RT PCR (ABI - TaqmanTM). Comparison of the patterns of expression for arrays of hybridized with RNA isolated from plants exposed to spaceflight compared to the control arrays revealed hundreds of genes that were differentially expressed in response to spaceflight, yet most genes that are hallmarks of hypoxic stress were unaffected. These results will be discussed in light of current models for plant responses to the spaceflight environment, and with regard to potential future flight opportunities.

  4. 17th International Conference on Arabidopsis Research

    SciTech Connect

    Bender, Judith

    2006-07-02

    The 17th International Conference on Arabidopsis Research was held at the University of Madison, Wisconsin from June 27- July 2, 2006. ICAR-2006 included approximately 625 scientists from across the world. The scientific program was of excellent quality featuring 73 talks, including 30 from invited speakers. There were also 6 community-organized workshops (facilitated by conference staff) featuring additional talks on topics including ‘Submitting data to long-term repositories,’ ‘TAIR introductory workshop,’ ‘Web services and demonstration,’ ‘Public engagement: broadening the impact of your research,’ ‘Systems biology approaches to analysis of metabolic and regulatory networks of Arabidopsis,’ and ‘Mechanotransduction in Arabidopsis.’ Approximately 440 posters were presented in general topic areas including, among others, Development, Modeling/Other Systems, Energy, Environment, and Genetic/Epigenetic mechanisms. Graduate students, postdoctoral researchers, junior faculty, and underrepresented minorities made up a significant portion of the oral presentations thereby promoting the training of young scientists and facilitating important career development opportunities for speakers. Several poster sessions provided an opportunity for younger participants to freely meet with more established scientists. The North American Arabidopsis Steering Committee (NAASC) continued its outreach effort and again sponsored two special luncheons to encourage personal and professional development of young scientists and also underrepresented minorities. The ‘Emerging Scientists Luncheon’ featured 10 graduate students selected on the basis of scientific excellence of their submitted research abstracts. The ‘Minority Funding Luncheon,’ featured 8 awardees selected by the NAASC through a widely-publicized application process. This luncheon was established specifically to provide an opportunity for underrepresented minorities, and/or scientists from

  5. Extraction of total protein from Arabidopsis.

    PubMed

    Larkin, Rob

    2007-01-01

    INTRODUCTIONThe functions of most Arabidopsis genes cannot be understood simply by studying the expression patterns of their mRNAs. The level of a protein may not be closely correlated with the level of the corresponding mRNA, or a protein may need to be modified to be active. Furthermore, the function of proteins often depends on specific subcellular localization, so knowledge of this can exclude some hypotheses about possible function. The simplest way to analyze proteins is in unfractionated extracts. However, it is often desirable to fractionate proteins, e.g, by size. This procedure extracts total protein from Arabidopsis samples. Typical yields are ~2-3 mg/ml (using rosette leaves) or 6-8 mg/ml (using young seedlings).

  6. Physiological Analysis of Phototropic Responses in Arabidopsis.

    PubMed

    Zeidler, Mathias

    2016-01-01

    Plants utilize light as sole energy source. To maximize light capture they are able to detect the light direction and orient themselves towards the light source. This phototropic response is mediated by the plant blue light photoreceptors phototropin1 and 2 (phot1 and phot2). Although fully differentiated plants also exhibit this response it can be best observed in etiolated seedlings. Differences in light between the illuminated and shaded site of a seedling stem lead to changes in the auxin-distribution, resulting in cell elongation on the shaded site. Since phototropism connects light perception, signaling, and auxin transport, it is of great interest to analyze this response with a fast and simple method.Here we describe a method to analyze the phototropic response of Arabidopsis seedlings. With numerous mutants available, its fast germination and its small size Arabidopsis is well suited for this analysis. Different genotypes can be simultaneously probed in less than a week.

  7. Evolutionary Divergence of Arabidopsis thaliana Classical Peroxidases.

    PubMed

    Kupriyanova, E V; Mamoshina, P O; Ezhova, T A

    2015-10-01

    Polymorphisms of 62 peroxidase genes derived from Arabidopsis thaliana were investigated to evaluate evolutionary dynamics and divergence of peroxidase proteins. By comparing divergence of duplicated genes AtPrx53-AtPrx54 and AtPrx36-AtPrx72 and their products, nucleotide and amino acid substitutions were identified that were apparently targets of positive selection. These substitutions were detected among paralogs of 461 ecotypes from Arabidopsis thaliana. Some of these substitutions are conservative and matched paralogous peroxidases in other Brassicaceae species. These results suggest that after duplication, peroxidase genes evolved under the pressure of positive selection, and amino acid substitutions identified during our study provided divergence of properties and physiological functions in peroxidases. Our predictions regarding functional significance for amino acid residues identified in variable sites of peroxidases may allow further experimental assessment of evolution of peroxidases after gene duplication.

  8. Arabidopsis thaliana telomeres exhibit euchromatic features

    PubMed Central

    Vaquero-Sedas, María I.; Gámez-Arjona, Francisco M.; Vega-Palas, Miguel A.

    2011-01-01

    Telomere function is influenced by chromatin structure and organization, which usually involves epigenetic modifications. We describe here the chromatin structure of Arabidopsis thaliana telomeres. Based on the study of six different epigenetic marks we show that Arabidopsis telomeres exhibit euchromatic features. In contrast, subtelomeric regions and telomeric sequences present at interstitial chromosomal loci are heterochromatic. Histone methyltransferases and the chromatin remodeling protein DDM1 control subtelomeric heterochromatin formation. Whereas histone methyltransferases are required for histone H3K92Me and non-CpG DNA methylation, DDM1 directs CpG methylation but not H3K92Me or non-CpG methylation. These results argue that both kinds of proteins participate in different pathways to reinforce subtelomeric heterochromatin formation. PMID:21071395

  9. Root gravitropism in maize and Arabidopsis

    NASA Technical Reports Server (NTRS)

    Evans, Michael L.

    1993-01-01

    Research during the period 1 March 1992 to 30 November 1993 focused on improvements in a video digitizer system designed to automate the recording of surface extension in plants responding to gravistimulation. The improvements included modification of software to allow detailed analysis of localized extension patterns in roots of Arabidopsis. We used the system to analyze the role of the postmitotic isodiametric growth zone (a region between the meristem and the elongation zone) in the response of maize roots to auxin, calcium, touch and gravity. We also used the system to analyze short-term auxin and gravitropic responses in mutants of Arabidopsis with reduced auxin sensitivity. In a related project, we studied the relationship between growth rate and surface electrical currents in roots by examining the effects of gravity and thigmostimulation on surface potentials in maize roots.

  10. DYn-2 Based Identification of Arabidopsis Sulfenomes*

    PubMed Central

    Akter, Salma; Huang, Jingjing; Bodra, Nandita; De Smet, Barbara; Wahni, Khadija; Rombaut, Debbie; Pauwels, Jarne; Gevaert, Kris; Carroll, Kate; Van Breusegem, Frank; Messens, Joris

    2015-01-01

    Identifying the sulfenylation state of stressed cells is emerging as a strategic approach for the detection of key reactive oxygen species signaling proteins. Here, we optimized an in vivo trapping method for cysteine sulfenic acids in hydrogen peroxide (H2O2) stressed plant cells using a dimedone based DYn-2 probe. We demonstrated that DYn-2 specifically detects sulfenylation events in an H2O2 dose- and time-dependent way. With mass spectrometry, we identified 226 sulfenylated proteins after H2O2 treatment of Arabidopsis cells, residing in the cytoplasm (123); plastid (68); mitochondria (14); nucleus (10); endoplasmic reticulum, Golgi and plasma membrane (7) and peroxisomes (4). Of these, 123 sulfenylated proteins have never been reported before to undergo cysteine oxidative post-translational modifications in plants. All in all, with this DYn-2 approach, we have identified new sulfenylated proteins, and gave a first glance on the locations of the sulfenomes of Arabidopsis thaliana. PMID:25693797

  11. Epigenetic variation in Arabidopsis disease resistance

    PubMed Central

    Stokes, Trevor L.; Kunkel, Barbara N.; Richards, Eric J.

    2002-01-01

    Plant pathogen resistance is mediated by a large repertoire of resistance (R) genes, which are often clustered in the genome and show a high degree of genetic variation. Here, we show that an Arabidopsis thaliana R-gene cluster is also subject to epigenetic variation. We describe a heritable but metastable epigenetic variant bal that overexpresses the R-like gene At4g16890 from a gene cluster on Chromosome 4. The bal variant and Arabidopsis transgenics overexpressing the At4g16890 gene are dwarfed and constitutively activate the salicylic acid (SA)-dependent defense response pathway. Overexpression of a related R-like gene also occurs in the ssi1 (suppressor of SA insensitivity 1) background, suggesting that ssi1 is mechanistically related to bal. PMID:11799061

  12. High-throughput TILLING for Arabidopsis.

    PubMed

    Till, Bradley J; Colbert, Trenton; Codomo, Christine; Enns, Linda; Johnson, Jessica; Reynolds, Steven H; Henikoff, Jorja G; Greene, Elizabeth A; Steine, Michael N; Comai, Luca; Henikoff, Steven

    2006-01-01

    Targeting induced local lesions in genomes (TILLING) is a general strategy for identifying induced point mutations that can be applied to almost any organism. In this chapter, we describe the basic methodology for high-throughput TILLING. Gene segments are amplified using fluorescently tagged primers, and products are denatured and reannealed to form heteroduplexes between the mutated sequence and its wild-type counterpart. These heteroduplexes are substrates for cleavage by the endonuclease CEL I. Following cleavage, products are analyzed on denaturing polyacrylamide gels using the LI-COR DNA analyzer system. High-throughput TILLING has been adopted by the Arabidopsis TILLING Project (ATP) to provide allelic series of point mutations for the general Arabidopsis community.

  13. Hypermethylated SUPERMAN epigenetic alleles in arabidopsis.

    PubMed

    Jacobsen, S E; Meyerowitz, E M

    1997-08-22

    Mutations in the SUPERMAN gene affect flower development in Arabidopsis. Seven heritable but unstable sup epi-alleles (the clark kent alleles) are associated with nearly identical patterns of excess cytosine methylation within the SUP gene and a decreased level of SUP RNA. Revertants of these alleles are largely demethylated at the SUP locus and have restored levels of SUP RNA. A transgenic Arabidopsis line carrying an antisense methyltransferase gene, which shows an overall decrease in genomic cytosine methylation, also contains a hypermethylated sup allele. Thus, disruption of methylation systems may yield more complex outcomes than expected and can result in methylation defects at known genes. The clark kent alleles differ from the antisense line because they do not show a general decrease in genomic methylation.

  14. Unraveling the circadian clock in Arabidopsis.

    PubMed

    Wang, Xiaoxue; Ma, Ligeng

    2013-02-01

    The circadian clock is an endogenous timing system responsible for coordinating an organism's biological processes with its environment. Interlocked transcriptional feedback loops constitute the fundamental architecture of the circadian clock. In Arabidopsis, three feedback loops, the core loop, morning loop and evening loop, comprise a network that is the basis of the circadian clock. The components of these three loops are regulated in distinct ways, including transcriptional, post-transcriptional and posttranslational mechanisms. The discovery of the DNA-binding and repressive activities of TOC1 has overturned our initial concept of its function in the circadian clock. The alternative splicing of circadian clock-related genes plays an essential role in normal functioning of the clock and enables organisms to sense environmental changes. In this review, we describe the regulatory mechanisms of the circadian clock that have been identified in Arabidopsis.

  15. Integrated analysis of transcriptome and metabolome of Arabidopsis albino or pale green mutants with disrupted nuclear-encoded chloroplast proteins.

    PubMed

    Satou, Masakazu; Enoki, Harumi; Oikawa, Akira; Ohta, Daisaku; Saito, Kazunori; Hachiya, Takushi; Sakakibara, Hitoshi; Kusano, Miyako; Fukushima, Atsushi; Saito, Kazuki; Kobayashi, Masatomo; Nagata, Noriko; Myouga, Fumiyoshi; Shinozaki, Kazuo; Motohashi, Reiko

    2014-07-01

    We used four mutants having albino or pale green phenotypes with disrupted nuclear-encoded chloroplast proteins to analyze the regulatory system of metabolites in chloroplast. We performed an integrated analyses of transcriptomes and metabolomes of the four mutants. Transcriptome analysis was carried out using the Agilent Arabidopsis 2 Oligo Microarray, and metabolome analysis with two mass spectrometers; a direct-infusion Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR/MS) and a gas chromatograph-time of flight mass spectrometer. Among approximately 200 known metabolites detected by the FT-ICR/MS, 71 metabolites showed significant changes in the mutants when compared with controls (Ds donor plants). Significant accumulation of several amino acids (glutamine, glutamate and asparagine) was observed in the albino and pale green mutants. Transcriptome analysis revealed altered expressions of genes in several metabolic pathways. For example, genes involved in the tricarboxylic acid cycle, the oxidative pentose phosphate pathway, and the de novo purine nucleotide biosynthetic pathway were up-regulated. These results suggest that nitrogen assimilation is constitutively promoted in the albino and pale green mutants. The accumulation of ammonium ions in the albino and pale green mutants was consistently higher than in Ds donor lines. Furthermore, genes related to pyridoxin accumulation and the de novo purine nucleotide biosynthetic pathway were up-regulated, which may have occurred as a result of the accumulation of glutamine in the albino and pale green mutants. The difference in metabolic profiles seems to be correlated with the disruption of chloroplast internal membrane structures in the mutants. In albino mutants, the alteration of metabolites accumulation and genes expression is stronger than pale green mutants.

  16. Comparative transcriptomics of Arabidopsis sperm cells.

    PubMed

    Borges, Filipe; Gomes, Gabriela; Gardner, Rui; Moreno, Nuno; McCormick, Sheila; Feijó, José A; Becker, Jörg D

    2008-10-01

    In flowering plants, the two sperm cells are embedded within the cytoplasm of the growing pollen tube and as such are passively transported to the embryo sac, wherein double fertilization occurs upon their release. Understanding the mechanisms and conditions by which male gametes mature and take part in fertilization are crucial goals in the study of plant reproduction. Studies of gene expression in male gametes of maize (Zea mays) and Plumbago and in lily (Lilium longiflorum) generative cells already showed that the previously held view of transcriptionally inert male gametes was not true, but genome-wide studies were lacking. Analyses in the model plant Arabidopsis (Arabidopsis thaliana) were hindered, because no method to isolate sperm cells was available. Here, we used fluorescence-activated cell sorting to isolate sperm cells from Arabidopsis, allowing GeneChip analysis of their transcriptome at a genome-wide level. Comparative analysis of the sperm cell transcriptome with those of representative sporophytic tissues and of pollen showed that sperm has a distinct and diverse transcriptional profile. Functional classifications of genes with enriched expression in sperm cells showed that DNA repair, ubiquitin-mediated proteolysis, and cell cycle progression are overrepresented Gene Ontology categories. Moreover, analysis of the small RNA and DNA methylation pathways suggests that distinct mechanisms might be involved in regulating the epigenetic state of the paternal genome. We identified numerous candidate genes whose involvement in sperm cell development and fertilization can now be directly tested in Arabidopsis. These results provide a roadmap to decipher the role of sperm-expressed proteins.

  17. Regulatory Proteolysis in Arabidopsis-Pathogen Interactions.

    PubMed

    Pogány, Miklós; Dankó, Tamás; Kámán-Tóth, Evelin; Schwarczinger, Ildikó; Bozsó, Zoltán

    2015-09-24

    Approximately two and a half percent of protein coding genes in Arabidopsis encode enzymes with known or putative proteolytic activity. Proteases possess not only common housekeeping functions by recycling nonfunctional proteins. By irreversibly cleaving other proteins, they regulate crucial developmental processes and control responses to environmental changes. Regulatory proteolysis is also indispensable in interactions between plants and their microbial pathogens. Proteolytic cleavage is simultaneously used both by plant cells, to recognize and inactivate invading pathogens, and by microbes, to overcome the immune system of the plant and successfully colonize host cells. In this review, we present available results on the group of proteases in the model plant Arabidopsis thaliana whose functions in microbial pathogenesis were confirmed. Pathogen-derived proteolytic factors are also discussed when they are involved in the cleavage of host metabolites. Considering the wealth of review papers available in the field of the ubiquitin-26S proteasome system results on the ubiquitin cascade are not presented. Arabidopsis and its pathogens are conferred with abundant sets of proteases. This review compiles a list of those that are apparently involved in an interaction between the plant and its pathogens, also presenting their molecular partners when available.

  18. Phosphorylation of plastoglobular proteins in Arabidopsis thaliana

    PubMed Central

    Lohscheider, Jens N.; Friso, Giulia; van Wijk, Klaas J.

    2016-01-01

    Plastoglobules (PGs) are plastid lipid–protein particles with a small specialized proteome and metabolome. Among the 30 core PG proteins are six proteins of the ancient ABC1 atypical kinase (ABC1K) family and their locations in an Arabidopsis mRNA-based co-expression network suggested central regulatory roles. To identify candidate ABC1K targets and a possible ABC1K hierarchical phosphorylation network within the chloroplast PG proteome, we searched Arabidopsis phosphoproteomics data from publicly available sources. Evaluation of underlying spectra and/or associated information was challenging for a variety of reasons, but supported pSer sites and a few pThr sites in nine PG proteins, including five FIBRILLINS. PG phosphorylation motifs are discussed in the context of possible responsible kinases. The challenges of collection and evaluation of published Arabidopsis phosphorylation data are discussed, illustrating the importance of deposition of all mass spectrometry data in well-organized repositories such as PRIDE and ProteomeXchange. This study provides a starting point for experimental testing of phosho-sites in PG proteins and also suggests that phosphoproteomics studies specifically designed toward the PG proteome and its ABC1K are needed to understand phosphorylation networks in these specialized particles. PMID:26962209

  19. Analysis of the Arabidopsis Mitochondrial Proteome1

    PubMed Central

    Millar, A. Harvey; Sweetlove, Lee J.; Giegé, Philippe; Leaver, Christopher J.

    2001-01-01

    The complete set of nuclear genes that encode proteins targeted to mitochondria in plants is currently undefined and thus the full range of mitochondrial functions in plants is unknown. Analysis of two-dimensional gel separations of Arabidopsis cell culture mitochondrial protein revealed approximately 100 abundant proteins and 250 low-abundance proteins. Comparison of subfractions of mitochondrial protein on two-dimensional gels provided information on the soluble, membrane, or integral membrane locations of this protein set. A total of 170 protein spots were excised, trypsin-digested, and matrix-assisted laser desorption ionization/time of flight mass spectrometry spectra obtained. Using this dataset, 91 of the proteins were identified by searching translated Arabidopsis genomic databases. Of this set, 81 have defined functions based on sequence comparison. These functions include respiratory electron transport, tricarboxylic acid cycle metabolism, amino acid metabolism, protein import, processing, and assembly, transcription, membrane transport, and antioxidant defense. A total of 10 spectra were matched to Arabidopsis putative open reading frames for which no specific function has been determined. A total of 64 spectra did not match to an identified open reading frame. Analysis of full-length putative protein sequences using bioinformatic tools to predict subcellular targeting (TargetP, Psort, and MitoProt) revealed significant variation in predictions, and also a lack of mitochondrial targeting prediction for several characterized mitochondrial proteins. PMID:11743115

  20. Arabidopsis alternative oxidase sustains Escherichia coli respiration.

    PubMed Central

    Kumar, A M; Söll, D

    1992-01-01

    Glutamyl-tRNA reductase, encoded by the hemA gene, is the first enzyme in porphyrin biosynthesis in many organisms. Hemes, important porphyrin derivatives, are essential components of redox enzymes, such as cytochromes. Thus a hemA Escherichia coli strain (SASX41B) is deficient in cytochrome-mediated aerobic respiration. Upon complementation of this strain with an Arabidopsis thaliana cDNA library, we isolated a clone which permitted the SASX41B strain to grow aerobically. The clone encodes the gene for Arabidopsis alternative oxidase, whose deduced amino acid sequence was found to have 71% identity with that of the enzyme from the voodoo lily, Sauromatum guttatum. The Arabidopsis protein is expressed as a 31-kDa protein in E. coli and confers on this organism cyanide-resistant growth, which in turn is sensitive to salicylhydroxamate. This implies that a single polypeptide is sufficient for alternative oxidase activity. Based on these observations we propose that a cyanide-insensitive respiratory pathway operates in the transformed E. coli hemA strain. Introduction of this pathway now opens the way to genetic/molecular biological investigations of alternative oxidase and its cofactor. Images PMID:1438286

  1. [Imprinting genes and it's expression in Arabidopsis].

    PubMed

    Zhang, Hong-Yu; Xu, Pei-Zhou; Yang, Hua; Wu, Xian-Jun

    2010-07-01

    Genomic imprinting refers to the phenomenon that the expression of a gene copy depends on its parent of origin. The Arabidopsis imprinted FIS (Fertilisation-independent seed) genes, mea, fis2, and fie, play essential roles in the repression of central cell and the regulation of early endosperm development. fis mutants display two phenotypes: autonomous diploid endosperm development when fertilization is absent and un-cellularised endosperm formation when fertilization occurs. The FIS Polycomb protein complex including the above three FIS proteins catalyzes histone H3 K27 tri-methylation on target loci. DME (DEMETER), a DNA glycosylase, and AtMET1 (Methyltransferase1), a DNA methyltransferase, are involved in the regulation of imprinted expression of both mea and fis2. This review summarizes the studies on the Arabidopsis imprinted FIS genes and other related genes. Recent works have shown that the insertion of transposons may affect nearby gene expression, which may be the main driving force behind the evolution of genomic imprinting. This summary covers the achievements on Arabidopsis imprinted genes will provide important information for studies on genomic imprinting in the important crops such as rice and maize.

  2. A Method for Characterizing Embryogenesis in Arabidopsis.

    PubMed

    Feng, Jinlin; Ma, Ligeng

    2017-08-04

    Given the highly predictable nature of their development, Arabidopsis embryos have been used as a model for studies of morphogenesis in plants. However, early stage plant embryos are small and contain few cells, making them difficult to observe and analyze. A method is described here for characterizing pattern formation in plant embryos under a microscope using the model organism Arabidopsis. Following the clearance of fresh ovules using Hoyer's solution, the cell number in and morphology of embryos could be observed, and their developmental stage could be determined by differential interference contrast microscopy using a 100X oil immersion lens. In addition, the expression of specific marker proteins tagged with Green Fluorescent Protein (GFP) was monitored to annotate cell identity specification during embryo patterning by confocal laser scanning microscopy. Thus, this method can be used to observe pattern formation in wild-type plant embryos at the cellular and molecular levels, and to characterize the role of specific genes in embryo patterning by comparing pattern formation in embryos from wild-type plants and embryo-lethal mutants. Therefore, the method can be used to characterize embryogenesis in Arabidopsis.

  3. Phytochrome regulation of branching in Arabidopsis.

    PubMed

    Finlayson, Scott A; Krishnareddy, Srirama R; Kebrom, Tesfamichael H; Casal, Jorge J

    2010-04-01

    The red light:far-red light ratio perceived by phytochromes controls plastic traits of plant architecture, including branching. Despite the significance of branching for plant fitness and productivity, there is little quantitative and mechanistic information concerning phytochrome control of branching responses in Arabidopsis (Arabidopsis thaliana). Here, we show that in Arabidopsis, the negative effects of the phytochrome B mutation and of low red light:far-red light ratio on branching were largely due to reduced bud outgrowth capacity and an increased degree of correlative inhibition acting on the buds rather than due to a reduced number of leaves and buds available for branching. Phytochrome effects on the degree of correlative inhibition required functional BRANCHED1 (BRC1), BRC2, AXR1, MORE AXILLARY GROWTH2 (MAX2), and MAX4. The analysis of gene expression in selected buds indicated that BRC1 and BRC2 are part of different gene networks. The BRC1 network is linked to the growth capacity of specific buds, while the BRC2 network is associated with coordination of growth among branches. We conclude that the branching integrators BRC1 and BRC2 are necessary for responses to phytochrome, but they contribute differentially to these responses, likely acting through divergent pathways.

  4. Sodium Influx and Accumulation in Arabidopsis1

    PubMed Central

    Essah, Pauline A.; Davenport, Romola; Tester, Mark

    2003-01-01

    Arabidopsis is frequently used as a genetic model in plant salt tolerance studies, however, its physiological responses to salinity remain poorly characterized. This study presents a characterization of initial Na+ entry and the effects of Ca2+ on plant growth and net Na+ accumulation in saline conditions. Unidirectional Na+ influx was measured carefully using very short influx times in roots of 12-d-old seedlings. Influx showed three components with distinct sensitivities to Ca2+, diethylpyrocarbonate, and osmotic pretreatment. Pharmacological agents and known mutants were used to test the contribution of different transport pathways to Na+ uptake. Influx was stimulated by 4-aminobutyric acid and glutamic acid; was inhibited by flufenamate, quinine, and cGMP; and was insensitive to modulators of K+ and Ca2+ channels. Influx did not differ from wild type in akt1 and hkt1 insertional mutants. These data suggested that influx was mediated by several different types of nonselective cation channels. Na+ accumulation in plants grown in 50 mm NaCl was strongly reduced by increasing Ca2+ activity (from 0.05-3.0 mm), and plant survival was improved. However, plant biomass was not affected by shoot Na+ concentration, suggesting that in Arabidopsis Na+ toxicity is not dependent on shoot Na+ accumulation. These data suggest that Arabidopsis is a good model for investigation of Na+ transport, but may be of limited utility as a model for the study of Na+ toxicity. PMID:12970496

  5. A randomized phase III trial of stereotactic radiosurgery (SRS) versus observation for patients with asymptomatic cerebral oligo-metastases in non-small-cell lung cancer.

    PubMed

    Lim, S H; Lee, J Y; Lee, M-Y; Kim, H S; Lee, J; Sun, J-M; Ahn, J S; Um, S-W; Kim, H; Kim, B S; Kim, S T; Na, D L; Sun, J Y; Jung, S H; Park, K; Kwon, O J; Lee, J-I; Ahn, M-J

    2015-04-01

    It is unclear whether treating brain metastasis before starting systemic chemotherapy can improve survival compared with upfront chemotherapy in non-small-cell lung cancer (NSCLC) with asymptomatic cerebral oligo-metastases. We undertook a randomized, controlled trial of 105 patients with one to four brain metastases, admitted to Samsung Medical Center between 2008 and 2013. Patients were randomly assigned to receive stereotactic radiosurgery (SRS) (49 patients) followed by chemotherapy or upfront chemotherapy (49 patients). The primary end point was overall survival (OS) and secondary end points included central nervous system (CNS) progression-free survival, progression to symptomatic brain metastasis and brain functional outcome. The median age was 58 years (range, 29-85) with ECOG 0-1 performance status, and 40% of patients were never smokers. Most patients had adenocarcinoma, and about half of patients had only one brain metastasis, while the rest had multiple cerebral metastases. The median OS time was 14.6 months [95% confidence interval (CI), 9.2-20.0] in the SRS group and 15.3 months (95% CI, 7.2-23.4) for the upfront chemotherapy group (P = 0.418). There was no significant difference in time to CNS disease progression [median, 9.4 months (SRS) versus 6.6 months (upfront chemotherapy), P = 0.248]. Symptomatic progression of brain metastases was observed more frequently in the upfront chemotherapy group (26.5%) than the SRS group (18.4%) but without statistical significance. Although this study included smaller sample size than initially anticipated due to early termination, SRS followed by chemotherapy did not improve OS in oligo-brain metastases NSCLC patients compared with upfront chemotherapy. Further study with large number of patients should be needed to confirm the use of upfront chemotherapy alone in this subgroup of patients. NCT01301560. © The Author 2014. Published by Oxford University Press on behalf of the European Society for Medical Oncology

  6. Gene expression profile analysis of Manila clam (Ruditapes philippinarum) hemocytes after a Vibrio alginolyticus challenge using an immune-enriched oligo-microarray

    PubMed Central

    2014-01-01

    Background The Manila clam (Ruditapes philippinarum) is a cultured bivalve with worldwide commercial importance, and diseases cause high economic losses. For this reason, interest in the immune genes in this species has recently increased. The present work describes the construction of the first R. philippinarum microarray containing immune-related hemocyte sequences and its application to study the gene transcription profiles of hemocytes from clams infected with V. alginolyticus through a time course. Results The complete set of sequences from R. philippinarum available in the public databases and the hemocyte sequences enriched in immune transcripts were assembled successfully. A total of 12,156 annotated sequences were used to construct the 8 ×15 k oligo-microarray. The microarray experiments yielded a total of 579 differentially expressed transcripts. Using the gene expression results, the associated Gene Ontology terms and the enrichment analysis, we found different response mechanisms throughout the experiment. Genes related to signaling, transcription and apoptosis, such as IL-17D, NF-κB or calmodulin, were typically expressed as early as 3 hours post-challenge (hpc), while characteristic immune genes, such as PGRPs, FREPs and defense proteins appeared later at 8 hpc. This immune-triggering response could have affected a high number of processes that seemed to be activated 24 hpc to overcome the Vibrio challenge, including the expression of many cytoskeleton molecules, which is indicative of the active movement of hemocytes. In fact functional studies showed an increment in apoptosis, necrosis or cell migration after the infection. Finally, 72 hpc, activity returned to normal levels, and more than 50% of the genes were downregulated in a negative feedback of all of the previously active processes. Conclusions Using a new version of the R. philippinarum oligo-microarray, a putative timing for the response against a Vibrio infection was established. The key

  7. Gene expression profile analysis of Manila clam (Ruditapes philippinarum) hemocytes after a Vibrio alginolyticus challenge using an immune-enriched oligo-microarray.

    PubMed

    Moreira, Rebeca; Milan, Massimo; Balseiro, Pablo; Romero, Alejandro; Babbucci, Massimiliano; Figueras, Antonio; Bargelloni, Luca; Novoa, Beatriz

    2014-04-07

    The Manila clam (Ruditapes philippinarum) is a cultured bivalve with worldwide commercial importance, and diseases cause high economic losses. For this reason, interest in the immune genes in this species has recently increased. The present work describes the construction of the first R. philippinarum microarray containing immune-related hemocyte sequences and its application to study the gene transcription profiles of hemocytes from clams infected with V. alginolyticus through a time course. The complete set of sequences from R. philippinarum available in the public databases and the hemocyte sequences enriched in immune transcripts were assembled successfully. A total of 12,156 annotated sequences were used to construct the 8 × 15 k oligo-microarray. The microarray experiments yielded a total of 579 differentially expressed transcripts. Using the gene expression results, the associated Gene Ontology terms and the enrichment analysis, we found different response mechanisms throughout the experiment. Genes related to signaling, transcription and apoptosis, such as IL-17D, NF-κB or calmodulin, were typically expressed as early as 3 hours post-challenge (hpc), while characteristic immune genes, such as PGRPs, FREPs and defense proteins appeared later at 8 hpc. This immune-triggering response could have affected a high number of processes that seemed to be activated 24 hpc to overcome the Vibrio challenge, including the expression of many cytoskeleton molecules, which is indicative of the active movement of hemocytes. In fact functional studies showed an increment in apoptosis, necrosis or cell migration after the infection. Finally, 72 hpc, activity returned to normal levels, and more than 50% of the genes were downregulated in a negative feedback of all of the previously active processes. Using a new version of the R. philippinarum oligo-microarray, a putative timing for the response against a Vibrio infection was established. The key point to overcome the

  8. Construction of an Ostrea edulis database from genomic and expressed sequence tags (ESTs) obtained from Bonamia ostreae infected haemocytes: Development of an immune-enriched oligo-microarray.

    PubMed

    Pardo, Belén G; Álvarez-Dios, José Antonio; Cao, Asunción; Ramilo, Andrea; Gómez-Tato, Antonio; Planas, Josep V; Villalba, Antonio; Martínez, Paulino

    2016-12-01

    The flat oyster, Ostrea edulis, is one of the main farmed oysters, not only in Europe but also in the United States and Canada. Bonamiosis due to the parasite Bonamia ostreae has been associated with high mortality episodes in this species. This parasite is an intracellular protozoan that infects haemocytes, the main cells involved in oyster defence. Due to the economical and ecological importance of flat oyster, genomic data are badly needed for genetic improvement of the species, but they are still very scarce. The objective of this study is to develop a sequence database, OedulisDB, with new genomic and transcriptomic resources, providing new data and convenient tools to improve our knowledge of the oyster's immune mechanisms. Transcriptomic and genomic sequences were obtained using 454 pyrosequencing and compiled into an O. edulis database, OedulisDB, consisting of two sets of 10,318 and 7159 unique sequences that represent the oyster's genome (WG) and de novo haemocyte transcriptome (HT), respectively. The flat oyster transcriptome was obtained from two strains (naïve and tolerant) challenged with B. ostreae, and from their corresponding non-challenged controls. Approximately 78.5% of 5619 HT unique sequences were successfully annotated by Blast search using public databases. A total of 984 sequences were identified as being related to immune response and several key immune genes were identified for the first time in flat oyster. Additionally, transcriptome information was used to design and validate the first oligo-microarray in flat oyster enriched with immune sequences from haemocytes. Our transcriptomic and genomic sequencing and subsequent annotation have largely increased the scarce resources available for this economically important species and have enabled us to develop an OedulisDB database and accompanying tools for gene expression analysis. This study represents the first attempt to characterize in depth the O. edulis haemocyte transcriptome in

  9. Randomized Trial Comparing the Effect of Endometrial Shedding With Medroxyprogesterone Acetate With Random Start of Clomiphene Citrate for Ovulation Induction in Oligo-ovulatory and Anovulatory Women.

    PubMed

    Jones, Claire Ann; Garbedian, Kimberly; Dixon, Marjorie; Murphy, Kellie; Shapiro, Heather

    2016-05-01

    A recent retrospective study demonstrated that anovulatory infertile women who did not have a progestogen-induced withdrawal bleed before treatment with clomiphene citrate (CC) had higher pregnancy rates than women who had a withdrawal bleed and those who had spontaneous menstrual bleeding. We sought to assess endometrial thickness at the time of ovulation in oligo-ovulatory and anovulatory women who took CC with or without a preceding progestogen-induced withdrawal bleed. We conducted a pilot randomized trial in which women with infertility and oligomenorrhea or amenorrhea were randomly assigned to take either CC after a withdrawal bleed induced by medroxyprogesterone acetate (MPA) 10 mg daily for 10 days or to take CC without such a bleed. Study participants underwent cycle monitoring with ultrasound assessment of endometrial thickness at the time of LH surge or a human chorionic gonadotropin trigger, followed by timed intercourse or intrauterine insemination. Women who had not ovulated by cycle day 21 took an increased dose of CC, with or without an MPA-induced withdrawal bleed, to a maximum of three cycles. Participants and nurses were asked to complete a questionnaire about the study. There was no significant difference in endometrial thickness on the day of LH surge or human chorionic gonadotropin trigger between women who had a progestogen-induced withdrawal bleed and those who did not (P = 0.65). On average, the time to ovulation was 15 days longer in women who took MPA than in women who did not, but this difference was not statistically significant (P = 0.65). Satisfaction with the study was reported as high by both patients and nurses. In anovulatory or oligo-ovulatory women treated with CC, we found no significant difference in endometrial thickness whether or not the use of CC was preceded by a withdrawal bleed induced by MPA. Copyright © 2016 The Society of Obstetricians and Gynaecologists of Canada/La Société des obstétriciens et gyn

  10. Oligo-dT anchored cDNA-SCoT: a novel differential display method for analyzing differential gene expression in response to several stress treatments in mango (Mangifera indica L.).

    PubMed

    Luo, Cong; He, Xin-Hua; Hu, Ying; Yu, Hai-xia; Ou, Shi-Jin; Fang, Zhong-Bin

    2014-09-15

    Differential display is a powerful technique for analyzing differences in gene expression. Oligo-dT cDNAstart codon targeted marker (cDNA-SCoT) technique is a novel, simple, cheap, rapid, and efficient method for differential gene expression research. In the present study, the oligo-dT anchored cDNA-SCoT technique was exploited to identify differentially expressed genes during several stress treatments in mango. A total of 37 primers combined with oligo-dT anchor primers 3side amplified approximately 150 fragments of 150 bp to 1500 bp in length. Up to 100 fragments were differentially expressed among the stress treatments and control samples, among which 92 were obtained and sequenced. Out of the 92 transcript derived fragments (TDFs), 70% were highly homologous to known genes, and 30% encoded unclassified proteins with unknown functions. The expression pattern of nine genes with known functions involved in several abiotic stresses in other species was confirmed by quantitative reverse transcription polymerase chain reaction (qRT-PCR) under cold (4 °C), salinity (NaCl), polyethylene glycol (PEG, MW 6000), and heavy metal treatments in leaves and stems at different time points (0, 24, 48, and 72 h). The expression patterns of the genes (TDF4, TDF7, TDF23, TDF45, TDF49, TDF50, TDF57, TDF91 and TDF92) that had direct or indirect relationships with cold, salinity, drought and heavy metal stress response were analyzed through qRT-PCR. The possible roles of these genes are discussed. This study suggests that the oligo-dT anchored cDNA-SCoT differential display method is a useful tool to serve as an initial step for characterizing transcriptional changes induced by abiotic stresses and provide gene information for further study and application in genetic improvement and breeding in mango.

  11. Parallel beta/alpha-barrels of alpha-amylase, cyclodextrin glycosyltransferase and oligo-1,6-glucosidase versus the barrel of beta-amylase: evolutionary distance is a reflection of unrelated sequences.

    PubMed

    Janecek, S

    1994-10-17

    The structures of functionally related beta/alpha-barrel starch hydrolases, alpha-amylase, beta-amylase, cyclodextrin glycosyltransferase and oligo-1,6-glucosidase, are discussed, their mutual sequence similarities being emphasized. Since these enzymes (except for beta-amylase) along with the predicted set of more than ten beta/alpha-barrels from the alpha-amylase enzyme superfamily fulfil the criteria characteristic of the products of divergent evolution, their unrooted distance tree is presented.

  12. The Arabidopsis TAC Position Viewer: a high-resolution map of transformation-competent artificial chromosome (TAC) clones aligned with the Arabidopsis thaliana Columbia-0 genome.

    PubMed

    Hirose, Yoshitsugu; Suda, Kunihiro; Liu, Yao-Guang; Sato, Shusei; Nakamura, Yukino; Yokoyama, Koji; Yamamoto, Naoki; Hanano, Shigeru; Takita, Eiji; Sakurai, Nozomu; Suzuki, Hideyuki; Nakamura, Yasukazu; Kaneko, Takakazu; Yano, Kentaro; Tabata, Satoshi; Shibata, Daisuke

    2015-09-01

    We present a high-resolution map of genomic transformation-competent artificial chromosome (TAC) clones extending over all Arabidopsis thaliana (Arabidopsis) chromosomes. The Arabidopsis genomic TAC clones have been valuable genetic tools. Previously, we constructed an Arabidopsis genomic TAC library consisting of more than 10,000 TAC clones harboring large genomic DNA fragments extending over the whole Arabidopsis genome. Here, we determined 13,577 end sequences from 6987 Arabidopsis TAC clones and mapped 5937 TAC clones to precise locations, covering approximately 90% of the Arabidopsis chromosomes. We present the large-scale data set of TAC clones with high-resolution mapping information as a Java application tool, the Arabidopsis TAC Position Viewer, which provides ready-to-go transformable genomic DNA clones corresponding to certain loci on Arabidopsis chromosomes. The TAC clone resources will accelerate genomic DNA cloning, positional walking, complementation of mutants and DNA transformation for heterologous gene expression.

  13. The impact of Arabidopsis on human health: diversifying our portfolio.

    PubMed

    Jones, Alan M; Chory, Joanne; Dangl, Jeffery L; Estelle, Mark; Jacobsen, Steven E; Meyerowitz, Elliot M; Nordborg, Magnus; Weigel, Detlef

    2008-06-13

    Studies of the model plant Arabidopsis thaliana may seem to have little impact on advances in medical research, yet a survey of the scientific literature shows that this is a misconception. Many discoveries with direct relevance to human health and disease have been elaborated using Arabidopsis, and several processes important to human biology are more easily studied in this versatile model plant.

  14. A survey of dominant mutations in Arabidopsis thaliana.

    PubMed

    Meinke, David W

    2013-02-01

    Following the recent publication of a comprehensive dataset of 2400 genes with a loss-of-function mutant phenotype in Arabidopsis (Arabidopsis thaliana), questions remain concerning the diversity of dominant mutations in Arabidopsis. Most of these dominant phenotypes are expected to result from inappropriate gene expression, novel protein function, or disrupted protein complexes. This review highlights the major classes of dominant mutations observed in model organisms and presents a collection of 200 Arabidopsis genes associated with a dominant or semidominant phenotype. Emphasis is placed on mutants identified through forward genetic screens of mutagenized or activation-tagged populations. These datasets illustrate the variety of genetic changes and protein functions that underlie dominance in Arabidopsis and may ultimately contribute to phenotypic variation in flowering plants.

  15. Push-Pull Type Oligo(N-annulated perylene)quinodimethanes: Chain Length and Solvent-Dependent Ground States and Physical Properties.

    PubMed

    Zeng, Zebing; Lee, Sangsu; Son, Minjung; Fukuda, Kotaro; Burrezo, Paula Mayorga; Zhu, Xiaojian; Qi, Qingbiao; Li, Run-Wei; Navarrete, Juan T López; Ding, Jun; Casado, Juan; Nakano, Masayoshi; Kim, Dongho; Wu, Jishan

    2015-07-08

    Research on stable open-shell singlet diradicaloids recently became a hot topic because of their unique optical, electronic, and magnetic properties and promising applications in materials science. So far, most reported singlet diradicaloid molecules have a symmetric structure, while asymmetric diradicaloids with an additional contribution of a dipolar zwitterionic form to the ground state were rarely studied. In this Article, a series of new push-pull type oligo(N-annulated perylene)quinodimethanes were synthesized. Their chain length and solvent-dependent ground states and physical properties were systematically investigated by various experimental methods such as steady-state and transient absorption, two-photon absorption, X-ray crystallographic analysis, electron spin resonance, superconducting quantum interference device, Raman spectroscopy, and electrochemistry. It was found that with extension of the chain length, the diradical character increases while the contribution of the zwitterionic form to the ground state becomes smaller. Because of the intramolecular charge transfer character, the physical properties of this push-pull system showed solvent dependence. In addition, density functional theory calculations on the diradical character and Hirshfeld charge were conducted to understand the chain length and solvent dependence of both symmetric and asymmetric systems. Our studies provided a comprehensive understanding on the fundamental structure- and environment-property relationships in the new asymmetric diradicaloid systems.

  16. Positively Charged Oligo[Poly(Ethylene Glycol) Fumarate] Scaffold Implantation Results in a Permissive Lesion Environment after Spinal Cord Injury in Rat

    PubMed Central

    Hakim, Jeffrey S.; Esmaeili Rad, Melika; Grahn, Peter J.; Chen, Bingkun K.; Knight, Andrew M.; Schmeichel, Ann M.; Isaq, Nasro A.; Dadsetan, Mahrokh; Yaszemski, Michael J.

    2015-01-01

    Positively charged oligo[poly(ethylene glycol) fumarate] (OPF+) scaffolds loaded with Schwann cells bridge spinal cord injury (SCI) lesions and support axonal regeneration in rat. The regeneration achieved is not sufficient for inducing functional recovery. Attempts to increase regeneration would benefit from understanding the effects of the scaffold and transplanted cells on lesion environment. We conducted morphometric and stereological analysis of lesions in rats implanted with OPF+ scaffolds with or without loaded Schwann cells 1, 2, 3, 4, and 8 weeks after thoracic spinal cord transection. No differences were found in collagen scarring, cyst formation, astrocyte reactivity, myelin debris, or chondroitin sulfate proteoglycan (CSPG) accumulation. However, when scaffold-implanted animals were compared with animals with transection injuries only, these barriers to regeneration were significantly reduced, accompanied by increased activated macrophages/microglia. This distinctive and regeneration permissive tissue reaction to scaffold implantation was independent of Schwann cell transplantation. Although the tissue reaction was beneficial in the short term, we observed a chronic fibrotic host response, resulting in scaffolds surrounded by collagen at 8 weeks. This study demonstrates that an appropriate biomaterial scaffold improves the environment for regeneration. Future targeting of the host fibrotic response may allow increased axonal regeneration and functional recovery. PMID:25891264

  17. Cationic Oligo(thiophene ethynylene) with Broad-Spectrum and High Antibacterial Efficiency under White Light and Specific Biocidal Activity against S. aureus in Dark.

    PubMed

    Zhao, Qi; Li, Junting; Zhang, Xiaoqian; Li, Zhengping; Tang, Yanli

    2016-01-13

    We designed and synthesized a novel oligo(thiophene ethynylene) (OTE) to investigate the antibacterial activities against Gram-positive (Staphylococcus aureus and Staphylococcus epidermidis) and Gram-negative (Ralstonia solanacearum and Escherichia coli) bacteria in vitro by photodynamic therapy (PDT). Notably, OTE presents broad-spectrum and greatly high antibacterial activities after white light irradiation at nanogram per milliliter concentrations. The half inhibitory concentrations (IC50) values obtained for S. aureus, S. epidermidis, E. coli, and R. solanacearum are 8, 13, 24, and 52 ng/mL after illumination for 30 min, respectively, which are lower than that of other PDT agents. Interestingly, OTE shows the specific and very strong dark killing capability against S. aureus at the concentration of 180 ng/mL for 30 min, which is the highest efficiency biocide against S. aureus without the need of irradiation to date. The antibacterial mechanism investigated demonstrated that reactive oxygen species or singlet-oxygen generated by OTE kills bacteria irreversibly upon white light irradiation, and OTE as a v-type oligomer exerts its toxicity directly on destroying bacterial cytoplasmic membrane in the dark. Importantly, the OTE shows no cell cytotoxicity and excellent biocompatibility. The results indicate that it is potential to provide versatile applications in the efficient control of pathogenic organisms and specific application for killing S. aureus.

  18. Rapid grafting of azido-labeled oligo(ethylene glycol)s onto an alkynyl-terminated monolayer on nonoxidized silicon via microwave-assisted "click" reaction.

    PubMed

    Li, Yan; Wang, Jun; Cai, Chengzhi

    2011-03-15

    Microwave (MW) irradiation was used for the grafting of azido-labeled oligo(ethylene oxide) (OEG) on alkynyl-terminated nonoxidized silicon substrates via copper-catalyzed "click" reaction. The "clickable" monolayers were prepared by photografting of an α,ω-alkynene, where the alkynyl terminus was protected by a trimethylgermanyl (TMG) group, onto hydrogen-terminated Si(111) surfaces. X-ray photoelectron spectroscopy (XPS) was primarily employed to characterize the monolayers, and the data obtained were utilized to calculate the surface density of the TMG-alkynyl-functionalized substrate. MW-assisted one-pot deprotection/click reaction was optimized on the surfaces using azido-tagged OEG derivatives. Using MW instead of conventional heating led to a substantial improvement in the rate of the reaction while suppressing the oxidation of the silicon interface and OEG degradation. The antifouling property of the resulting substrates was evaluated using fibrinogen as a model protein. Results show that the OEG-modification reduced the protein adsorption by >90%.

  19. Development of a sensitive surface plasmon resonance immunosensor for detection of 2,4-dinitrotoluene with a novel oligo (ethylene glycol)-based sensor surface.

    PubMed

    Nagatomo, Kazutaka; Kawaguchi, Toshikazu; Miura, Norio; Toko, Kiyoshi; Matsumoto, Kiyoshi

    2009-09-15

    A surface plasmon resonance (SPR) immunosensor for detection of 2,4-dinitrotoluene (2,4-DNT), which is a signature compound of 2,4,6-trinitrotoluene-related explosives, was developed by using a novel oligo (ethylene glycol) (OEG)-based sensor surface. A rabbit polyclonal antibody against 2,4-DNT (anti-DNPh-KLH-400 antibody) was prepared, and the avidity for 2,4-DNT and recognition capability were investigated by indirect competitive ELISA. The sensor surface was fabricated by immobilizing a 2,4-DNT analog onto an OEG-based self-assembled monolayer formed on a gold surface via an OEG linker. The fabricated surface was characterized by Fourier-transform infrared-refractive absorption spectrometry (FTIR-RAS). The immunosensing of 2,4-DNT is based on the indirect competitive principle, in which the immunoreaction between the anti-DNPh-KLH-400 antibody and 2,4-DNT on the sensor surface was inhibited in the presence of free 2,4-DNT in solution. The limit of detection for the immunosensor, calculated as three times the standard deviation of a blank value, was 20 pg mL(-1), and the linear dynamic range was found to be between 1 and 100 ng mL(-1). Additionally, the fabricated OEG-based surface effectively prevented non-specific adsorption of proteins, and the specific response to anti-DNPh-KLH-400 antibody was maintained for more than 30 measurement cycles.

  20. Programmed Synthesis of Molecular Wires with Fixed Insulation and Defined Length Based on Oligo(phenylene ethynylene) and Permethylated α-Cyclodextrins.

    PubMed

    Masai, Hiroshi; Fujihara, Tetsuaki; Tsuji, Yasushi; Terao, Jun

    2017-06-03

    The development of new tuning methods for π-conjugated insulated molecular wires with strictly defined axle lengths as well as positions and degrees of macrocycle coverage would provide unprecedented insight into insulation effects in functionalized materials. Herein, iterative reactions of oligo(phenylene ethynylene) (OPE) linked with permethylated α-cyclodextrins were carried out to fabricate insulated molecular wires with a defined length and insulation in desired areas. Insulated OPEs were elongated in a stepwise manner by performing sequential coupling/deprotection reactions. The insulated areas on the OPE units in each expansion step were selectively controlled by means of programmed solvent conditions (high/low polarity). Moreover, a completely insulated OPE (up to a linked [11]rotaxane) with high structural regularity and high covering ratio was synthesized by appropriate tuning of the Pd catalyst and an extension unit bearing a traceless capping unit based on a tert-butyldimethylsilyl group. This strategy may guide the development of the selective synthesis of fully insulated, partially insulated, and uninsulated molecular wires with well-defined lengths and covered/uncovered areas. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. A novel sequence-specific RNA quantification method using nicking endonuclease, dual-labeled fluorescent DNA probe, and conformation-interchangeable oligo-DNA

    PubMed Central

    Hosoda, Kazufumi; Matsuura, Tomoaki; Kita, Hiroshi; Ichihashi, Norikazu; Tsukada, Koji; Urabe, Itaru; Yomo, Tetsuya

    2008-01-01

    We have developed a novel, single-step, isothermal, signal-amplified, and sequence-specific RNA quantification method (L-assay). The L-assay consists of nicking endonuclease, a dual-labeled fluorescent DNA probe (DL-probe), and conformation-interchangeable oligo-DNA (L-DNA). This signal-amplified assay can quantify target RNA concentration in a sequence-specific manner with a coefficient of variation (Cv) of 5% and a lower limit of detection of 0.1 nM. Moreover, this assay allows quantification of target RNA even in the presence of a several thousandfold excess by weight of cellular RNA. In addition, this assay can be used to measure the changes in RNA concentration in real-time and to quantify short RNAs (<30 nucleotides). The L-assay requires only incubation under isothermal conditions, is inexpensive, and is expected to be useful for basic research requiring high-accuracy, easy-to-use RNA quantification, and real-time quantification. PMID:18230763

  2. Synthesis and Properties of Trehalose-Based Flexible Polymers Prepared from Difurfurylidene Trehalose and Maleimide- Terminated Oligo(dimethylsiloxane) by Diels-Alder Reactions

    PubMed Central

    Teramoto, Naozumi; Niwa, Masashi; Shibata, Mitsuhiro

    2010-01-01

    Difurfurylidene trehalose (DFTreh) was synthesized from trehalose and furfural by an acetalization reaction. Maleimide-terminated dimethylsiloxane oligomers (DMS-BMI) were synthesized from amine-terminated dimethylsiloxane oligomers by condensation with maleic anhydride. Three types of DMS-BMI with different length were prepared. Trehalose-based polymers were synthesized by Diels-Alder reaction of DFTreh and DMS-BMI. The reaction proceeded at 40~70 °C to produce a polymer with a maximum weight average molecular weight of ~19,000. The thermal degradation temperature increased with the increase of the length of the oligo(dimethylsiloxane) units. The differential scanning calorimetry (DSC) measurements revealed the glass transition temperature (Tg) of the polymer at -130~-120 °C, and no distinct Tg not observed above room temperature in the DSC measurement. The polymer products are not liquid at room temperature, and solid films can be obtained by casting from solution, implying a phase-separated structure made up of soft and hard segments. The phase-separated structure was confirmed by transmission electron microscope (TEM) study. The DSC curve of the polymer showed a broad endothermic peak at 110~160 °C, suggesting that a retro-Diels-Alder reaction occurred. When a N,N-dimethylformamide solution of the polymer was kept at 100 °C and the resulting solution was analyzed by gel permeation chromatography (GPC), the molecular weight decreased and monomers appeared.

  3. Preparation of highly pure daidzin on oligo-β-cyclodextrin-Sepharose HP and investigation of chromatographic behavior of isoflavones by molecular docking.

    PubMed

    Yang, Li; Li, Cong; Yuan, Tianhu; Tan, Tianwei; Zhang, Liqun

    2011-06-15

    A novel method using column chromatography on oligo-β-cyclodextrin-Sepharose HP for the preparation of high purity daidzin from crude soybean samples was proposed in this work. The isoflavone of daidzin in sample A and B was purified under the optimum mobile phase composed of methanol/acetic acid/water=20.0/8.0/72.0 (v/v/v) at a flow-rate of 1.0 mL/min in one-step operation with a purity of 97.2% and 98.1%, a recovery of 95.3% and 96.3% respectively. The target products in isolated fraction were detected and characterized by HPLC analysis and ESI-MS spectrum. Preparative separation with sample-load of up to 2.42 mg/mL medium gave satisfactory results for daidzin with the purities over 97% and recoveries approximately 90%. Molecular docking simulations were utilized to help demonstrate the inclusion complexation between β-cyclodextrin and the isoflavones in samples through inclusion geometries and calculations of the binding energies. The prediction of the elution orders with AUTODOCK and SURFLEX-DOCK were validated by the chromatographic results.

  4. Saccharomyces cerevisiae and Kluyveromyces marxianus Cocultures Allow Reduction of Fermentable Oligo-, Di-, and Monosaccharides and Polyols Levels in Whole Wheat Bread.

    PubMed

    Struyf, Nore; Laurent, Jitka; Verspreet, Joran; Verstrepen, Kevin J; Courtin, Christophe M

    2017-09-22

    Fermentable oligo-, di-, and monosaccharides and polyols (FODMAPs) are small molecules that are poorly absorbed in the small intestine and rapidly fermented in the large intestine. There is evidence that a diet low in FODMAPs reduces abdominal symptoms in approximately 70% of the patients suffering from irritable bowel syndrome. Wheat contains relatively high fructan levels and is therefore a major source of FODMAPs in our diet. In this study, a yeast-based strategy was developed to reduce FODMAP levels in (whole wheat) bread. Fermentation of dough with an inulinase-secreting Kluyveromyces marxianus strain allowed to reduce fructan levels in the final product by more than 90%, while only 56%  reduction was achieved when a control Saccharomyces cerevisiae strain was used. To ensure sufficient CO2 production, cocultures of S. cerevisiae and K. marxianus were prepared. Bread prepared with a coculture of K. marxianus and S. cerevisiae had fructan levels ≤0.2% dm, and a loaf volume comparable with that of control bread. Therefore, this approach is suitable to effectively reduce FODMAP levels in bread.

  5. Effect of oligochitosan and oligo-β-glucan supplementation on growth, innate immunity, and disease resistance of striped catfish (Pangasianodon hypophthalmus).

    PubMed

    Nguyen, Ngoc Duy; Van Dang, Phu; Le, Anh Quoc; Nguyen, Thi Kim Lan; Pham, Duy Hai; Van Nguyen, Nguyen; Nguyen, Quoc Hien

    2016-06-01

    Oligochitosan (COS) and oligo-β-glucan (βOG) were prepared by gamma Co-60 irradiation of chitosan/H2 O2 and β-glucan/H2 O2 solutions. The striped catfish (Pangasianodon hypophthalmus) was fed diets containing 0-200 mg COS, βOG, and a mixture of COS/βOG per kg feed for 45 days, and then challenged with Edwardsiella ictaluri bacterium. The effects of supplemented COS, βOG, and a mixture of COS/βOG on immune stimulation and growth performance in striped catfish were investigated. The results indicated that when striped catfish fed with 100-200 mg COS or βOG/kg feed the growth performance was significantly improved and the mortality was considerably decreased. Furthermore, striped catfish fed with supplementation of 50 mg COS + 50 mg βOG/kg feed was the best for increasing weight gain (∼26%) and for decreasing mortality (∼38%) compared with the control group. Moreover, phagocytic activity and lysozyme activity of fish were enhanced by feeding diet-supplemented COS and/or βOG. Thus, COS and/or βOG can be potentially utilized as the immunostimulants and growth promoters for aquaculture.

  6. Trimodal Control of Ion-Transport Activity on Cyclo-oligo-(1→6)-β-D-glucosamine-Based Artificial Ion-Transport Systems.

    PubMed

    Roy, Arundhati; Saha, Tanmoy; Gening, Marina L; Titov, Denis V; Gerbst, Alexey G; Tsvetkov, Yury E; Nifantiev, Nikolay E; Talukdar, Pinaki

    2015-11-23

    Cyclo-oligo-(1→6)-β-D-glucosamines functionalized with hydrophobic tails are reported as a new class of transmembrane ion-transport system. These macrocycles with hydrophilic cavities were introduced as an alternative to cyclodextrins, which are supramolecular systems with hydrophobic cavities. The transport activities of these glycoconjugates were manipulated by altering the oligomericity of the macrocycles, as well as the length and number of attached tails. Hydrophobic tails of 3 different sizes were synthesized and coupled with each glucosamine scaffold through the amide linkage to obtain 18 derivatives. The ion-transport activity increased from di- to tetrameric glucosamine macrocycles, but decreased further when flexible pentameric glucosamine was introduced. The ion-transport activity also increased with increasing length of attached linkers. For a fixed length of linkers, the transport activity decreased when the number of such tails was reduced. All glycoconjugates displayed a uniform anion-selectivity sequence: Cl(-) >Br(-) >I(-) . From theoretical studies, hydrogen bonding between the macrocycle backbone and the anion bridged through water molecules was observed. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Synthesis and characterization of star-shaped oligo(ethylene glycol) with tyrosine derived moieties under variation of their molecular weight.

    PubMed

    Julich-Gruner, Konstanze K; Roch, Toralf; Ma, Nan; Neffe, Axel T; Lendlein, Andreas

    2015-01-01

    Desamino tyrosine (DAT) and desamino tyrosyl tyrosine (DATT) can be used to functionalize the end groups of water soluble polymers. The phenolic groups may enable physical interactions by π- π interaction and hydrogen bonds, which might lead to the formation of a hydrogel by physical crosslinking. However, using star-shaped oligo(ethylene glycols) (sOEG) with a molecular weight of 5 kDa for functionalization with DAT or DATT resulted in the formation of surfactants and not in hydrogels.As the molecular weight of the sOEG polymer chain can have an influence on forming physical cross links, DAT(T)-fuctionalization of sOEGs with higher molecular weight was investigated, the polymers were structurally characterized and for their mechanical properties were evaluated by rheological measurements.Aqueous solutions of DAT(T)-sOEGs with 10 and 20 kDa showed lower storage and loss moduli compared to unfunctionalized sOEGs indicating also the formation of surfactants. Cell-based assays showed that all sOEG solutions did not impair cell viability and were free of endotoxins, which could otherwise induce uncontrolled immune responses.Conclusively, our data suggested that the sOEG solutions have surface active properties without inducing unwanted cellular responses, which is required e.g. in pharmaceutical applications to solubilize hydophobic substances.

  8. 4'-Thio-oligo-beta-D-ribonucleotides: synthesis of beta-4'-thio-oligouridylates, nuclease resistance, base pairing properties, and interaction with HIV-1 reverse transcriptase.

    PubMed Central

    Bellon, L; Barascut, J L; Maury, G; Divita, G; Goody, R; Imbach, J L

    1993-01-01

    We present the synthesis and the study of properties of a new series of modified oligonucleotides, namely 4'-thio-oligo-beta-D-ribonucleotides (4'-S-RNA). Homo-oligonucleotides of this class (4'-SU6 and 4'-SU12) were prepared from the previously known thionucleosides using the phosphoramidite methodology. The comparison of the substrate properties of 4'-SU6 and its natural analog U6 with respect to four nucleases indicates that the former is much more resistant than the latter. Such resistance to nucleases in addition to relatively high Tm values for 4'-SU12 hybridized with Poly(A) show that these new 4'-S-RNA are good candidates for potential antisense effects. The oligonucleotides 4'-SU6 and 4'-SU12 have been also evaluated as non sequence specific inhibitors of HIV-1 reverse transcriptase. All available evidences, based primarily on fluorescence measurements, are consistent with the binding of 4'-SU6 and 4'-SU12 to RT at a site which is different from the polymerase site of the enzyme. PMID:7683133

  9. Copolymer Networks From Oligo(ε-caprolactone) and n-Butyl Acrylate Enable a Reversible Bidirectional Shape-Memory Effect at Human Body Temperature.

    PubMed

    Saatchi, Mersa; Behl, Marc; Nöchel, Ulrich; Lendlein, Andreas

    2015-05-01

    Exploiting the tremendous potential of the recently discovered reversible bidirectional shape-memory effect (rbSME) for biomedical applications requires switching temperatures in the physiological range. The recent strategy is based on the reduction of the melting temperature range (ΔT m ) of the actuating oligo(ε-caprolactone) (OCL) domains in copolymer networks from OCL and n-butyl acrylate (BA), where the reversible effect can be adjusted to the human body temperature. In addition, it is investigated whether an rbSME in the temperature range close or even above Tm,offset (end of the melting transition) can be obtained. Two series of networks having mixtures of OCLs reveal broad ΔTm s from 2 °C to 50 °C and from -10 °C to 37 °C, respectively. In cyclic, thermomechanical experiments the rbSME can be tailored to display pronounced actuation in a temperature interval between 20 °C and 37 °C. In this way, the application spectrum of the rbSME can be extended to biomedical applications. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Fluorescent oligo(p-phenyleneethynylene) contained amphiphiles-encapsulated magnetic nanoparticles for targeted magnetic resonance and two-photon optical imaging in vitro and in vivo

    NASA Astrophysics Data System (ADS)

    Yin, Chao; Hong, Binbin; Gong, Zhaocui; Zhao, Hui; Hu, Wenbo; Lu, Xiaomei; Li, Jie; Li, Xiang; Yang, Zhen; Fan, Quli; Yao, Yuyu; Huang, Wei

    2015-05-01

    Folate receptor-targeted multifunctional fluorescent magnetic nanoparticles (FMNPs) composed of cores containing iron oxide nanocrystals and amphiphilic oligo(p-phenyleneethynylene) shells with multimodal imaging capability were successfully prepared through a convenient hydrophobic encapsulation approach. The iron oxide nanoparticles in the core provided T2-weighted magnetic resonance imaging (MRI), whereas the amphiphilic oligomers on the surface of the nanoparticles introduced good water-solubility, biocompatibility, excellent fluorescent properties and cancer-targeting. These nanoparticles exhibited superparamagnetic properties with saturation magnetization (Ms) of 23 emu g-1 and a transverse relaxivity rate of 140.89 mM-1 s-1. In vitro studies indicated that the dual-modal FMNPs can serve as an effective two-photon fluorescent and a magnetic probe to achieve the targeted imaging of Hela cells without obvious cytotoxicity. In vivo two-photon fluorescence and MRI results demonstrated that the FMNPs were able to preferentially accumulate in tumor tissues to allow dual-modal detection of tumors in a living body. These studies provided insight in developing novel multifunctional probes for multimodal imaging, which would play an important role for theranostics in biomedical science.

  11. Fluorescent oligo(p-phenyleneethynylene) contained amphiphiles-encapsulated magnetic nanoparticles for targeted magnetic resonance and two-photon optical imaging in vitro and in vivo.

    PubMed

    Yin, Chao; Hong, Binbin; Gong, Zhaocui; Zhao, Hui; Hu, Wenbo; Lu, Xiaomei; Li, Jie; Li, Xiang; Yang, Zhen; Fan, Quli; Yao, Yuyu; Huang, Wei

    2015-05-21

    Folate receptor-targeted multifunctional fluorescent magnetic nanoparticles (FMNPs) composed of cores containing iron oxide nanocrystals and amphiphilic oligo(p-phenyleneethynylene) shells with multimodal imaging capability were successfully prepared through a convenient hydrophobic encapsulation approach. The iron oxide nanoparticles in the core provided T2-weighted magnetic resonance imaging (MRI), whereas the amphiphilic oligomers on the surface of the nanoparticles introduced good water-solubility, biocompatibility, excellent fluorescent properties and cancer-targeting. These nanoparticles exhibited superparamagnetic properties with saturation magnetization (Ms) of 23 emu g(-1) and a transverse relaxivity rate of 140.89 mM(-1) s(-1). In vitro studies indicated that the dual-modal FMNPs can serve as an effective two-photon fluorescent and a magnetic probe to achieve the targeted imaging of Hela cells without obvious cytotoxicity. In vivo two-photon fluorescence and MRI results demonstrated that the FMNPs were able to preferentially accumulate in tumor tissues to allow dual-modal detection of tumors in a living body. These studies provided insight in developing novel multifunctional probes for multimodal imaging, which would play an important role for theranostics in biomedical science.

  12. Interferon-induced inhibition of parainfluenza virus type 5; the roles of MxA, PKR and oligo A synthetase/RNase L.

    PubMed

    Carlos, T S; Young, D; Stertz, S; Kochs, G; Randall, R E

    2007-06-20

    We have previously reported that the addition of interferon (IFN) to the culture medium of Vero cells (which cannot produce IFN) that were infected with the CPI- strain of parainfluenza virus 5 (PIV5, formally known as SV5), that fails to block IFN signaling, rapidly induces alterations in the relative levels of virus mRNA and protein synthesis. In addition, IFN treatment also caused a rapid redistribution of virus proteins and enhanced the formation of cytoplasmic viral inclusion bodies. The most studied IFN-induced genes with known anti-viral activity are MxA, PKR and the Oligo A synthetase/RNase L system. We therefore examined the effects of these proteins on the replication cycle of PIV5. These studies revealed that while these proteins had some anti-viral activity against PIV5 they were not primarily responsible for the very rapid alteration in virus protein synthesis observed following IFN treatment, nor for the IFN-induced formation of virus inclusion bodies, in CPI- infected cells.

  13. Selection of conformational states in self-assembled surface structures formed from an oligo(naphthylene-ethynylene) 3-bit binary switch

    NASA Astrophysics Data System (ADS)

    Ning, Y.; Cramer, J. R.; Nuermaimaiti, A.; Svane, K.; Yu, M.; Lægsgaard, E.; Besenbacher, F.; Xue, Q.-K.; Ma, X.; Hammer, B.; Gothelf, K. V.; Linderoth, T. R.

    2015-03-01

    Supra-molecular self-assembly on surfaces often involves molecular conformational flexibility which may act to enrich the variation and complexity of the structures formed. However, systematic and explicit investigations of how molecular conformational states are selected in surface self-assembly processes are relatively scarce. Here, we use a combination of high-resolution scanning tunneling microscopy and Density Functional Theory (DFT) calculations to investigate self-assembly for a custom-designed molecule capable of assuming eight distinct surface conformations (four enantiomeric pairs). The conformations result from binary positions of n = 3 naphtalene units on a linear oligo(naphthylene-ethynylene) backbone. On Au(111), inter-molecular interactions involving carboxyl and bulky tert-butyl-phenyl functional groups induce the molecules to form two ordered phases with brick-wall and lamella structure, respectively. These structures each involve molecules in two conformational states, and there is a clear separation between the conformers involved in the two types of structures. On Cu(111), individual molecules isolated by carboxylate-substrate binding show a distribution involving all possible conformational states. Together these observations imply selection and adaptation of conformational states upon molecular self-assembly. From DFT modeling and statistical analysis of the molecular conformations, the observed selection of conformational states is attributed to steric interaction between the naphthalene units. The present study enhances our understanding of how ordering and selection of molecular conformations is controlled by intermolecular interactions in a complex situation with many distinct conformational states for the participating molecules.

  14. Antimicrobial Contact-Active Oligo(2-oxazoline)s-Grafted Surfaces for Fast Water Disinfection at the Point-of-Use.

    PubMed

    Correia, Vanessa G; Ferraria, Ana M; Pinho, Mariana G; Aguiar-Ricardo, Ana

    2015-12-14

    Water is one of the most valuable resources today and its purity is crucial to health and society well-being. The access to safe drinking water is decreasing in the world, which can have a huge socio-economic impact especially in developing countries, more prone to water-associated diseases. The goal of this work was to develop an innovative, fast, and cost-effective 3D material capable of decontaminating water. We have used an eco-friendly strategy, combining plasma surface activation and supercritical fluid technology to produce, for the first time, a 2-oxazoline-grafted 3D surface with broad-spectrum contact-active antimicrobial properties. Oligo(2-methyl-2-oxazoline) quaternized with N,N-dimethyldodecylamine and grafted to a chitosan (CHT) scaffold (CHT-OMetOx-DDA) efficiently and quickly (<3 min) killed >99.999% of Staphylococcus aureus and Escherichia coli cells upon direct contact and avoided bacterial adhesion to the materials surface, which is important for the prevention of biofilm formation. As a proof of concept, CHT-OMetOx-DDA scaffold was demonstrated to be suitable for water purification efficiently killing the microorganisms present in different water samples within minutes of contact and without leaching to the water. Additionally, we report for the first time a new method to clearly distinguish two mechanisms of action of bioactive surfaces: contact-active and releasing systems.

  15. Oligo(ethylene glycol)-sidechain microgels prepared in absence of cross-linking agent: Polymerization, characterization and variation of particle deformability.

    PubMed

    Welsch, Nicole; Lyon, L Andrew

    2017-01-01

    We present a systematic study of self-cross-linked microgels formed by precipitation polymerization of oligo ethylene glycol methacrylates. The cross-linking density of these microgels and, thus, the network flexibility can be easily tuned through the modulation of the reaction temperature during polymerization. Microgels prepared in absence of any difunctional monomer, i.e. cross-linker, show enhanced deformability and particle spreading on solid surfaces as compared to microgels cross-linked with varying amounts of poly(ethylene glycol diacrylate) (PEG-DA) in addition to self-crosslinking. Particles prepared at low reaction temperatures exhibit the highest degree of spreading due to the lightly cross-linked and flexible polymer network. Moreover, AFM force spectroscopy studies suggest that cross-linker-free microgels constitute of a more homogeneous polymer network than PEG-DA cross-linked particles and have elastic moduli at the particle apex that are ~5 times smaller than the moduli of 5 mol-% PEG-DA cross-linked microgels. Resistive pulse sensing experiments demonstrate that microgels prepared at 75 and 80°C without PEG-DA are able to deform significantly to pass through nanopores that are smaller than the microgel size. Additionally, we found that polymer network flexibility of microgels is a useful tool to control the formation of particle dewetting patterns. This offers a promising new avenue for build-up of 2D self-assembled particle structures with patterned chemical and mechanical properties.

  16. Thermo- and pH-Responsive Copolymers Bearing Cholic Acid and Oligo(ethylene glycol) Pendants: Self-Assembly and pH-Controlled Release.

    PubMed

    Jia, Yong-Guang; Zhu, X X

    2015-11-11

    A family of block and random copolymers of norbornene derivatives bearing cholic acid and oligo(ethylene glycol) pendants were prepared in the presence of Grubbs' catalyst. The phase transition temperature of the copolymers in aqueous solutions may be tuned by the variation of comonomer ratios and pH values. Both types of copolymers formed micellar nanostructures with a hydrophilic poly(ethylene glycol) shell and a hydrophobic core containing cholic acid residues. The micellar size increased gradually with increasing pH due to the deprotonation of the carboxylic acid groups. These micelles were capable of encapsulating hydrophobic compounds such as Nile Red (NR). A higher hydrophobicity/hydrophilicity ratio in both copolymers resulted in a higher loading capacity for NR. With similar molecular weights and monomer compositions, the block copolymers showed a higher loading capacity for NR than the random copolymers. The NR-loaded micelles exhibited a pH-triggered release behavior. At pH 7.4 within 96 h, the micelles formed by the block and random of copolymers released 56 and 97% NR, respectively. Therefore, these micelles may have promise for use as therapeutic nanocarriers in drug delivery systems.

  17. Enzymatic Synthesis of Oligo(ethylene glycol)-Bearing Cellulose Oligomers for in Situ Formation of Hydrogels with Crystalline Nanoribbon Network Structures.

    PubMed

    Nohara, Takatoshi; Sawada, Toshiki; Tanaka, Hiroshi; Serizawa, Takeshi

    2016-11-29

    Enzymatic synthesis of cellulose and its derivatives has gained considerable attention for use in the production of artificial crystalline nanocelluloses with unique structural and functional properties. However, the poor colloidal stability of the nanocelluloses during enzymatic synthesis in aqueous solutions limits their crystallization-based self-assembly to greater architectures. In this study, oligo(ethylene glycol) (OEG)-bearing cellulose oligomers with different OEG chain lengths were systematically synthesized via cellodextrin phosphorylase-catalyzed oligomerization of α-d-glucose l-phosphate monomers against OEG-bearing β-d-glucose primers. The products were self-assembled into extremely well-grown crystalline nanoribbon network structures with the cellulose II allomorph, potentially due to OEG-derived colloidal stability of the nanoribbon's precursors, followed by the in situ formation of physically cross-linked hydrogels. The monomer conversions, average degree of polymerization, and morphologies of the nanoribbons changed significantly, depending on the OEG chain length. Taken together, our findings open a new avenue for the enzymatic reaction-based facile production of novel cellulosic soft materials with regular nanostructures.

  18. Degradative properties and cytocompatibility of a mixed-mode hydrogel containing oligo[poly(ethylene glycol)fumarate] and poly(ethylene glycol)dithiol.

    PubMed

    Brink, Kelly S; Yang, Peter J; Temenoff, Johnna S

    2009-02-01

    Our laboratory is currently exploring synthetic oligo(poly(ethylene glycol)fumarate) (OPF)-based biomaterials as a means to deliver fibroblasts to promote regeneration of central/partial defects in tendons and ligaments. In order to further modulate the swelling and degradative characteristics of OPF-based hydrogels, OPF crosslinking via a radically initiated, mixed-mode reaction involving poly(ethylene glycol) (PEG)-diacrylate and PEG-dithiol was investigated. Results demonstrate that mixed-mode hydrogels containing OPF can be formed and that the presence of 20 wt.% PEG-dithiol increases swelling and decreases degradation time vs. 10 wt.% PEG-dithiol and non-thiol-containing hydrogels (20% thiol fold swelling 28.7+/-0.8; 10% thiol fold swelling 11.6+/-1.4; non-thiol 8.7+/-0.2; 20% thiol-containing hydrogels degrade within 15 days in vitro). After encapsulation, tendon/ligament fibroblasts remained largely viable over 8 days of static culture. While the presence of PEG-dithiol did not significantly affect cellularity or collagen production within the constructs over this time period, image analysis revealed that the 20% PEG-dithiol gels did appear to promote cell clustering, with greater values for aggregate area observed by day 8. These experiments suggest that mixed-mode OPF-based hydrogels may provide an interesting alternative as a cell carrier for engineering a variety of soft orthopedic tissues, particularly for applications when it is important to encourage cell-cell contact.

  19. Oligo(FcDC-co-CholDEA) with ferrocene in the main chain and cholesterol as a pendant group-preparation and unusual properties.

    PubMed

    Yan, Junlin; Liu, Jing; Sun, Yuanhui; Jing, Ping; He, Panli; Gao, Di; Fang, Yu

    2010-10-21

    With ever-increasing need for thin, flexible, and functional materials in electrochemical systems, various techniques have been explored for creating materials used in fuel cells, batteries, electrochromic devices, solar cells, and sensors. In the present study, a novel ferrocene (Fc) and cholesterol (Chol)-containing oligomer, oligo(FcDC-co-CholDEA), was specially designed and prepared by putting Fc in the main chain and Chol as a side group. MALDI-TOF MS and freezing point depression measurements revealed that in average each oligomer contains three Fc units and three Chol units. Cyclic voltammetric measurements revealed that the oligomer displays superior electrochemical stability if compared with other Fc derivatives containing only one Fc unit and one or two Chol unit and with poly(ferrocenylsilane) with Fc in the main chain. In particular, the Fc-containing oligomer possesses an unusual oxidation center, of which the oxidation potential could be as high as 1.81 V. The oligomer is also superior in self-assembly, as demonstrated by forming an LB film of layered structures. Furthermore, supramolecular films with high mechanical strength in the wet state can be prepared by employing a simple solution casting method. This finding demonstrates that self-assembly is a simple but effective way to create films of potential uses in real-life applications provided proper building blocks are designed and employed.

  20. RNA in situ hybridization in Arabidopsis.

    PubMed

    Wu, Miin-Feng; Wagner, Doris

    2012-01-01

    RNA in situ hybridization using digoxigenin-labeled riboprobes on tissue sections is a powerful technique for revealing microscopic spatial gene expression. Here, we describe an in situ hybridization method commonly practiced in Arabidopsis research labs. The highly stringent hybridization condition eliminates the usage of Ribonlucease A and gives highly specific signals. This also allows the use of longer probes which enhance signal strength without cross hybridization to closely related genes. In addition, using spin columns in template and riboprobe purification greatly reduces background signals.

  1. Effects of vertical rotation on Arabidopsis development

    NASA Technical Reports Server (NTRS)

    Brown, A. H.; Chapman, D. K.; Dahl, A. O.

    1975-01-01

    Various gross morphological end points of Arabidopsis development are examined in an attempt to separate the effects of growth on the horizontal clinostat into a component caused by rotation alone and another component caused by the altered position with respect to the direction of the g-vector. In a series of tests which involved comparisons between vertical stationary plants, vertical rotated plants, and plants rotated on clinostats, certain characters were consistently influenced by vertical rotation alone. The characters for which this effect was statistically significant were petiole length and leaf blade width.

  2. Carotenoid Biosynthesis in Arabidopsis: A Colorful Pathway

    PubMed Central

    Ruiz-Sola, M. Águila; Rodríguez-Concepción, Manuel

    2012-01-01

    Plant carotenoids are a family of pigments that participate in light harvesting and are essential for photoprotection against excess light. Furthermore, they act as precursors for the production of apocarotenoid hormones such as abscisic acid and strigolactones. In this review, we summarize the current knowledge on the genes and enzymes of the carotenoid biosynthetic pathway (which is now almost completely elucidated) and on the regulation of carotenoid biosynthesis at both transcriptional and post-transcriptional levels. We also discuss the relevance of Arabidopsis as a model system for the study of carotenogenesis and how metabolic engineering approaches in this plant have taught important lessons for carotenoid biotechnology. PMID:22582030

  3. Molecular mechanisms underlying the Arabidopsis circadian clock.

    PubMed

    Nakamichi, Norihito

    2011-10-01

    A wide range of biological processes exhibit circadian rhythm, enabling plants to adapt to the environmental day-night cycle. This rhythm is generated by the so-called 'circadian clock'. Although a number of genetic approaches have identified >25 clock-associated genes involved in the Arabidopsis clock mechanism, the molecular functions of a large part of these genes are not known. Recent comprehensive studies have revealed the molecular functions of several key clock-associated proteins. This progress has provided mechanistic insights into how key clock-associated proteins are integrated, and may help in understanding the essence of the clock's molecular mechanisms.

  4. The defense response in Arabidopsis thaliana against Fusarium sporotrichioides

    PubMed Central

    2012-01-01

    Background Certain graminaceous plants such as Zea mays and Triticum aestivum serve as hosts for Fusarium sporotrichioides; however, molecular interactions between the host plants and F. sporotrichioides remain unknown. It is also not known whether any interaction between Arabidopsis thaliana and F. sporotrichioides can occur. To understand these interactions, we performed proteomic analysis. Results Arabidopsis leaves and flowers were inoculated with F. sporotrichioides. Accumulation of PLANT DEFENSIN1.2 (PDF1.2) and PATHOGENESIS RELATED1 (PR1) mRNA in Arabidopsis were increased by inoculation of F. sporotrichioides. Furthermore, mitogen-activated protein kinase 3 (MPK3) and mitogen-activated protein kinase 6 (MPK6), which represent MAP kinases in Arabidopsis, were activated by inoculation of F. sporotrichioides. Proteomic analysis revealed that some defense-related proteins were upregulated, while the expression of photosynthesis- and metabolism-related proteins was down regulated, by inoculation with F. sporotrichioides. We carried out the proteomic analysis about upregulated proteins by inoculation with Fusarium graminearum. The glutathione S-transferases (GSTs), such as GSTF4 and GSTF7 were upregulated, by inoculation with F. graminearum-infected Arabidopsis leaves. On the other hand, GSTF3 and GSTF9 were uniquely upregulated, by inoculation with F. sporotrichioides. Conclusions These results indicate that Arabidopsis is a host plant for F. sporotrichioides. We revealed that defense response of Arabidopsis is initiated by infection with F. sporotrichioides. PMID:23110430

  5. Linkage maps for Arabidopsis lyrata subsp. lyrata and Arabidopsis lyrata subsp. petraea combining anonymous and Arabidopsis thaliana-derived markers.

    PubMed

    Beaulieu, Julien; Jean, Martine; Belzile, François

    2007-02-01

    Arabidopsis lyrata, a close relative of the model plant Arabidopsis thaliana, is 1 of a few plant species for which the genome is to be entirely sequenced, which promises to yield important insights into genome evolution. Only 2 sparse linkage maps have been published, and these were based solely on markers derived from the A. thaliana genome. Because the genome of A. lyrata is practically twice as large as that of A. thaliana, the extent of map coverage of the A. lyrata genome remains uncertain. In this study, a 2-way pseudo-testcross strategy was used to construct genetic linkage maps of A. lyrata subsp. petraea and A. lyrata subsp. lyrata, using simple sequence repeat (SSR) and cleaved amplified polymorphic sequence (CAPS) markers from the A. thaliana genome, and anonymous amplified fragment length polymorphism (AFLP) markers that could potentially uncover regions unique to the A. lyrata genome. The SSR and CAPS markers largely confirmed the relationships between linkage groups in A. lyrata and A. thaliana. AFLP markers slightly increased the coverage of the A. lyrata maps, but mostly increased marker density on the linkage groups. We noted a much lower level of polymorphism and a greater segregation distortion in A. lyrata subsp. lyrata markers. The implications of these findings for the sequencing of the A. lyrata genome are discussed.

  6. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.

    PubMed

    Riechmann, J L; Heard, J; Martin, G; Reuber, L; Jiang, C; Keddie, J; Adam, L; Pineda, O; Ratcliffe, O J; Samaha, R R; Creelman, R; Pilgrim, M; Broun, P; Zhang, J Z; Ghandehari, D; Sherman, B K; Yu, G

    2000-12-15

    The completion of the Arabidopsis thaliana genome sequence allows a comparative analysis of transcriptional regulators across the three eukaryotic kingdoms. Arabidopsis dedicates over 5% of its genome to code for more than 1500 transcription factors, about 45% of which are from families specific to plants. Arabidopsis transcription factors that belong to families common to all eukaryotes do not share significant similarity with those of the other kingdoms beyond the conserved DNA binding domains, many of which have been arranged in combinations specific to each lineage. The genome-wide comparison reveals the evolutionary generation of diversity in the regulation of transcription.

  7. Reducible Poly(Oligo-D-Arginine) as an Efficient Carrier of the Thymidine Kinase Gene in the Intracranial Glioblastoma Animal Model.

    PubMed

    Kim, Hyun Ah; Lee, Hyun-Lin; Choi, Eunji; Kim, Yong-Hee; Lee, Minhyung

    2015-11-01

    Gene therapy has been considered as an alternative treatment for glioblastoma therapy. In this study, a glioblastoma-specific suicide gene, pEpo-NI2-SV-TK, was delivered into the intracranial glioblastoma model using reducible poly(oligo-d-arginines) (rPOA). pEpo-NI2-SV-TK has the erythropoietin (Epo) enhancer and the nestin intron 2 (NI2) for glioblastoma specific gene expression. The in vitro studies showed that the rPOA formed stable complexes with pEpo-NI2-SV-TK. In the MTT and TUNEL assays, rPOA showed lower cytotoxicity than polyethylenimine (25 kDa, PEI25k). In addition, the rPOA/pEpo-NI2-SV-TK complex induced higher glioblastoma cell death under hypoxic condition than normoxic condition, suggesting that pEpo-NI2-SV-TK induced gene expression in the hypoxic tumor tissue. For in vivo therapeutic efficacy evaluation, the rPOA/pEpo-NI2-SV-TK complex was injected into the brains of an intracranial glioblastoma rat model. The rPOA/pEpo-NI2-SV-TK injected group had a significantly reduced tumor size, compared with the control and the PEI25k/pEpo-NI2-SV-TK injected group. The TUNEL assay showed that the rPOA-pEpo-NI2-SV-TK complex had more apoptotic cells than the control and PEI25k/pEpo-NI2-SV-TK injected groups. These results suggest that the rPOA is an efficient carrier for pEpo-NI2-SV-TK and increased the therapeutic efficacy in the intracranial glioblastoma models. Therefore, the rPOA/pEpo-NI2-SV-TK complex may be useful for glioblastoma specific gene therapy.

  8. Synthesis and antitumor activity of new amphiphilic alkylglycerolipids substituted with a polar head group, 2-(2-trimethylammonioethoxy)ethyl or a congeneric oligo(ethyleneoxy)ethyl group.

    PubMed

    Ukawa, K; Imamiya, E; Yamamoto, H; Aono, T; Kozai, Y; Okutani, T; Nomura, H; Honma, Y; Hozumi, M; Kudo, I

    1989-12-01

    A new series of amphiphilic 1-octadecyl glycerolipids (eleven compounds, 1a-k) were designed and synthesized, in which the 3-phosphocholine portion of platelet-activating factor (1-alkyl-2-acetyl-sn-glycero-3-phosphocholine, PAF) was replaced by the 2-(2-trimethylammonioethoxy)ethyl group and congeneric groups having oligo(ethyleneoxy)ethyl bridges of various lengths at position 3, together with modification at position 2 (lower alkyl, acetonyl, acetoacetyl, carboxymethyl and pyrimidin-2-yl groups). These ether lipids, characterized by a nonphosphorus lysoglycerolipid structure, showed potent antitumor activity in vitro (human promyelocytic leukemia cells, HL-60, and human epidermoid carcinoma cells, KB) and in vivo (mouse sarcoma S180 and mouse mammary carcinoma MM46). Maximal in vitro potency was obtained with 1-O-octadecyl-2-O-(2-pyrimidinyl)-3-O-[2-(2-trimethylammonioethoxy )ethyl] glycerol (1g; IC50 values for both HL-60 and KB were 0.32 microgram/ml, indicating a higher activity than alkyl-lysophospholipid, ET18-OMe). Several appropriately 2-substituted 1-octadecylglycerolipids with the 3-[2-(2-trimethylammonioethoxy)ethyl] group (e.g., methyl, 1b; butyl, 1f; 2,2,2-trifluoroethyl, 1j; and acetonyl, 1k) showed a potent life-span-prolonging effect on mice with ascites sarcoma S180 and on those with mammary carcinoma MM46, when administered intraperitoneally at 16.5 and 12.5 mg/kg/d, respectively. Compounds 1b and 1k showed definite tumor growth inhibition against solid sarcoma S180 in mice, whether given p.o. or i.v. at 16.5 mg/kg/d. Studies on the structure-activity relationships indicate that the metabolic stability to phospholipase C or related enzymes is at least partly responsible for the potent antitumor activity of this series of ether lipids.

  9. Radiation-induced synthesis and swelling properties of p(2-hydroxyethyl methacrylate/itaconic acid/oligo (ethylene glycol) acrylate) terpolymeric hydrogels

    NASA Astrophysics Data System (ADS)

    Micic, M.; Stamenic, D.; Suljovrujic, E.

    2012-09-01

    Since it is presumed that by incorporation of pH-responsive (IA) and temperature-responsive (OEGA) co-monomers, it is possible to prepare P(HEMA/IA/OEGA) hydrogels with dual (pH and thermo) responsiveness, the main purpose of our study is to investigate the influence of different mole fractions of IA and especially OEGA on the diversity of the swelling properties of the obtained hydrogels. For that reason, a series of terpolymeric hydrogels with different mole ratios of 2-hydroxyethyl methacrylate (HEMA), itaconic acid (IA) and oligo(ethylene glycol) acrylates (OEGA) was synthesised by gamma radiation. The obtained hydrogels were characterised by swelling studies in the wide pH (2.2-9.0) and temperature range (20-70 °C), confirming dual (pH and thermo) responsiveness and a large variation in the swelling capability. It was observed that the equilibrium swelling of P(HEMA/IA/OEGA) hydrogels, for a constant amount of IA, increased progressively with an increase in OEGA share. On the other hand, the dissociation of carboxyl groups from IA occurs at pH>4; therefore, small mole fractions of IA render good pH sensitivity and a large increase in the swelling capacity of these hydrogels at higher pH values. Additional characterisation of structure and properties was conducted by Fourier transform infrared (FTIR) spectroscopy, scanning electron microscopy (SEM) and mechanical measurements, confirming that the inherent properties of P(HEMA/IA/OEGA) hydrogels can be significantly tuned by variation in their composition. According to all presented, it seems that the obtained hydrogels can be a beneficial synergetic combination for controlled delivery of bioactive molecules such as drugs, peptides, proteins, etc.

  10. Donor-acceptor random copolyesters containing perylenebisimide (PBI) and oligo(p-phenylene vinylene) (OPV) by melt condensation polymerization: energy transfer studies.

    PubMed

    Nisha, S Kumari; Asha, S K

    2013-10-31

    Novel copolyesters consisting of oligo(p-phenylene vinylene) (OPV) as donor (D) and perylenebisimide (PBI) as acceptor (A) were synthesized by melt polycondensation. Photoinduced energy transfer and photoinduced charge separation in these polyesters were studied in solution as well as in the solid state. Selective excitation of OPV moiety resulted in the energy transfer with >90% efficiency from OPV to PBI chromophore in the solution state. The direct excitation of PBI in the D-A copolyester resulted in reduced fluorescence emission of acceptor, indicating electron transfer between the D and A moieties. The effect of distance between donor and acceptor on the energy transfer efficiency from donor to acceptor was studied. Compared to a physical mixture of D and A polyesters alone, the energy transfer was 4 times more efficient in the D-A copolyester, highlighting the influence of covalently linking D and A in a single polymer chain. A strong fluorescence quenching (∼ 100%) of both chromophores in solid state indicated an efficient photoinduced charge transfer after photoexcitation of either D or A. Thus, OPV-PBI main chain copolyester is an excellent system for the study of energy- and electron-transfer processes in organic semiconductor. Reactive blend of D/A copolyester was also prepared by the transesterification reaction between D and A alone copolyesters. The energy transfer efficiency from D to A moiety upon selective excitation of D chromophore in the D/A copolyester blend was ∼4 times higher compared to a physical mixture of D and A alone copolyesters, which gave direct proof for the transesterification reaction in polyester/polyester reactive blending.

  11. Rotational motion of rhodamine 6G tethered to actin through oligo(ethylene glycol) linkers studied by frequency-domain fluorescence anisotropy

    PubMed Central

    Wazawa, Tetsuichi; Morimoto, Nobuyuki; Nagai, Takeharu; Suzuki, Makoto

    2015-01-01

    Investigation of the rotational motion of a fluorescent probe tethered to a protein helps to elucidate the local properties of the solvent and protein near the conjugation site of the probe. In this study, we have developed an instrument for frequency-domain fluorescence (FDF) anisotropy measurements, and studied how the local properties around a protein, actin, can be elucidated from the rotational motion of a dye tethered to actin. Rhodamine 6G (R6G) was attached to Cys-374 using newly-synthesized R6G-maleimide with three different oligo(ethylene glycol) (OEG) linker lengths. The time-resolved anisotropy decay of R6G tethered to G-actin was revealed to be a combination of the two modes of the wobbling motion of R6G and the tumbling motion of G-actin. The rotational diffusion coefficient (RDC) of R6G wobbling was ~0.1 ns−1 at 20°C and increased with OEG linker length. The use of the three R6G-actin conjugates of different linker lengths was useful to not only figure out the linker length dependence of the rotational motion of R6G but also validate the analyses. In the presence of a cosolvent of glycerol, although the tumbling motion of G-actin was retarded in response to the bulk viscosity, the wobbling motion of R6G tethered to actin exhibited an increase of RDC as glycerol concentration increased. This finding suggests an intricate relationship between the fluid properties of the bulk solvent and the local environment around actin. PMID:27493858

  12. Long-term protection against tobacco mosaic virus induced by the marine alga oligo-sulphated-galactan Poly-Ga in tobacco plants.

    PubMed

    Vera, Jeannette; Castro, Jorge; González, Alberto; Barrientos, Herna; Matsuhiro, Betty; Arce, Patricio; Zuñiga, Gustavo; Moenne, Alejandra

    2011-06-01

    In order to study the antiviral effect of the oligo-sulphated galactan Poly-Ga, the leaves of tobacco plants Xhanti(NN) were sprayed with water (control), with increasing concentrations of Poly-Ga, for increasing numbers of treatments or cultivated for increasing times after treatment. Control and treated plants were infected with tobacco mosaic virus (TMV) and the numbers of necrotic lesions were measured in infected leaves. The number of necrotic lesions decreased with increasing concentrations of Poly-Ga, with increasing numbers of treatments and with increasing time after treatment, indicating a long-term protection against TMV that mimicks vaccination. In addition, control Xhanti(nn) plants and plants treated with Poly-Ga and cultivated for increasing times after treatment were infected with TMV in the middle part of the plant, and the levels of TMV-capsid protein (CP) transcripts were measured in apical leaves. TMV-CP transcripts decreased in distant leaves, indicating that Poly-Ga induces systemic protection against TMV. The activities of the defence enzymes phenylalanine ammonia lyase (PAL) and lipoxygenase (LOX) and the amounts of several phenylpropanoid compounds (PPCs) were measured in control and treated plants without infection. A progressive increase in PAL activity was observed with increasing time after treatment, together with the accumulation of free and conjugated PPCs. In contrast, LOX activity remained unchanged. Interestingly, the increase in PAL activity showed a linear correlation with the decrease in necrotic lesions and the decrease in TMV-CP transcript level. Thus, Poly-Ga induced systemic and long-term protection against TMV in tobacco plants that is determined, at least in part, by a sustained activation of PAL and the accumulation of PPCs with potential antiviral activity.

  13. In vitro inhibition of promyelocytic leukemia/retinoic acid receptor-alpha (PML/RARalpha) expression and leukemogenic activity by DNA/LNA chimeric antisense oligos.

    PubMed

    Caprodossi, Sara; Galluzzi, Luca; Biagetti, Simona; Della Chiara, Giulia; Pelicci, Pier Giuseppe; Magnani, Mauro; Fanelli, Mirco

    2005-01-01

    Acute promyelocytic leukemia (APL) is a subtype of myeloid leukemia characterized by the chromosomal translocation t(15:17) that leads to the expression of promyelocytic leukemia/retinoic acid receptor-alpha (PML/ RARalpha) oncofusion protein. The block of differentiation at the promyelocytic stage of the blasts and their increased survival induced by PML/RARalpha are the principal biological features of the disease. Therapies based on pharmacological doses of retinoic acid (RA, 10(-6) M) are able to restore APL cell differentiation in most cases, but not to achieve complete hematological remission because retinoic acid resistance occurs in many patients. In order to elaborate alternative therapeutic approaches, we focused our attention on the use of antisense oligonucleotides as gene-specific drug directed to PML/RARalpha mRNA target. We used antisense molecules containing multiple locked nucleic acid (LNA) modifications. The LNAs are nucleotide analogues that are able to form duplexes with complementary DNA or RNA sequences with highly increased thermal stability and are resistant to 3'-exonuclease degradation in vitro. The DNA/LNA chimeric molecules were designed on the fusion sequence of PML and RARalpha genes to specifically target the oncofusion protein. Cell-free and in vitro experiments using U937-PR9-inducible cell line showed that DNA/LNA oligonucleotides were able to interfere with PML/RARalpha expression more efficiently than the corresponding unmodified DNA oligo. Moreover, the treatment of U937-PR9 cells with these chimeric antisense molecules was able to abrogate the block of differentiation induced by PML/RARalpha oncoprotein. These data suggest a possible application of oligonucleotides containing LNA in an antisense therapeutic strategy for APL.

  14. Dynamic in vitro hemocompatibility testing of poly(ether imide) membranes functionalized with linear, methylated oligoglycerol and oligo(ethylene glycol).

    PubMed

    Braune, Steffen; von Ruesten-Lange, Maik; Mrowietz, Christof; Lützow, Karola; Roch, Toralf; Neffe, Axel T; Lendlein, Andreas; Jung, Friedrich

    2013-01-01

    Linear, side-chain methylated oligoglycerols (OGMe) were recently reported as potential surface passivating molecules for improving the protein resistance of cardiovascular application relevant poly(ether imide) (PEI) membranes. A previously reported in vitro screening under static test conditions allowed an end-point evaluation of the adhesion and activation of adherent thrombocytes performed on the material surfaces and revealed similar levels of thrombogenicity on PEI membranes, functionalized with OGMe and oligo(ethylene glycol) (OEG) of similar molecular weight (Mn = 1,300 g·mol-1 - 1,800 g·mol-1). In the present study, we investigated the hemocompatibility of these materials in a dynamic closed loop system, in order to study time-dependent thrombocyte material interactions also of the circulating thrombocytes by mimicking in vivo relevant flow conditions in a dynamic test system with multiple material contacts. Activation and aggregation of circulating thrombocytes as well as complement activation and plasmatic coagulation were evaluated after 40 circulations of thrombocyte rich plasma in the closed loop system. The results of the dynamic tests revealed no differences between the OGMe and OEG functionalized PEI membranes. Furthermore, no differences were observed between the latter and a PEI membrane treated under the conditions of functionalization at pH 11 (PEI-pH11) without an oligoether being present. Blood plasma protein adsorption, as well as activation, and adherence of circulating thrombocytes occurred in a comparable, but minor manner on all investigated PEI membranes. From this we conclude that the OGMe and OEG surface functionalization did not lead to an improvement of the already good hemocompatibility of the PEI-pH11 membrane.

  15. Modulation of marrow stromal osteoblast adhesion on biomimetic oligo[poly(ethylene glycol) fumarate] hydrogels modified with Arg-Gly-Asp peptides and a poly(ethyleneglycol) spacer.

    PubMed

    Shin, Heungsoo; Jo, Seongbong; Mikos, Antonios G

    2002-08-01

    Novel oligo[poly(ethylene glycol) fumarate] (OPF) hydrogels functionalized with cell adhesion peptides were prepared, and the effects of incorporated peptide density and macromolecular structure of hydrogels on attachment and morphology of marrow stromal cells (MSCs) were evaluated. Poly(ethylene glycol) (PEG; number average molecular weight of 930, 2860, and 6090) was used to synthesize OPF. A model peptide, Gly-Arg-Gly-Asp (GRGD), was incorporated into OPF hydrogels after being coupled to acrylated PEG of molecular weight 3400. The increase of incorporated peptide concentration enhanced MSC attachment to OPF hydrogels of PEG of molecular weight of 930 and 2860. However, the number of attached MSCs to OPF hydrogels of PEG (molecular weight 6090) remained constant regardless of the peptide density. The length of PEG in OPF also influenced cell attachment. When 1 micromole peptide/g hydrogel was incorporated into the OPF hydrogels, the degree of cell attachment at 12 h relative to the initial seeding density was 93.9 +/- 5.9%, 64.7 +/- 8.2%, and 9.3 +/- 6.6% for OPF hydrogels prepared with PEG of molecular weights of 930, 2860, and 6090, respectively. However, the crosslinking density of hydrogels did not significantly affect cell attachment. The interaction was sequence specific, in that MSC attachment to GRGD-modified hydrogels was competitively inhibited when cells were incubated in the presence of 0.5 mM soluble GRGD before cell seeding. These results suggest that we can modulate MSC attachment to OPF hydrogels by altering the peptide density and the molecular structure of OPF hydrogels.

  16. Effect of poly(ethylene glycol) molecular weight on tensile and swelling properties of oligo(poly(ethylene glycol) fumarate) hydrogels for cartilage tissue engineering.

    PubMed

    Temenoff, Johnna S; Athanasiou, Kyriacos A; LeBaron, Richard G; Mikos, Antonios G

    2002-03-05

    This study was designed to determine the effect of changes in poly(ethylene glycol) (PEG) molecular weight on swelling and mechanical properties of hydrogels made from a novel polymer, oligo(poly(ethylene glycol) fumarate) (OPF), recently developed in our laboratory. Properties of hydrogels made from OPF with initial PEG molecular weights of 860, 3900, and 9300 were examined. The PEG 3900 formulation had a tensile modulus of 23.1 +/- 12.4 kPa and percent elongation at fracture of 53.2 +/- 13.7%; the PEG 9300 formulation had similar tensile properties (modulus: 16.5 +/- 4.6 kPa, elongation: 76.0 +/- 26.4%). However, the PEG 860 gels had a significantly higher modulus (89.5 +/- 50.7 kPa) and a significantly smaller percent elongation at fracture (30.1 +/- 6.4%), when compared with other formulations. Additionally, there were significant differences in percent swelling between each of the formulations. Molecular weight between crosslinks (M(c)) and mesh size were calculated for each OPF formulation. M(c) increased from 2010 +/- 116 g/mol with PEG 860 to 6250 +/- 280 g/mol with PEG 9300. Mesh size calculations showed a similar trend (76 +/- 2 A for PEG 860 to 160 +/- 6 A for PEG 9300). It was also found that these hydrogels could be laminated if a second layer was added before the first had completely crosslinked. Mechanical testing of these laminated gels revealed that the presence of an interfacial area did not significantly alter their tensile properties. These results suggest that the material properties of OPF-based hydrogels can be altered by changing the molecular weight of PEG used in synthesis and that multilayered OPF hydrogel constructs can be produced, with each layer having distinct mechanical properties.

  17. Reconstruction of pre-rift Pyrenean relief in the Oligo-Quitanian Camargue Basin (Gulf of Lion passive margin, SE France): Implications on thermal history of basins

    SciTech Connect

    Benedicto, A.; Labaume, P.; Seranne, M.

    1995-08-01

    Fault reconstruction techniques commonly assume horizontal pre-rift level datum to calculate fault geometry from hanging-wall geometry or viceversa. Example from Camargue basin shows that neglecting pre-rift relief may lead to important errors in calculating the fault and hanging-wall geometries, and the total extension. These errors have direct implications on reconstruction of the thermal history of basins. The Camargue basin results front NW-SE extension and rifting of the Gulf of Lion passive margin. More than 4000m of Oligo-Aquitanian syn-rift series unconformably overlie a crust previously thickened during Pyrenean orogeny. The half-graben basin is controlled by the SE-dipping listric Nimes basement fault which generated a typical roll-over. As both fault and hanging-wall geometries are constrained, the pre-rift surface topography can be restored, using three reconstruction techniques. Either the constant-bed-length and constant-heave techniques produce a depression in the axis of the basin and a relief (1500m and 12(X)m respectively) atop the roll-over. The simple-shear (a=60{degrees}) technique generates a 1500m topography atop the roll-over, more coherent with regional data. Testing the hypothesis of a pre-rift horizontal datum leads to a roll-over 1400m too deep. Pre-rift surface elevation corresponds to the residual topography herited from the Pyrenean orogeny. Consequently, there has been some 1000m subsidence more than predicted by the syn-rift sedimentary record.

  18. Gene expression in breast muscle associated with feed efficiency in a single male broiler line using a chicken 44K oligo microarray. I. Top differentially expressed genes.

    PubMed

    Kong, B-W; Song, J J; Lee, J Y; Hargis, B M; Wing, T; Lassiter, K; Bottje, W

    2011-11-01

    Global RNA expression in breast muscle obtained from a male broiler line phenotyped for high or low feed efficiency (FE) was investigated. Pooled RNA samples (n = 6/phenotype) labeled with cyanine 3 or cyanine 5 fluorescent dyes to generate cRNA probes were hybridized on a 4 × 44K chicken oligo microarray. Local polynomial regression normalization was applied to background-corrected red and green intensities with a moderated t-statistic. Corresponding P-values were computed and adjusted for multiple testing by false discovery rate to identify differentially expressed genes. Microarray validation was carried out by comparing findings with quantitative reverse-transcription PCR. A 1.3-fold difference in gene expression was set as a cutoff value, which encompassed 20% (782 of 4,011) of the total number of genes that were differentially expressed between FE phenotypes. Using an online software program (Ingenuity Pathway Analysis), the top 10 upregulated genes identified by Ingenuity Pathway Analysis in the high-FE group were generally associated with anabolic processes. In contrast, 7 of the top 10 downregulated genes in the high-FE phenotype (upregulated in the low-FE phenotype) were associated with muscle fiber development, muscle function, and cytoskeletal organization, with the remaining 3 genes associated with self-recognition or stress-responding genes. The results from this study focusing on only the top differentially expressed genes suggest that the high-FE broiler phenotype is derived from the upregulation of genes associated with anabolic processes as well as a downregulation of genes associated with muscle fiber development, muscle function, cytoskeletal organization, and stress response.

  19. Oligo-antigenic diet in the treatment of chronic anal fissures. Evidence for a relationship between food hypersensitivity and anal fissures.

    PubMed

    Carroccio, Antonio; Mansueto, Pasquale; Morfino, Giuditta; D'Alcamo, Alberto; Di Paola, Valentina; Iacono, Giuseppe; Soresi, Maurizio; Scerrino, Gregorio; Maresi, Emiliano; Gulotta, Gaspare; Rini, Giovambattista; Bonventre, Sebastiano

    2013-05-01

    Patients with chronic constipation due to food hypersensitivity (FH) had an elevated anal sphincter resting pressure. No studies have investigated a possible role of FH in anal fissures (AFs). We aimed to evaluate (1) the effectiveness of diet in curing AFs and to evaluate (2) the clinical effects of a double-blind placebo-controlled (DBPC) challenge, using cow's milk protein or wheat. One hundred and sixty-one patients with AFs were randomized to receive a "true-elimination diet" or a "sham-elimination diet" for 8 weeks; both groups also received topical nifedipine and lidocaine. Sixty patients who were cured with the "true-elimination diet" underwent DBPC challenge in which cow's milk and wheat were used. At the end of the study, 69% of the "true-diet group" and 45% of the "sham-diet group" showed complete healing of AFs (P<0.0002). Thirteen of the 60 patients had AF recurrence during the 2-week cow's milk DBPC challenge and 7 patients had AF recurrence on wheat challenge. At the end of the challenge, anal sphincter resting pressure significantly increased in the patients who showed AF reappearance (P<0.0001), compared with the baseline values. The patients who reacted to the challenges had a significantly higher number of eosinophils in the lamina propria and intraepithelial lymphocytes than those who did not react to the challenges. An oligo-antigenic diet combined with medical treatment improved the rate of chronic AF healing. In more than 20% of the patients receiving medical and dietary treatment, AFs recurred on DBPC food challenge.

  20. The Oligo-Acyl Lysyl Antimicrobial Peptide C12K-2β12 Exhibits a Dual Mechanism of Action and Demonstrates Strong In Vivo Efficacy against Helicobacter pylori

    PubMed Central

    Makobongo, Morris O.; Gancz, Hanan; Carpenter, Beth M.; McDaniel, Dennis P.

    2012-01-01

    Helicobacter pylori has developed antimicrobial resistance to virtually all current antibiotics. Thus, there is a pressing need to develop new anti-H. pylori therapies. We recently described a novel oligo-acyl-lysyl (OAK) antimicrobial peptidomimetic, C12K-2β12, that shows potent in vitro bactericidal activity against H. pylori. Herein, we define the mechanism of action and evaluate the in vivo efficacy of C12K-2β12 against H. pylori after experimental infection of Mongolian gerbils. We demonstrate using a 1-N-phenylnaphthylamine (fluorescent probe) uptake assay and electron microscopy that C12K-2β12 rapidly permeabilizes the bacterial membrane and creates pores that cause bacterial cell lysis. Furthermore, using nucleic acid binding assays, Western blots, and confocal microscopy, we show that C12K-2β12 can cross the bacterial membranes into the cytoplasm and tightly bind to bacterial DNA, RNA, and proteins, a property that may result in inhibition of enzymatic activities and macromolecule synthesis. To define the in vivo efficacy of C12K-2β12, H. pylori-infected gerbils were orogastrically treated with increasing doses and concentrations of C12K-2β12 1 day or 1 week postinfection. The efficacy of C12K-2β12 was strongest in animals that received the largest number of doses at the highest concentration, indicating dose-dependent activity of the peptide (P < 0.001 by analysis of variance [ANOVA]) regardless of the timing of the treatment with C12K-2β12. Overall, our results demonstrate a dual mode of action of C12K-2β12 against the H. pylori membrane and cytoplasmic components. Moreover, and consistent with the previously reported in vitro efficacy, C12K-2β12 shows significant in vivo efficacy against H. pylori when used as monotherapy. Therefore, OAK peptides may be a valuable resource for therapeutic treatment of H. pylori infection. PMID:22064541

  1. Estimating In Situ Zooplankton Non-Predation Mortality in an Oligo-Mesotrophic Lake from Sediment Trap Data: Caveats and Reality Check.

    PubMed

    Dubovskaya, Olga P; Tang, Kam W; Gladyshev, Michail I; Kirillin, Georgiy; Buseva, Zhanna; Kasprzak, Peter; Tolomeev, Aleksandr P; Grossart, Hans-Peter

    2015-01-01

    Mortality is a main driver in zooplankton population biology but it is poorly constrained in models that describe zooplankton population dynamics, food web interactions and nutrient dynamics. Mortality due to non-predation factors is often ignored even though anecdotal evidence of non-predation mass mortality of zooplankton has been reported repeatedly. One way to estimate non-predation mortality rate is to measure the removal rate of carcasses, for which sinking is the primary removal mechanism especially in quiescent shallow water bodies. We used sediment traps to quantify in situ carcass sinking velocity and non-predation mortality rate on eight consecutive days in 2013 for the cladoceran Bosmina longirostris in the oligo-mesotrophic Lake Stechlin; the outcomes were compared against estimates derived from in vitro carcass sinking velocity measurements and an empirical model correcting in vitro sinking velocity for turbulence resuspension and microbial decomposition of carcasses. Our results show that the latter two approaches produced unrealistically high mortality rates of 0.58-1.04 d(-1), whereas the sediment trap approach, when used properly, yielded a mortality rate estimate of 0.015 d(-1), which is more consistent with concurrent population abundance data and comparable to physiological death rate from the literature. Zooplankton carcasses may be exposed to water column microbes for days before entering the benthos; therefore, non-predation mortality affects not only zooplankton population dynamics but also microbial and benthic food webs. This would be particularly important for carbon and nitrogen cycles in systems where recurring mid-summer decline of zooplankton population due to non-predation mortality is observed.

  2. Antimicrobial and bacteria-releasing multifunctional surfaces: oligo (p-phenylene-ethynylene)/poly (N-isopropylacrylamide) films deposited by RIR-MAPLE.

    PubMed

    Yu, Qian; Ge, Wangyao; Atewologun, Ayomide; Stiff-Roberts, Adrienne D; López, Gabriel P

    2015-02-01

    Antimicrobial oligo (p-phenylene-ethynylene) (OPE) films have previously been demonstrated to show effective ultraviolet A (UVA) light-induced biocidal activity; however, a serious problem arises from the accumulation of dead bacteria and debris on the films that limits their effectiveness and application. In this work, we address this challenge by incorporating thermally-responsive poly (N-isopropylacrylamide) (PNIPAAm), which provides on-demand bacteria-releasing functionality. Multifunctional surfaces comprising blended films of OPE and PNIPAAm were deposited on substrates by resonant infrared, matrix-assisted pulsed laser evaporation (RIR-MAPLE) using a sequential co-deposition mode. In this way, RIR-MAPLE enabled the deposition of multifunctional films with surface properties and film functionality that can be tailored, precisely and systematically, by controlling the chemical composition of the deposited film. The surface properties of these films were characterized by UV-visible (UV-vis) absorbance spectroscopy, X-ray photoelectron spectroscopy (XPS), atomic force microscopy (AFM), and water contact angle measurements. The interactions between bacteria and the deposited films were tested using two model bacteria: Escherichia coli K12 (Gram-negative) and Staphylococcus epidermidis (Gram-positive). The antimicrobial and bacteria-release properties of the blended films were controlled by varying the OPE/PNIPAAm ratio in the RIR-MAPLE emulsion target, providing an easy way to optimize the multifunctional surface. The OPE/PNIPAAm blended films with optimized composition killed a majority of attached E. coli bacteria at 37 °C and under UVA exposure, and the dead bacteria were then removed from the films simply by rinsing with water at 25 °C. Copyright © 2014 Elsevier B.V. All rights reserved.

  3. Therapeutic effects of a reducible poly (oligo-D-arginine) carrier with the heme oxygenase-1 gene in the treatment of hypoxic-ischemic brain injury.

    PubMed

    Hyun, Hyesun; Won, Young-Wook; Kim, Kyung-Min; Lee, Jiyoung; Lee, Minhyung; Kim, Yong-Hee

    2010-12-01

    Non-viral carriers for gene therapy have been developed to minimize carrier cytotoxicity and to enhance transfection efficiency. Previously, we synthesized a 9-arginine-based reducible high molecular weight peptide for gene delivery. For the reducible poly(oligo-D-arginines) (rPOA), 9-arginine oligopeptides are connected by internal disulfide linkages to produce a high molecular weight peptide. In this study, rPOA was evaluated as a carrier of the heme oxygenase-1 (HO-1) gene for the treatment of ischemia/reperfusion (I/R) -induced brain stroke. An in vitro transfection assay showed that rPOA had higher transfection efficiency and lower toxicity than polyethylenimine (PEI). For in vivo evaluation, I/R rat models were produced by middle cerebral artery occlusion (MCAO). rPOA/HO-1 expression plasmid (pHO-1) polyplexes were injected into the brain at 1 h before MCAO, and HO-1 expression levels in the brain were then measured by ELISA. The results indicated that rPOA/pHO-1 polyplexes had higher transfection efficiencies than PEI/pHO-1 polyplexes. The rPOA/pHO-1 polyplexes significantly reduced infarct volumes. In addition, tumor necrosis factor-alpha (TNF-α) was reduced in the rPOA/pHO-1 polyplex injection group, suggesting that HO-1 had an anti-inflammatory effect, while the PEI/pHO-1 polyplex did not show this effect. These results suggest that rPOA is a potential non-viral vector for HO-1 gene therapy to protect brain cells from I/R-related neuronal injury including stroke. Copyright © 2010 Elsevier Ltd. All rights reserved.

  4. A Factorial Analysis of the Combined Effects of Hydrogel Fabrication Parameters on the in vitro Swelling and Degradation of Oligo(poly(ethylene glycol) fumarate) Hydrogels

    PubMed Central

    Lam, Johnny; Kim, Kyobum; Lu, Steven; Tabata, Yasuhiko; Scott, David W.; Mikos, Antonios G.; Kasper, F. Kurtis

    2014-01-01

    In this study, a full factorial approach was employed to investigate the effects of poly(ethylene glycol) (PEG) molecular weight (10,000 vs. 35,000 nominal molecular weight), crosslinker-to-macromer carbon-carbon double bond ratio (40 vs. 60), crosslinker type (PEG-diacrylate (PEGDA) vs. N,N′–methylene bisacrylamide (MB)), crosslinking extent of incorporated gelatin microparticles (low vs. high), and incubation medium composition (with or without collagenase) on the swelling and degradation characteristics of oligo(poly(ethylene glycol) fumarate) (OPF) hydrogel composites as indicated by the swelling ratio and the % mass remaining, respectively. Each factor consisted of two levels, which were selected based on previous in vitro and in vivo studies utilizing these hydrogels for various tissue engineering applications. Fractional factorial analyses of the main effects indicated that the mean swelling ratio and the mean % mass remaining of OPF composite hydrogels were significantly affected by every factor. In particular, increasing the PEG chain MW of OPF macromers significantly increased the mean swelling ratio and decreased the mean % mass remaining by 5.7±0.3 and 17.2±0.6 %, respectively. However, changing the crosslinker from MB to PEGDA reduced the mean swelling ratio and increased the mean % mass remaining of OPF composite hydrogels by 4.9±0.2 and 9.4±0.9 %, respectively. Additionally, it was found that the swelling characteristics of hydrogels fabricated with higher PEG chain MW or with MB were more sensitive to increases in DBR. Collectively, the main and cross effects observed between factors enables informed tuning of the swelling and degradation properties of OPF-based hydrogels for various tissue engineering applications. PMID:24243766

  5. A factorial analysis of the combined effects of hydrogel fabrication parameters on the in vitro swelling and degradation of oligo(poly(ethylene glycol) fumarate) hydrogels.

    PubMed

    Lam, Johnny; Kim, Kyobum; Lu, Steven; Tabata, Yasuhiko; Scott, David W; Mikos, Antonios G; Kasper, F Kurtis

    2014-10-01

    In this study, a full factorial approach was used to investigate the effects of poly(ethylene glycol) (PEG) molecular weight (MW; 10,000 vs. 35,000 nominal MW), crosslinker-to-macromer carbon-carbon double bond ratio (DBR; 40 vs. 60), crosslinker type (PEG-diacrylate (PEGDA) vs. N,N'-methylene bisacrylamide (MB)), crosslinking extent of incorporated gelatin microparticles (low vs. high), and incubation medium composition (with or without collagenase) on the swelling and degradation characteristics of oligo[(poly(ethylene glycol) fumarate)] (OPF) hydrogel composites as indicated by the swelling ratio and the percentage of mass remaining, respectively. Each factor consisted of two levels, which were selected based on previous in vitro and in vivo studies utilizing these hydrogels for various tissue engineering applications. Fractional factorial analyses of the main effects indicated that the mean swelling ratio and the mean percentage of mass remaining of OPF composite hydrogels were significantly affected by every factor. In particular, increasing the PEG chain MW of OPF macromers significantly increased the mean swelling ratio and decreased the mean percentage of mass remaining by 5.7 ± 0.3 and 17.2 ± 0.6%, respectively. However, changing the crosslinker from MB to PEGDA reduced the mean swelling ratio and increased the mean percentage of mass remaining of OPF composite hydrogels by 4.9 ± 0.2 and 9.4 ± 0.9%, respectively. Additionally, it was found that the swelling characteristics of hydrogels fabricated with higher PEG chain MW or with MB were more sensitive to increases in DBR. Collectively, the main and cross effects observed between factors enables informed tuning of the swelling and degradation properties of OPF-based hydrogels for various tissue engineering applications. © 2013 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 102A: 3477-3487, 2014. © 2013 Wiley Periodicals, Inc.

  6. Estimating In Situ Zooplankton Non-Predation Mortality in an Oligo-Mesotrophic Lake from Sediment Trap Data: Caveats and Reality Check

    PubMed Central

    Dubovskaya, Olga P.; Tang, Kam W.; Gladyshev, Michail I.; Kirillin, Georgiy; Buseva, Zhanna; Kasprzak, Peter; Tolomeev, Aleksandr P.; Grossart, Hans-Peter

    2015-01-01

    Background Mortality is a main driver in zooplankton population biology but it is poorly constrained in models that describe zooplankton population dynamics, food web interactions and nutrient dynamics. Mortality due to non-predation factors is often ignored even though anecdotal evidence of non-predation mass mortality of zooplankton has been reported repeatedly. One way to estimate non-predation mortality rate is to measure the removal rate of carcasses, for which sinking is the primary removal mechanism especially in quiescent shallow water bodies. Objectives and Results We used sediment traps to quantify in situ carcass sinking velocity and non-predation mortality rate on eight consecutive days in 2013 for the cladoceran Bosmina longirostris in the oligo-mesotrophic Lake Stechlin; the outcomes were compared against estimates derived from in vitro carcass sinking velocity measurements and an empirical model correcting in vitro sinking velocity for turbulence resuspension and microbial decomposition of carcasses. Our results show that the latter two approaches produced unrealistically high mortality rates of 0.58-1.04 d-1, whereas the sediment trap approach, when used properly, yielded a mortality rate estimate of 0.015 d-1, which is more consistent with concurrent population abundance data and comparable to physiological death rate from the literature. Ecological implications Zooplankton carcasses may be exposed to water column microbes for days before entering the benthos; therefore, non-predation mortality affects not only zooplankton population dynamics but also microbial and benthic food webs. This would be particularly important for carbon and nitrogen cycles in systems where recurring mid-summer decline of zooplankton population due to non-predation mortality is observed. PMID:26146995

  7. Synthesis of carbohydrate-functionalised sequence-defined oligo(amidoamine)s by photochemical thiol-ene coupling in a continuous flow reactor.

    PubMed

    Wojcik, Felix; O'Brien, Alexander G; Götze, Sebastian; Seeberger, Peter H; Hartmann, Laura

    2013-02-25

    Poly/oligo(amidoamine)s (PAAs) have recently been recognised for their potential as well-defined scaffolds for multiple carbohydrate presentation and as multivalent ligands. Herein, we report two complimentary strategies for the preparation of such sequence-defined carbohydrate-functionalised PAAs that use photochemical thiol-ene coupling (TEC) as an alternative to the established azide-alkyne cycloaddition ("click") reaction. In the first approach, PAAs that contained multiple olefins were synthesised on a solid support from a new building block and subsequent conjugation with unprotected thio-carbohydrates. Alternatively, a pre-functionalised building block was prepared by using TEC and assembled on a solid support to provide a carbohydrate-functionalised PAA. Both methods rely on the use of a continuous flow photoreactor for the TEC reactions. This system is highly efficient, owing to its short path length, and requires no additional radical initiator. Performing the reactions at 254 nm in Teflon AF-2400 tubing provides a highly efficient TEC procedure for carbohydrate conjugation, as demonstrated in the reactions of O-allyl glycosides with thiols. This method allowed the complete functionalisation of all of the reactive sites on the PAA backbone in a single step, thereby obtaining a defined homogeneous sequence. Furthermore, reaction at 366 nm in FEP tubing in the flow reactor enabled the large-scale synthesis of an fluorenylmethyloxycarbonyl (Fmoc)-protected glycosylated building block, which was shown to be suitable for solid-phase synthesis and will also allow heterogeneous sequence control of different carbohydrates along the oligomeric backbone. These developments enable the synthesis of sequence-defined carbohydrate-functionalised PAAs with potential biological applications. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Small Angle Neutron Scattering Study of Conformation of Oligo(ethylene glycol) Grafted Polystyrene in Dilute Solutions: Effect of the Backbone Length

    SciTech Connect

    Cheng, Gang; Hong, Kunlun; Hua, Fengjun; Melnichenko, Yuri B; Wignall, George D; Mays, Jimmy

    2008-01-01

    The conformation and clusterization of comb like polymers of polystyrene densely grafted with oligo(ethylene glycol) (OEG) side chains in 1.0 wt% solutions of D2O, toluene-d8 and methanol-d4 was investigated as a function of the degree of polymerization (DP) of the backbone by small angle neutron scattering (SANS). Each side chain had four EG repeat units and the DP of the polystyrene backbone was varied from 8 to 85. The global conformation of the polymers in toluene and methanol was shown to assume ellipsoidal, cylindrical or worm-like chain morphologies with increasing DP of the polystyrene backbone. At the same time, in D2O, the polymer conformation was described by the form factor of rigid cylinders. The second viral coefficient was measured for the polymer with a DP of 85 in all three solvents and the solvent quality of toluene, methanol and D2O was identified as good, marginal and poor for this polymer. Due to a poor solvent quality, the PS backbone (DP = 85) is partially collapsed in D2O whereas it is moderately expanded in toluene and methanol. Polymers with the DP of 8 were found to aggregate into clusters in all three solvents, with the characteristic size between 100 and 200 ?and a fractal dimension of 2. With increase of the DP, the clusters diminished in D2O and completely disappeared in toluene and methanol. This observation suggests that the clusterization of these short side-chain polymers is caused by end group and hydrogen bonding interactions between different chains.

  9. Local evolution of seed flotation in Arabidopsis.

    PubMed

    Saez-Aguayo, Susana; Rondeau-Mouro, Corinne; Macquet, Audrey; Kronholm, Ilkka; Ralet, Marie-Christine; Berger, Adeline; Sallé, Christine; Poulain, Damien; Granier, Fabienne; Botran, Lucy; Loudet, Olivier; de Meaux, Juliette; Marion-Poll, Annie; North, Helen M

    2014-03-01

    Arabidopsis seeds rapidly release hydrophilic polysaccharides from the seed coat on imbibition. These form a heavy mucilage layer around the seed that makes it sink in water. Fourteen natural Arabidopsis variants from central Asia and Scandinavia were identified with seeds that have modified mucilage release and float. Four of these have a novel mucilage phenotype with almost none of the released mucilage adhering to the seed and the absence of cellulose microfibrils. Mucilage release was modified in the variants by ten independent causal mutations in four different loci. Seven distinct mutations affected one locus, coding the MUM2 β-D-galactosidase, and represent a striking example of allelic heterogeneity. The modification of mucilage release has thus evolved a number of times independently in two restricted geographical zones. All the natural mutants identified still accumulated mucilage polysaccharides in seed coat epidermal cells. Using nuclear magnetic resonance (NMR) relaxometry their production and retention was shown to reduce water mobility into internal seed tissues during imbibition, which would help to maintain seed buoyancy. Surprisingly, despite released mucilage being an excellent hydrogel it did not increase the rate of water uptake by internal seed tissues and is more likely to play a role in retaining water around the seed.

  10. Diuretics prime plant immunity in Arabidopsis thaliana.

    PubMed

    Noutoshi, Yoshiteru; Ikeda, Mika; Shirasu, Ken

    2012-01-01

    Plant activators are agrochemicals that activate the plant immune system, thereby enhancing disease resistance. Due to their prophylactic and durable effects on a wide spectrum of diseases, plant activators can provide synergistic crop protection when used in combination with traditional pest controls. Although plant activators have achieved great success in wet-rice farming practices in Asia, their use is still limited. To isolate novel plant activators applicable to other crops, we screened a chemical library using a method that can selectively identify immune-priming compounds. Here, we report the isolation and characterization of three diuretics, bumetanide, bendroflumethiazide and clopamide, as immune-priming compounds. These drugs upregulate the immunity-related cell death of Arabidopsis suspension-cultured cells induced with an avirulent strain of Pseudomonas syringae pv. tomato in a concentration-dependent manner. The application of these compounds to Arabidopsis plants confers disease resistance to not only the avirulent but also a virulent strain of the pathogen. Unlike salicylic acid, an endogenous phytohormone that governs disease resistance in response to biotrophic pathogens, the three diuretic compounds analyzed here do not induce PR1 or inhibit plant growth, showing potential as lead compounds in a practical application.

  11. Arabidopsis MET1 cytosine methyltransferase mutants.

    PubMed Central

    Kankel, Mark W; Ramsey, Douglas E; Stokes, Trevor L; Flowers, Susan K; Haag, Jeremy R; Jeddeloh, Jeffrey A; Riddle, Nicole C; Verbsky, Michelle L; Richards, Eric J

    2003-01-01

    We describe the isolation and characterization of two missense mutations in the cytosine-DNA-methyltransferase gene, MET1, from the flowering plant Arabidopsis thaliana. Both missense mutations, which affect the catalytic domain of the protein, led to a global reduction of cytosine methylation throughout the genome. Surprisingly, the met1-2 allele, with the weaker DNA hypomethylation phenotype, alters a well-conserved residue in methyltransferase signature motif I. The stronger met1-1 allele caused late flowering and a heterochronic delay in the juvenile-to-adult rosette leaf transition. The distribution of late-flowering phenotypes in a mapping population segregating met1-1 indicates that the flowering-time phenotype is caused by the accumulation of inherited defects at loci unlinked to the met1 mutation. The delay in flowering time is due in part to the formation and inheritance of hypomethylated fwa epialleles, but inherited defects at other loci are likely to contribute as well. Centromeric repeat arrays hypomethylated in met1-1 mutants are partially remethylated when introduced into a wild-type background, in contrast to genomic sequences hypomethylated in ddm1 mutants. ddm1 met1 double mutants were constructed to further our understanding of the mechanism of DDM1 action and the interaction between two major genetic loci affecting global cytosine methylation levels in Arabidopsis. PMID:12663548

  12. The mitochondrial lysine acetylome of Arabidopsis.

    PubMed

    König, Ann-Christine; Hartl, Markus; Boersema, Paul J; Mann, Matthias; Finkemeier, Iris

    2014-11-01

    Posttranslational modifications are essential regulators of protein functions as they can modify enzyme activities or protein-molecule interactions by changing the charge state or chemical properties of their target amino acid. The acetyl moiety of the central energy metabolite acetyl-CoA can be transferred to the ε-amino group of lysine, a process known as lysine acetylation which is implicated in the regulation of key metabolic enzymes in various organisms. Since plant mitochondria are of great importance for plant growth and development and as they house key enzymes of oxidative phosphorylation and photorespiration, it is essential to investigate the occurrence of lysine acetylation in this organelle. Here we characterised the plant mitochondrial acetylome of Arabidopsis mitochondria by LC-MS/MS analysis. In total 120 lysine-acetylated mitochondrial proteins containing 243 acetylated sites were identified. These proteins were mapped into functional categories showing that many proteins with essential functions from the tricaboxylic cycle and the respiratory chain are lysine-acetylated, as well as proteins involved in photorespiration, amino acid and protein metabolism, and redox regulation. Immuno-detection of mitochondrial proteins revealed that many lysine-acetylated proteins reside in native protein complexes. Furthermore, in vitro experiments demonstrated that lysine acetylation can occur non-enzymatically in Arabidopsis mitochondria at physiological matrix pH. Copyright © 2014 Elsevier B.V. and Mitochondria Research Society. All rights reserved.

  13. Local Evolution of Seed Flotation in Arabidopsis

    PubMed Central

    Saez-Aguayo, Susana; Rondeau-Mouro, Corinne; Macquet, Audrey; Kronholm, Ilkka; Ralet, Marie-Christine; Berger, Adeline; Sallé, Christine; Poulain, Damien; Granier, Fabienne; Botran, Lucy; Loudet, Olivier; de Meaux, Juliette; Marion-Poll, Annie; North, Helen M.

    2014-01-01

    Arabidopsis seeds rapidly release hydrophilic polysaccharides from the seed coat on imbibition. These form a heavy mucilage layer around the seed that makes it sink in water. Fourteen natural Arabidopsis variants from central Asia and Scandinavia were identified with seeds that have modified mucilage release and float. Four of these have a novel mucilage phenotype with almost none of the released mucilage adhering to the seed and the absence of cellulose microfibrils. Mucilage release was modified in the variants by ten independent causal mutations in four different loci. Seven distinct mutations affected one locus, coding the MUM2 β-D-galactosidase, and represent a striking example of allelic heterogeneity. The modification of mucilage release has thus evolved a number of times independently in two restricted geographical zones. All the natural mutants identified still accumulated mucilage polysaccharides in seed coat epidermal cells. Using nuclear magnetic resonance (NMR) relaxometry their production and retention was shown to reduce water mobility into internal seed tissues during imbibition, which would help to maintain seed buoyancy. Surprisingly, despite released mucilage being an excellent hydrogel it did not increase the rate of water uptake by internal seed tissues and is more likely to play a role in retaining water around the seed. PMID:24625826

  14. Diuretics Prime Plant Immunity in Arabidopsis thaliana

    PubMed Central

    Noutoshi, Yoshiteru; Ikeda, Mika; Shirasu, Ken

    2012-01-01

    Plant activators are agrochemicals that activate the plant immune system, thereby enhancing disease resistance. Due to their prophylactic and durable effects on a wide spectrum of diseases, plant activators can provide synergistic crop protection when used in combination with traditional pest controls. Although plant activators have achieved great success in wet-rice farming practices in Asia, their use is still limited. To isolate novel plant activators applicable to other crops, we screened a chemical library using a method that can selectively identify immune-priming compounds. Here, we report the isolation and characterization of three diuretics, bumetanide, bendroflumethiazide and clopamide, as immune-priming compounds. These drugs upregulate the immunity-related cell death of Arabidopsis suspension-cultured cells induced with an avirulent strain of Pseudomonas syringae pv. tomato in a concentration-dependent manner. The application of these compounds to Arabidopsis plants confers disease resistance to not only the avirulent but also a virulent strain of the pathogen. Unlike salicylic acid, an endogenous phytohormone that governs disease resistance in response to biotrophic pathogens, the three diuretic compounds analyzed here do not induce PR1 or inhibit plant growth, showing potential as lead compounds in a practical application. PMID:23144763

  15. Stress promotes Arabidopsis - Piriformospora indica interaction

    PubMed Central

    Vahabi, Khabat; Dorcheh, Sedigheh Karimi; Monajembashi, Shamci; Westermann, Martin; Reichelt, Michael; Falkenberg, Daniela; Hemmerich, Peter; Sherameti, Irena; Oelmüller, Ralf

    2016-01-01

    ABSTRACT The endophytic fungus Piriformospora indica colonizes Arabidopsis thaliana roots and promotes plant performance, growth and resistance/tolerance against abiotic and biotic stress. Here we demonstrate that the benefits for the plant increase when the two partners are co-cultivated under stress (limited access to nutrient, exposure to heavy metals and salt, light and osmotic stress, pathogen infection). Moreover, physical contact between P. indica and Arabidopsis roots is necessary for optimal growth promotion, and chemical communication cannot replace the physical contact. Lower nutrient availability down-regulates and higher nutrient availability up-regulates the plant defense system including the expression of pathogenesis-related genes in roots. High light, osmotic and salt stresses support the beneficial interaction between the plant and the fungus. P. indica reduces stomata closure and H2O2 production after Alternaria brassicae infection in leaves and suppresses the defense-related accumulation of the phytohormone jasmonic acid. Thus, shifting the growth conditions toward a stress promotes the mutualistic interaction, while optimal supply with nutrients or low stress diminishes the benefits for the plant in the symbiosis. PMID:27167761

  16. Stress promotes Arabidopsis - Piriformospora indica interaction.

    PubMed

    Vahabi, Khabat; Dorcheh, Sedigheh Karimi; Monajembashi, Shamci; Westermann, Martin; Reichelt, Michael; Falkenberg, Daniela; Hemmerich, Peter; Sherameti, Irena; Oelmüller, Ralf

    2016-05-03

    The endophytic fungus Piriformospora indica colonizes Arabidopsis thaliana roots and promotes plant performance, growth and resistance/tolerance against abiotic and biotic stress. Here we demonstrate that the benefits for the plant increase when the two partners are co-cultivated under stress (limited access to nutrient, exposure to heavy metals and salt, light and osmotic stress, pathogen infection). Moreover, physical contact between P. indica and Arabidopsis roots is necessary for optimal growth promotion, and chemical communication cannot replace the physical contact. Lower nutrient availability down-regulates and higher nutrient availability up-regulates the plant defense system including the expression of pathogenesis-related genes in roots. High light, osmotic and salt stresses support the beneficial interaction between the plant and the fungus. P. indica reduces stomata closure and H2O2 production after Alternaria brassicae infection in leaves and suppresses the defense-related accumulation of the phytohormone jasmonic acid. Thus, shifting the growth conditions toward a stress promotes the mutualistic interaction, while optimal supply with nutrients or low stress diminishes the benefits for the plant in the symbiosis.

  17. Brassinosteroid functions in Arabidopsis seed development

    PubMed Central

    Jiang, Wen-Bo; Lin, Wen-Hui

    2013-01-01

    Seed development of flowering plant is a complicated process controlled by a signal network. Double fertilization generates 2 zygotic products (embryo and endosperm). Embryo gives rise to a daughter plant while endosperm provides nutrients for embryo during embryogenesis and germination. Seed coat differentiates from maternally derived integument and encloses embryo and endosperm. Seed size/mass and number comprise final seed yield, and seed shape also contributes to seed development and weight. Seed size is coordinated by communication among endosperm, embryo, and integument. Seed number determination is more complex to investigate and shows differencies between monocot and eudicot. Total seed number depends on sillique number and seed number per sillique in Arabidopsis. Seed comes from fertilized ovule, hence the ovule number per flower determines the maximal seed number per sillique. Early studies reported that engineering BR levels increased the yield of ovule and seed; however the molecular mechanism of BR regulation in seed development still remained unclear. Our recent studies demonstrated that BR regulated seed size, shape, and number by transcriptionally modulating specific seed developmental pathways. This review summarizes roles of BR in Arabidopsis seed development and gives clues for future application of BR in agricultural production. PMID:24270689

  18. Defining the core Arabidopsis thaliana root microbiome

    PubMed Central

    Gehring, Jase; Malfatti, Stephanie; Tremblay, Julien; Engelbrektson, Anna; Kunin, Victor; del Rio, Tijana Glavina; Edgar, Robert C.; Eickhorst, Thilo; Ley, Ruth E.; Hugenholtz, Philip; Tringe, Susannah Green; Dangl, Jeffery L.

    2014-01-01

    Land plants associate with a root microbiota distinct from the complex microbial community present in surrounding soil. The microbiota colonizing therhizosphere(immediately surroundingthe root) and the endophytic compartment (within the root) contribute to plant growth, productivity, carbon sequestration and phytoremediation1-3. Colonization of the root occurs despite a sophisticated plant immune system4,5, suggesting finely tuned discrimination of mutualists and commensals from pathogens. Genetic principles governing the derivation of host-specific endophyte communities from soil communities are poorly understood. Here we report the pyrosequencing of the bacterial 16S ribosomal RNA gene of more than 600 Arabidopsis thaliana plants to test the hypotheses that the root rhizosphere and endophytic compartment microbiota of plants grown under controlled conditions in natural soils are sufficiently dependent on the host to remain consistent across different soil types and developmental stages, and sufficiently dependent on host genotype to vary between inbred Arabidopsis accessions. We describe different bacterial communities in two geochemically distinct bulk soils and in rhizosphere and endophytic compartments prepared from roots grown in these soils. The communities in each compartment are strongly influenced by soil type. Endophytic compartments from both soils feature overlapping, low-complexity communities that are markedly enriched in Actinobacteria and specific families from other phyla, notably Proteobacteria. Some bacteria vary quantitatively between plants of different developmental stage and genotype. Our rigorous definition of an endophytic compartment microbiome should facilitate controlled dissection of plantmicrobe interactions derived from complex soil communities. PMID:22859206

  19. Polyploidization increases meiotic recombination frequency in Arabidopsis

    PubMed Central

    2011-01-01

    Background Polyploidization is the multiplication of the whole chromosome complement and has occurred frequently in vascular plants. Maintenance of stable polyploid state over generations requires special mechanisms to control pairing and distribution of more than two homologous chromosomes during meiosis. Since a minimal number of crossover events is essential for correct chromosome segregation, we investigated whether polyploidy has an influence on the frequency of meiotic recombination. Results Using two genetically linked transgenes providing seed-specific fluorescence, we compared a high number of progeny from diploid and tetraploid Arabidopsis plants. We show that rates of meiotic recombination in reciprocal crosses of genetically identical diploid and autotetraploid Arabidopsis plants were significantly higher in tetraploids compared to diploids. Although male and female gametogenesis differ substantially in meiotic recombination frequency, both rates were equally increased in tetraploids. To investigate whether multivalent formation in autotetraploids was responsible for the increased recombination rates, we also performed corresponding experiments with allotetraploid plants showing strict bivalent pairing. We found similarly increased rates in auto- and allotetraploids, suggesting that the ploidy effect is independent of chromosome pairing configurations. Conclusions The evolutionary success of polyploid plants in nature and under domestication has been attributed to buffering of mutations and sub- and neo-functionalization of duplicated genes. Should the data described here be representative for polyploid plants, enhanced meiotic recombination, and the resulting rapid creation of genetic diversity, could have also contributed to their prevalence. PMID:21510849

  20. Epigenetic natural variation in Arabidopsis thaliana.

    PubMed

    Vaughn, Matthew W; Tanurdzić, Milos; Lippman, Zachary; Jiang, Hongmei; Carrasquillo, Robert; Rabinowicz, Pablo D; Dedhia, Neilay; McCombie, W Richard; Agier, Nicolas; Bulski, Agnès; Colot, Vincent; Doerge, R W; Martienssen, Robert A

    2007-07-01

    Cytosine methylation of repetitive sequences is widespread in plant genomes, occurring in both symmetric (CpG and CpNpG) as well as asymmetric sequence contexts. We used the methylation-dependent restriction enzyme McrBC to profile methylated DNA using tiling microarrays of Arabidopsis Chromosome 4 in two distinct ecotypes, Columbia and Landsberg erecta. We also used comparative genome hybridization to profile copy number polymorphisms. Repeated sequences and transposable elements (TEs), especially long terminal repeat retrotransposons, are densely methylated, but one third of genes also have low but detectable methylation in their transcribed regions. While TEs are almost always methylated, genic methylation is highly polymorphic, with half of all methylated genes being methylated in only one of the two ecotypes. A survey of loci in 96 Arabidopsis accessions revealed a similar degree of methylation polymorphism. Within-gene methylation is heritable, but is lost at a high frequency in segregating F(2) families. Promoter methylation is rare, and gene expression is not generally affected by differences in DNA methylation. Small interfering RNA are preferentially associated with methylated TEs, but not with methylated genes, indicating that most genic methylation is not guided by small interfering RNA. This may account for the instability of gene methylation, if occasional failure of maintenance methylation cannot be restored by other means.

  1. Epigenetic Natural Variation in Arabidopsis thaliana

    PubMed Central

    Jiang, Hongmei; Carrasquillo, Robert; Rabinowicz, Pablo D; Dedhia, Neilay; McCombie, W. Richard; Agier, Nicolas; Bulski, Agnès; Colot, Vincent; Doerge, R.W; Martienssen, Robert A

    2007-01-01

    Cytosine methylation of repetitive sequences is widespread in plant genomes, occurring in both symmetric (CpG and CpNpG) as well as asymmetric sequence contexts. We used the methylation-dependent restriction enzyme McrBC to profile methylated DNA using tiling microarrays of Arabidopsis Chromosome 4 in two distinct ecotypes, Columbia and Landsberg erecta. We also used comparative genome hybridization to profile copy number polymorphisms. Repeated sequences and transposable elements (TEs), especially long terminal repeat retrotransposons, are densely methylated, but one third of genes also have low but detectable methylation in their transcribed regions. While TEs are almost always methylated, genic methylation is highly polymorphic, with half of all methylated genes being methylated in only one of the two ecotypes. A survey of loci in 96 Arabidopsis accessions revealed a similar degree of methylation polymorphism. Within-gene methylation is heritable, but is lost at a high frequency in segregating F 2 families. Promoter methylation is rare, and gene expression is not generally affected by differences in DNA methylation. Small interfering RNA are preferentially associated with methylated TEs, but not with methylated genes, indicating that most genic methylation is not guided by small interfering RNA. This may account for the instability of gene methylation, if occasional failure of maintenance methylation cannot be restored by other means. PMID:17579518

  2. Brassinosteroids promote Arabidopsis pollen germination and growth.

    PubMed

    Vogler, Frank; Schmalzl, Christina; Englhart, Maria; Bircheneder, Martin; Sprunck, Stefanie

    2014-09-01

    Pollen tubes are among the fastest tip-growing plant cells and represent an excellent experimental system for studying the dynamics and spatiotemporal control of polarized cell growth. However, investigating pollen tube tip growth in the model plant Arabidopsis remains difficult because in vitro pollen germination and pollen tube growth rates are highly variable and largely different from those observed in pistils, most likely due to growth-promoting properties of the female reproductive tract. We found that in vitro grown Arabidopsis pollen respond to brassinosteroid (BR) in a dose-dependent manner. Pollen germination and pollen tube growth increased nine- and fivefold, respectively, when media were supplemented with 10 µM epibrassinolide (epiBL), resulting in growth kinetics more similar to growth in vivo. Expression analyses show that the promoter of one of the key enzymes in BR biosynthesis, CYP90A1/CPD, is highly active in the cells of the reproductive tract that form the pathway for pollen tubes from the stigma to the ovules. Pollen tubes grew significantly shorter through the reproductive tract of a cyp90a1 mutant compared to the wild type, or to a BR perception mutant. Our results show that epiBL promotes pollen germination and tube growth in vitro and suggest that the cells of the reproductive tract provide BR compounds to stimulate pollen tube growth.

  3. Epigenetic regulation of gene responsiveness in Arabidopsis

    PubMed Central

    To, Taiko K.; Kim, Jong Myong

    2014-01-01

    The regulation of chromatin structure is inevitable for proper transcriptional response in eukaryotes. Recent reports in Arabidopsis have suggested that gene responsiveness is modulated by particular chromatin status. One such feature is H2A.Z, a histone variant conserved among eukaryotes. In Arabidopsis, H2A.Z is enriched within gene bodies of transcriptionally variable genes, which is in contrast to genic DNA methylation found within constitutive genes. In the absence of H2A.Z, the genes normally harboring H2A.Z within gene bodies are transcriptionally misregulated, while DNA methylation is unaffected. Therefore, H2A.Z may promote variability of gene expression without affecting genic DNA methylation. Another epigenetic information that could be important for gene responsiveness is trimethylation of histone H3 lysine 4 (H3K4me3). The level of H3K4me3 increases when stress responsive genes are transcriptionally activated, and it decreases after recovery from the stress. Even after the recovery, however, H3K4me3 is kept at some atypical levels, suggesting possible role of H3K4me3 for a stress memory. In this review, we summarize and discuss the growing evidences connecting chromatin features and gene responsiveness. PMID:24432027

  4. FPF1 promotes flowering in Arabidopsis.

    PubMed Central

    Kania, T; Russenberger, D; Peng, S; Apel, K; Melzer, S

    1997-01-01

    We have characterized the gene flowering promoting factor1 (FPF1), which is expressed in apical meristems immediately after the photoperiodic induction of flowering in the long-day plants mustard and Arabidopsis. In early transition stages, expression is only detectable in the peripheral zone of apical meristems; however, later on, it can also be found in floral meristems and in axillary meristems that form secondary inflorescences. The FPF1 gene encodes a 12.6-kD protein that has no homology to any previously identified protein of known function. Constitutive expression of the gene in Arabidopsis under control of the cauliflower mosaic virus 35S promoter resulted in a dominant heritable trait of early flowering under both short- and long-day conditions. Treatments with gibberellin (GA) and paclobutrazol, a GA biosynthesis inhibitor, as well as crosses with GA-deficient mutants indicate that FPF1 is involved in a GA-dependent signaling pathway and modulates a GA response in apical meristems during the transition to flowering. PMID:9286110

  5. MTHFD1 controls DNA methylation in Arabidopsis

    PubMed Central

    Groth, Martin; Moissiard, Guillaume; Wirtz, Markus; Wang, Haifeng; Garcia-Salinas, Carolina; Ramos-Parra, Perla A.; Bischof, Sylvain; Feng, Suhua; Cokus, Shawn J.; John, Amala; Smith, Danielle C.; Zhai, Jixian; Hale, Christopher J.; Long, Jeff A.; Hell, Ruediger; Díaz de la Garza, Rocío I.; Jacobsen, Steven E.

    2016-01-01

    DNA methylation is an epigenetic mechanism that has important functions in transcriptional silencing and is associated with repressive histone methylation (H3K9me). To further investigate silencing mechanisms, we screened a mutagenized Arabidopsis thaliana population for expression of SDCpro-GFP, redundantly controlled by DNA methyltransferases DRM2 and CMT3. Here, we identify the hypomorphic mutant mthfd1-1, carrying a mutation (R175Q) in the cytoplasmic bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase (MTHFD1). Decreased levels of oxidized tetrahydrofolates in mthfd1-1 and lethality of loss-of-function demonstrate the essential enzymatic role of MTHFD1 in Arabidopsis. Accumulation of homocysteine and S-adenosylhomocysteine, genome-wide DNA hypomethylation, loss of H3K9me and transposon derepression indicate that S-adenosylmethionine-dependent transmethylation is inhibited in mthfd1-1. Comparative analysis of DNA methylation revealed that the CMT3 and CMT2 pathways involving positive feedback with H3K9me are mostly affected. Our work highlights the sensitivity of epigenetic networks to one-carbon metabolism due to their common S-adenosylmethionine-dependent transmethylation and has implications for human MTHFD1-associated diseases. PMID:27291711

  6. Metallochaperone-like genes in Arabidopsis thaliana.

    PubMed

    Tehseen, Muhammad; Cairns, Narelle; Sherson, Sarah; Cobbett, Christopher S

    2010-08-01

    A complete inventory of metallochaperone-like proteins containing a predicted HMA domain in Arabidopsis revealed a large family of 67 proteins. 45 proteins, the HIPPs, have a predicted isoprenylation site while 22 proteins, the HPPs, do not. Sequence comparisons divided the proteins into seven major clusters (I-VII). Cluster IV is notable for the presence of a conserved Asp residue before the CysXXCys, metal binding motif, analogous to the Zn binding motif in E. coli ZntA. HIPP20, HIPP21, HIPP22, HIPP26 and HIPP27 in Cluster IV were studied in more detail. All but HIPP21 could rescue the Cd-sensitive, ycf1 yeast mutant but failed to rescue the growth of zrt1zrt2, zrc1cot1 and atx1 mutants. In Arabidopsis, single and double mutants did not show a phenotype but the hipp20/21/22 triple mutant was more sensitive to Cd and accumulated less Cd than the wild-type suggesting the HIPPs can have a role in Cd-detoxification, possibly by binding Cd. Promoter-GUS reporter expression studies indicated variable expression of these HIPPs. For example, in roots, HIPP22 and HIPP26 are only expressed in lateral root tips while HIPP20 and HIPP25 show strong expression in the root vasculature.

  7. Photoperiodic flowering regulation in Arabidopsis thaliana

    PubMed Central

    Golembeski, Greg S.; Kinmonth-Schultz, Hannah A.; Song, Young Hun; Imaizumi, Takato

    2015-01-01

    Photoperiod, or the duration of light in a given day, is a critical cue that flowering plants utilize to effectively assess seasonal information and coordinate their reproductive development in synchrony with the external environment. The use of the model plant, Arabidopsis thaliana, has greatly improved our understanding of the molecular mechanisms that determine how plants process and utilize photoperiodic information to coordinate a flowering response. This mechanism is typified by the transcriptional activation of FLOWERING LOCUS T (FT) gene by the transcription factor CONSTANS (CO) under inductive long-day conditions in Arabidopsis. FT protein then moves from the leaves to the shoot apex, where floral meristem development can be initiated. As a point of integration from a variety of environmental factors in the context of a larger system of regulatory pathways that affect flowering, the importance of photoreceptors and the circadian clock in CO regulation throughout the day has been a key feature of the photoperiodic flowering pathway. In addition to these established mechanisms, the recent discovery of a photosynthate derivative trehalose-6-phosphate as an activator of FT in leaves has interesting implications for the involvement of photosynthesis in the photoperiodic flowering response that were suggested from previous physiological experiments in flowering induction. PMID:25684830

  8. Protein expression in Arabidopsis thaliana after chronic clinorotation

    NASA Technical Reports Server (NTRS)

    Piastuch, William C.; Brown, Christopher S.

    1994-01-01

    Soluble protein expression in Arabidopsis thaliana L. (Heynh.) leaf and stem tissue was examined after chronic clinorotation. Seeds of Arabidopsis were germinated and plants grown to maturity on horizontal or vertical slow-rotating clinostats (1 rpm) or in stationary vertical control units. Total soluble proteins and in vivo-labeled soluble proteins isolated from these plants were analyzed by two-dimensional sodium doedocyl sulfate polyacrylamide gel electrophoresis (SDS PAGE) and subsequent fluorography. Visual and computer analysis of the resulting protein patterns showed no significant differences in either total protein expression or in active protein synthesis between horizontal clinorotation and vertical controls in the Arabidopsis leaf and stem tissue. These results show chronic clinorotation does not cause gross changes in protein expression in Arabidopsis.

  9. Protein expression in Arabidopsis thaliana after chronic clinorotation

    NASA Technical Reports Server (NTRS)

    Piastuch, W. C.; Brown, C. S.

    1995-01-01

    Soluble protein expression in Arabidopsis thaliana L. (Heynh.) leaf and stem tissue was examined after chronic clinorotation. Seeds of Arabidopsis were germinated and plants grown to maturity on horizontal or vertical slow-rotating clinostats (1 rpm) or in stationary vertical control units. Total soluble proteins and in vivo-labeled soluble proteins isolated from these plants were analyzed by two-dimensional SDS PAGE and subsequent fluorography. Visual and computer analysis of the resulting protein patterns showed no significant differences in either total protein expression or in active protein synthesis between horizontal clinorotation and vertical controls in the Arabidopsis leaf and stem tissue. These results show chronic clinorotation does not cause gross changes in protein expression in Arabidopsis.

  10. The development of Arabidopsis as a model plant.

    PubMed

    Koornneef, Maarten; Meinke, David

    2010-03-01

    Twenty-five years ago, Arabidopsis thaliana emerged as the model organism of choice for research in plant biology. A consensus was reached about the need to focus on a single organism to integrate the classical disciplines of plant science with the expanding fields of genetics and molecular biology. Ten years after publication of its genome sequence, Arabidopsis remains the standard reference plant for all of biology. We reflect here on the major advances and shared resources that led to the extraordinary growth of the Arabidopsis research community. We also underscore the importance of continuing to expand and refine our detailed knowledge of Arabidopsis while seeking to appreciate the remarkable diversity that characterizes the plant kingdom.

  11. VIZARD: analysis of Affymetrix Arabidopsis GeneChip data

    NASA Technical Reports Server (NTRS)

    Moseyko, Nick; Feldman, Lewis J.

    2002-01-01

    SUMMARY: The Affymetrix GeneChip Arabidopsis genome array has proved to be a very powerful tool for the analysis of gene expression in Arabidopsis thaliana, the most commonly studied plant model organism. VIZARD is a Java program created at the University of California, Berkeley, to facilitate analysis of Arabidopsis GeneChip data. It includes several integrated tools for filtering, sorting, clustering and visualization of gene expression data as well as tools for the discovery of regulatory motifs in upstream sequences. VIZARD also includes annotation and upstream sequence databases for the majority of genes represented on the Affymetrix Arabidopsis GeneChip array. AVAILABILITY: VIZARD is available free of charge for educational, research, and not-for-profit purposes, and can be downloaded at http://www.anm.f2s.com/research/vizard/ CONTACT: moseyko@uclink4.berkeley.edu.

  12. Protein expression in Arabidopsis thaliana after chronic clinorotation

    NASA Technical Reports Server (NTRS)

    Piastuch, W. C.; Brown, C. S.

    1995-01-01

    Soluble protein expression in Arabidopsis thaliana L. (Heynh.) leaf and stem tissue was examined after chronic clinorotation. Seeds of Arabidopsis were germinated and plants grown to maturity on horizontal or vertical slow-rotating clinostats (1 rpm) or in stationary vertical control units. Total soluble proteins and in vivo-labeled soluble proteins isolated from these plants were analyzed by two-dimensional SDS PAGE and subsequent fluorography. Visual and computer analysis of the resulting protein patterns showed no significant differences in either total protein expression or in active protein synthesis between horizontal clinorotation and vertical controls in the Arabidopsis leaf and stem tissue. These results show chronic clinorotation does not cause gross changes in protein expression in Arabidopsis.

  13. VIZARD: analysis of Affymetrix Arabidopsis GeneChip data

    NASA Technical Reports Server (NTRS)

    Moseyko, Nick; Feldman, Lewis J.

    2002-01-01

    SUMMARY: The Affymetrix GeneChip Arabidopsis genome array has proved to be a very powerful tool for the analysis of gene expression in Arabidopsis thaliana, the most commonly studied plant model organism. VIZARD is a Java program created at the University of California, Berkeley, to facilitate analysis of Arabidopsis GeneChip data. It includes several integrated tools for filtering, sorting, clustering and visualization of gene expression data as well as tools for the discovery of regulatory motifs in upstream sequences. VIZARD also includes annotation and upstream sequence databases for the majority of genes represented on the Affymetrix Arabidopsis GeneChip array. AVAILABILITY: VIZARD is available free of charge for educational, research, and not-for-profit purposes, and can be downloaded at http://www.anm.f2s.com/research/vizard/ CONTACT: moseyko@uclink4.berkeley.edu.

  14. Nespoli works with Arabidopsis Seeds in the Columbus Module

    NASA Image and Video Library

    2011-02-17

    ISS026-E-027966 (17 Feb. 2011) --- European Space Agency astronaut Paolo Nespoli, Expedition 26 flight engineer, works with hardware containing Arabidopsis seeds in the Columbus laboratory of the International Space Station.

  15. 3D Gel Map of Arabidopsis Complex I

    PubMed Central

    Peters, Katrin; Belt, Katharina; Braun, Hans-Peter

    2013-01-01

    Complex I has a unique structure in plants and includes extra subunits. Here, we present a novel study to define its protein constituents. Mitochondria were isolated from Arabidopsis thaliana cell cultures, leaves, and roots. Subunits of complex I were resolved by 3D blue-native (BN)/SDS/SDS-PAGE and identified by mass spectrometry. Overall, 55 distinct proteins were found, seven of which occur in pairs of isoforms. We present evidence that Arabidopsis complex I consists of 49 distinct types of subunits, 40 of which represent homologs of bovine complex I. The nine other subunits represent special proteins absent in the animal linage of eukaryotes, most prominently a group of subunits related to bacterial gamma-type carbonic anhydrases. A GelMap http://www.gelmap.de/arabidopsis-3d-complex-i/ is presented for promoting future complex I research in Arabidopsis thaliana. PMID:23761796

  16. Bacillus thermoamyloliquefaciens KP1071 alpha-glucosidase II is a thermostable M(r) 540,000 homohexameric alpha-glucosidase with both exo-alpha-1,4-glucosidase and oligo-1,6-glucosidase activities.

    PubMed

    Suzuki, Y; Nobiki, M; Matsuda, M; Sawai, T

    1997-04-01

    alpha-Glucosidase II of the facultative thermophile Bacillus thermoamyloliquefaciens KP1071 (FERM-P8477; growth over 30-66 degrees C) was purified to a homogeneous state. Its M(r) was estimated as 90000 by SDS/PAGE. However, the enzyme behaved as an active Mr 540000 protein on gel filtration with each of two gels of different matrices as well as on gel electrophoresis under native conditions. The enzyme was not glycosylated. Its isoelectric point was estimated as 5.7. The N-terminal sequence of 20 residues was determined asAla1-Ile-Gln-Pro-Glu-Gln-Asp-Asp-Lys-Thr-Gln-Glu-Asp-Gly- Tyr-Ile-Asp-Ile-Gly-Asn20. The sequence did not resemble those of procaryotic and eucaryotic proteins hitherto reported including the monomeric exo-alpha-1,4-glucosidase and the monomeric oligo-1,6-glucosidase from the same microorganism. The alpha-glucosidase II had no antigenic group shared with the latter two enzymes. Analysis of substrate specificity showed that the alpha-glucosidase II has dual activity towards oligo-1,6-glucosidases and exo-alpha-1,4-glucosidases, but its preference is for non-reducing terminal alpha-1,4 glucosidic bonds in substrates. Kinetic studies proved that both activities are attributed to the same catalytic site. The enzyme was most active at 81 degrees C and pH 7.0. Its half-life at pH 6.8 was 10 min at 81 degrees C, and 5 h at 55 degrees C in 6.4 M urea, 26% ethanol or 2.5% SDS. We suggest that the alpha-glucosidase II is a thermostable, homohexameric enzyme of origin distinct from the exo-alpha-1,4-glucosidase and the oligo-1,6-glucosidase present in the same strain.

  17. Hormonal stimulation of starfish oocytes induces partial degradation of the 3' termini of cyclin B mRNAs with oligo(U) tails, followed by poly(A) elongation.

    PubMed

    Ochi, Hiroe; Chiba, Kazuyoshi

    2016-06-01

    In yeast, plant, and mammalian somatic cells, short poly(A) tails on mRNAs are subject to uridylation, which mediates mRNA decay. Although mRNA uridylation has never been reported in animal oocytes, maternal mRNAs with short poly(A) tails are believed to be translationally repressed. In this study, we found that 96% of cyclin B mRNAs with short poly(A) tails were uridylated in starfish oocytes. Hormonal stimulation induced poly(A) elongation of cyclin B mRNA, and 62% of long adenine repeats did not contain uridine residues. To determine whether uridylated short poly(A) tails destabilize cyclin B mRNA, we developed a method for producing RNAs with the strict 3' terminal sequences of cyclin B, with or without oligo(U) tails. When we injected these synthetic RNAs into starfish oocytes prior to hormonal stimulation, we found that uridylated RNAs were as stable as nonuridylated RNAs. Following hormonal stimulation, the 3' termini of short poly(A) tails of synthesized RNAs containing oligo(U) tails were trimmed, and their poly(A) tails were subsequently elongated. These results indicate that uridylation of short poly(A) tails in cyclin B mRNA of starfish oocytes does not mediate mRNA decay; instead, hormonal stimulation induces partial degradation of uridylated short poly(A) tails in the 3'-5' direction, followed by poly(A) elongation. Oligo(U) tails may be involved in translational inactivation of mRNAs. © 2016 Ochi and Chiba; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  18. Hormonal stimulation of starfish oocytes induces partial degradation of the 3′ termini of cyclin B mRNAs with oligo(U) tails, followed by poly(A) elongation

    PubMed Central

    Ochi, Hiroe; Chiba, Kazuyoshi

    2016-01-01

    In yeast, plant, and mammalian somatic cells, short poly(A) tails on mRNAs are subject to uridylation, which mediates mRNA decay. Although mRNA uridylation has never been reported in animal oocytes, maternal mRNAs with short poly(A) tails are believed to be translationally repressed. In this study, we found that 96% of cyclin B mRNAs with short poly(A) tails were uridylated in starfish oocytes. Hormonal stimulation induced poly(A) elongation of cyclin B mRNA, and 62% of long adenine repeats did not contain uridine residues. To determine whether uridylated short poly(A) tails destabilize cyclin B mRNA, we developed a method for producing RNAs with the strict 3′ terminal sequences of cyclin B, with or without oligo(U) tails. When we injected these synthetic RNAs into starfish oocytes prior to hormonal stimulation, we found that uridylated RNAs were as stable as nonuridylated RNAs. Following hormonal stimulation, the 3′ termini of short poly(A) tails of synthesized RNAs containing oligo(U) tails were trimmed, and their poly(A) tails were subsequently elongated. These results indicate that uridylation of short poly(A) tails in cyclin B mRNA of starfish oocytes does not mediate mRNA decay; instead, hormonal stimulation induces partial degradation of uridylated short poly(A) tails in the 3′–5′ direction, followed by poly(A) elongation. Oligo(U) tails may be involved in translational inactivation of mRNAs. PMID:27048146

  19. Light responses in Photoperiodism in Arabidopsis thaliana

    SciTech Connect

    Anthony R. Cashmore

    2006-08-01

    ADO1: An Arabidopsis blue light photoreceptor We have reported the characterization of an Arabidopsis gene encoding the ADAGIO 1 (ADO1) protein (Jarillo et al., 2001a). ADO1 contains a LOV domain, similar to WHITE COLLAR 1 (WC1), a photoreceptor for entrainment of Neurospora circadian rhythms (Froehlich et al., 2002), as well as PHOT1 and PHOT2, the blue light photoreceptors for phototropism (Briggs et al., 2001; Christie et al., 1998; Jarillo et al., 2001b; Kinoshita et al., 2001). Loss of function ado1 mutants show an unusually long periodicity for their free running circadian rhythm (Jarillo et al., 2001a). This observation holds for plants grown under white light as well as blue light and surprisingly, plants grown under red light also show altered circadian properties. The similarity of the LOV domain of ADO1 to those of PHOT1, PHOT2 and WC1 (known flavoprotein photoreceptors) as well as the genetic and molecular properties of ADO1, indicate that ADO1 is likely a new class of blue light photoreceptor. Indeed, the LOV domain of the related FKF1/ADO3 has been shown to bind FMN, and exhibit the in vitro photochemistry characteristic of PHOT1 (Imaizumi et al., 2003). Furthermore, ZTL/ADO1 has been shown to participate in the circadian and proteasome mediated degradation of the Arabidopsis clock protein, TOC1 (Mas et al., 2003). We also showed that the ado1 mutation selectively confers hypersensitivity to red light — when grown under red light (but not blue light) the ado1 mutant possesses an unusually short hypocotyl. This red light hypersensivity is even more severe in a triple ado1 ado2 ado3 mutant — ADO2 and ADO3 being the two other members of this ADAGIO gene family. This finding of a mutant phenotype under red light is somewhat unexpected for a protein thought to function as a photoreceptor for blue light. We have pursued our studies of ADO1 by preparing a mutant gene for which we have altered the codon for the cysteine residue conserved in all LOV

  20. Double helix formation of poly(m-phenylene)s bearing achiral oligo(ethylene oxide) pendants and transformation into an excess of one-handed single helix through cholate binding in water.

    PubMed

    Ben, Teng; Furusho, Yoshio; Goto, Hidetoshi; Miwa, Kazuhiro; Yashima, Eiji

    2009-06-21

    A water-soluble poly(m-phenylene) bearing an achiral oligo(ethylene oxide) chain at the 5-position was synthesized by the Ni(0)-mediated homo-coupling polycondensation of a 3,5-dibromophenol monomer. The poly(m-phenylene) adopted a single helical conformation in protic media and self-assembled into a double helix in water through aromatic interaction, while it took a random-coil conformation in chloroform. Upon the addition of sodium cholate in water, the double helical poly(m-phenylene) was transformed into single strands, which bound the cholate molecules to form an excess of one-handed single helix.

  1. Using Arabidopsis to study shoot branching in biomass willow.

    PubMed

    Ward, Sally P; Salmon, Jemma; Hanley, Steven J; Karp, Angela; Leyser, Ottoline

    2013-06-01

    The success of the short-rotation coppice system in biomass willow (Salix spp.) relies on the activity of the shoot-producing meristems found on the coppice stool. However, the regulation of the activity of these meristems is poorly understood. In contrast, our knowledge of the mechanisms behind axillary meristem regulation in Arabidopsis (Arabidopsis thaliana) has grown rapidly in the past few years through the exploitation of integrated physiological, genetic, and molecular assays. Here, we demonstrate that these assays can be directly transferred to study the control of bud activation in biomass willow and to assess similarities with the known hormone regulatory system in Arabidopsis. Bud hormone response was found to be qualitatively remarkably similar in Salix spp. and Arabidopsis. These similarities led us to test whether Arabidopsis hormone mutants could be used to assess allelic variation in the cognate Salix spp. hormone genes. Allelic differences in Salix spp. strigolactone genes were observed using this approach. These results demonstrate that both knowledge and assays from Arabidopsis axillary meristem biology can be successfully applied to Salix spp. and can increase our understanding of a fundamental aspect of short-rotation coppice biomass production, allowing more targeted breeding.

  2. Overexpression of Arabidopsis AnnAt8 Alleviates Abiotic Stress in Transgenic Arabidopsis and Tobacco

    PubMed Central

    Yadav, Deepanker; Ahmed, Israr; Shukla, Pawan; Boyidi, Prasanna; Kirti, Pulugurtha Bharadwaja

    2016-01-01

    Abiotic stress results in massive loss of crop productivity throughout the world. Because of our limited knowledge of the plant defense mechanisms, it is very difficult to exploit the plant genetic resources for manipulation of traits that could benefit multiple stress tolerance in plants. To achieve this, we need a deeper understanding of the plant gene regulatory mechanisms involved in stress responses. Understanding the roles of different members of plant gene families involved in different stress responses, would be a step in this direction. Arabidopsis, which served as a model system for the plant research, is also the most suitable system for the functional characterization of plant gene families. Annexin family in Arabidopsis also is one gene family which has not been fully explored. Eight annexin genes have been reported in the genome of Arabidopsis thaliana. Expression studies of different Arabidopsis annexins revealed their differential regulation under various abiotic stress conditions. AnnAt8 (At5g12380), a member of this family has been shown to exhibit ~433 and ~175 fold increase in transcript levels under NaCl and dehydration stress respectively. To characterize Annexin8 (AnnAt8) further, we have generated transgenic Arabidopsis and tobacco plants constitutively expressing AnnAt8, which were evaluated under different abiotic stress conditions. AnnAt8 overexpressing transgenic plants exhibited higher seed germination rates, better plant growth, and higher chlorophyll retention when compared to wild type plants under abiotic stress treatments. Under stress conditions transgenic plants showed comparatively higher levels of proline and lower levels of malondialdehyde compared to the wild-type plants. Real-Time PCR analyses revealed that the expression of several stress-regulated genes was altered in AnnAt8 over-expressing transgenic tobacco plants, and the enhanced tolerance exhibited by the transgenic plants can be correlated with altered expressions of

  3. N-Glycopeptide Profiling in Arabidopsis Inflorescence.

    PubMed

    Xu, Shou-Ling; Medzihradszky, Katalin F; Wang, Zhi-Yong; Burlingame, Alma L; Chalkley, Robert J

    2016-06-01

    This study presents the first large-scale analysis of plant intact glycopeptides. Using wheat germ agglutinin lectin weak affinity chromatography to enrich modified peptides, followed by electron transfer dissociation (ETD)(1) fragmentation tandem mass spectrometry, glycan compositions on over 1100 glycopeptides from 270 proteins found in Arabidopsis inflorescence tissue were characterized. While some sites were only detected with a single glycan attached, others displayed up to 16 different glycoforms. Among the identified glycopeptides were four modified in nonconsensus glycosylation motifs. While most of the modified proteins are secreted, membrane, endoplasmic reticulum (ER), or Golgi-localized proteins, surprisingly, N-linked sugars were detected on a protein predicted to be cytosolic or nuclear. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  4. The ethylene response pathway in Arabidopsis

    NASA Technical Reports Server (NTRS)

    Kieber, J. J.; Evans, M. L. (Principal Investigator)

    1997-01-01

    The simple gas ethylene influences a diverse array of plant growth and developmental processes including germination, senescence, cell elongation, and fruit ripening. This review focuses on recent molecular genetic studies, principally in Arabidopsis, in which components of the ethylene response pathway have been identified. The isolation and characterization of two of these genes has revealed that ethylene sensing involves a protein kinase cascade. One of these genes encodes a protein with similarity to the ubiquitous Raf family of Ser/Thr protein kinases. A second gene shows similarity to the prokaryotic two-component histidine kinases and most likely encodes an ethylene receptor. Additional elements involved in ethylene signaling have only been identified genetically. The characterization of these genes and mutants will be discussed.

  5. Molecular genetic analysis of phototropism in Arabidopsis.

    PubMed

    Sakai, Tatsuya; Haga, Ken

    2012-09-01

    Plant life is strongly dependent on the environment, and plants regulate their growth and development in response to many different environmental stimuli. One of the regulatory mechanisms involved in these responses is phototropism, which allows plants to change their growth direction in response to the location of the light source. Since the study of phototropism by Darwin, many physiological studies of this phenomenon have been published. Recently, molecular genetic analyses of Arabidopsis have begun to shed light on the molecular mechanisms underlying this response system, including phototropin blue light photoreceptors, phototropin signaling components, auxin transporters, auxin action mechanisms and others. This review highlights some of the recent progress that has been made in further elucidating the phototropic response, with particular emphasis on mutant phenotypes.

  6. Molecular Genetic Analysis of Phototropism in Arabidopsis

    PubMed Central

    Sakai, Tatsuya; Haga, Ken

    2012-01-01

    Plant life is strongly dependent on the environment, and plants regulate their growth and development in response to many different environmental stimuli. One of the regulatory mechanisms involved in these responses is phototropism, which allows plants to change their growth direction in response to the location of the light source. Since the study of phototropism by Darwin, many physiological studies of this phenomenon have been published. Recently, molecular genetic analyses of Arabidopsis have begun to shed light on the molecular mechanisms underlying this response system, including phototropin blue light photoreceptors, phototropin signaling components, auxin transporters, auxin action mechanisms and others. This review highlights some of the recent progress that has been made in further elucidating the phototropic response, with particular emphasis on mutant phenotypes. PMID:22864452

  7. Regulation of the Arabidopsis defense transcriptome.

    PubMed

    Eulgem, Thomas

    2005-02-01

    Transcriptional re-programming is a key step of plant defense in response to pathogen recognition. Microarray analyses combined with genetic and biochemical approaches are now enabling us to study basic principles and details of regulatory mechanisms controlling the defense transcriptome in Arabidopsis. Recent results show that signaling pathways used by different defense systems converge and target overlapping gene sets. Furthermore, a quantitative mechanism common to multiple defense systems modulates transcript levels of these defense-associated genes. Most importantly, some transcription factors have been proven to play a pivotal role in disease resistance. Regulatory circuits linking signaling and gene regulation are emerging, suggesting that a complex interplay of transcriptional activators and repressors fine-tunes expression of the defense transcriptome.

  8. The Arabidopsis Cyclophilin Gene Family1

    PubMed Central

    Romano, Patrick G.N.; Horton, Peter; Gray, Julie E.

    2004-01-01

    Database searching has allowed the identification of a number of previously unreported single and multidomain isoform members of the Arabidopsis cyclophilin gene family. In addition to the cyclophilin-like peptidyl-prolyl cis-trans isomerase domain, the latter contain a variety of other domains with characterized functions. Transcriptional analysis showed they are expressed throughout the plant, and different isoforms are present in all parts of the cell including the cytosol, nucleus, mitochondria, secretory pathway, and chloroplast. The abundance and diversity of cyclophilin isoforms suggests that, like their animal counterparts, plant cyclophilins are likely to be important proteins involved in a wide variety of cellular processes. As well as fulfilling the basic role of protein folding, they may also play important roles in mRNA processing, protein degradation, and signal transduction and thus may be crucial during both development and stress responsiveness. PMID:15051864

  9. A Space Flight Cultivation Protocol for Arabidopsis

    NASA Astrophysics Data System (ADS)

    Levine, H. G.

    2008-06-01

    A tube-based method is presented for the cultivation and manipulation of Arabidopsis thaliana during space flight experimentation. Seeds were germinated on rock-wool plugs and subsequently transferred into modified polypropylene conical tubes (cut to 5 cm lengths) at 7 days after planting. Each tube contained four side-situated slits through which capillary mat strips were woven. An additional capillary mat wick extended from below the tube up through the bottom to the mid-interior portion. The incorporation of Fibrous Ion Exchange Resin Substrate provided nutrients. The tubes were transferred to plant compartments containing a horticulture foam matrix that received water inputs. Vigorous seedling development through to seed production was achieved. Dispersed seeds frequently germinated on top of the foam substrate, yielding a 2nd generation of seedlings. The methods used herein could be applied to other plant species to be flown in space.

  10. Radiation-sensitive mutants of Arabidopsis thaliana

    SciTech Connect

    Jenkins, M.E.; Harlow, G.R.; Liu, Z.

    1995-06-01

    Five Arabidopsis mutants have been isolated on the basis of hypersensitivity of leaf tissue to UV light. For each mutant, the UV-hypersensitive phenotype (uvh) was inherited as a single recessive Mendelian trait. In addition, each uvh mutant represented a separate complementation group. Three of the mutations producing the UV hypersensitive phenotype have been mapped relative to either genetic markers or physical microsatellite polymorphisms. Locus UVH1 is linked to nga76 on chromosome 5, UVH3 to GL1 on chromosome three, and UVH6 to nga59 on chromosome 1. Each uvh mutant has a characteristic pattern of sensitivity based on UV sensitivity of leaf tissue, UV sensitivity of root tissue, and ionizing radiation sensitivity of seeds. On the basis of these patterns, possible molecular defects in these mutants are discussed. 30 refs., 3 figs., 5 tabs.

  11. The ethylene signal transduction pathway in Arabidopsis

    NASA Technical Reports Server (NTRS)

    Kieber, J. J.; Evans, M. L. (Principal Investigator)

    1997-01-01

    The gaseous hormone ethylene is an important regulator of plant growth and development. Using a simple response of etiolated seedlings to ethylene as a genetic screen, genes involved in ethylene signal transduction have been identified in Arabidopsis. Analysis of two of these genes that have been cloned reveals that ethylene signalling involves a combination of a protein (ETR1) with similarity to bacterial histidine kinases and a protein (CTR1) with similarity to Raf-1, a protein kinase involved in multiple signalling cascades in eukaryotic cells. Several lines of investigation provide compelling evidence that ETR1 encodes an ethylene receptor. For the first time there is a glimpse of the molecular circuitry underlying the signal transduction pathway for a plant hormone.

  12. ELF3 controls thermoresponsive growth in Arabidopsis.

    PubMed

    Box, Mathew S; Huang, B Emma; Domijan, Mirela; Jaeger, Katja E; Khattak, Asif Khan; Yoo, Seong Jeon; Sedivy, Emma L; Jones, D Marc; Hearn, Timothy J; Webb, Alex A R; Grant, Alastair; Locke, James C W; Wigge, Philip A

    2015-01-19

    Plant development is highly responsive to ambient temperature, and this trait has been linked to the ability of plants to adapt to climate change. The mechanisms by which natural populations modulate their thermoresponsiveness are not known. To address this, we surveyed Arabidopsis accessions for variation in thermal responsiveness of elongation growth and mapped the corresponding loci. We find that the transcriptional regulator EARLY FLOWERING3 (ELF3) controls elongation growth in response to temperature. Through a combination of modeling and experiments, we show that high temperature relieves the gating of growth at night, highlighting the importance of temperature-dependent repressors of growth. ELF3 gating of transcriptional targets responds rapidly and reversibly to changes in temperature. We show that the binding of ELF3 to target promoters is temperature dependent, suggesting a mechanism where temperature directly controls ELF3 activity.

  13. Endoplasmic Reticulum Stress Response in Arabidopsis Roots

    PubMed Central

    Cho, Yueh; Kanehara, Kazue

    2017-01-01

    Roots are the frontier of plant body to perceive underground environmental change. Endoplasmic reticulum (ER) stress response represents circumvention of cellular stress caused by various environmental changes; however, a limited number of studies are available on the ER stress responses in roots. Here, we report the tunicamycin (TM) -induced ER stress response in Arabidopsis roots by monitoring expression patterns of immunoglobulin-binding protein 3 (BiP3), a representative marker for the response. Roots promptly responded to the TM-induced ER stress through the induction of similar sets of ER stress-responsive genes. However, not all cells responded uniformly to the TM-induced ER stress in roots, as BiP3 was highly expressed in root tips, an outer layer in elongation zone, and an inner layer in mature zone of roots. We suggest that ER stress response in roots has tissue specificity. PMID:28298914

  14. Live confocal imaging of Arabidopsis flower buds.

    PubMed

    Prunet, Nathanaël; Jack, Thomas P; Meyerowitz, Elliot M

    2016-11-01

    Recent advances in confocal microscopy, coupled with the development of numerous fluorescent reporters, provide us with a powerful tool to study the development of plants. Live confocal imaging has been used extensively to further our understanding of the mechanisms underlying the formation of roots, shoots and leaves. However, it has not been widely applied to flowers, partly because of specific challenges associated with the imaging of flower buds. Here, we describe how to prepare and grow shoot apices of Arabidopsis in vitro, to perform both single-point and time-lapse imaging of live, developing flower buds with either an upright or an inverted confocal microscope. Copyright © 2016 Elsevier Inc. All rights reserved.

  15. RNA structure, binding, and coordination in Arabidopsis.

    PubMed

    Foley, Shawn W; Kramer, Marianne C; Gregory, Brian D

    2017-09-01

    From the moment of transcription, up through degradation, each RNA transcript is bound by an ever-changing cohort of RNA binding proteins. The binding of these proteins is regulated by both the primary RNA sequence, as well as the intramolecular RNA folding, or secondary structure, of the transcript. Thus, RNA secondary structure regulates many post-transcriptional processes. With the advent of next generation sequencing, several techniques have been developed to generate global landscapes of both RNA-protein interactions and RNA secondary structure. In this review, we describe the current state of the field detailing techniques to globally interrogate RNA secondary structure and/or RNA-protein interaction sites, as well as our current understanding of these features in the transcriptome of the model plant Arabidopsis thaliana. WIREs RNA 2017, 8:e1426. doi: 10.1002/wrna.1426 For further resources related to this article, please visit the WIREs website. © 2017 Wiley Periodicals, Inc.

  16. Cation channels in the Arabidopsis plasma membrane.

    PubMed

    Véry, Anne Aliénor; Sentenac, Hervé

    2002-04-01

    In vivo analyses have identified different functional types of ion channels in various plant tissues and cells. The Arabidopsis genome contains approximately 70 genes for ion channels, of which 57 might be cation-selective channels (K(+), Ca(2+) or poorly discriminating channels). Here, we describe the different families of (putative) cation channels: the Shakers, the two-P-domain and Kir K(+) channels (encoded by the KCO genes), the cyclic-nucleotide-gated channels, the glutamate receptors, and the Ca(2+) channel TPC1. We also compare molecular data with the data obtained in planta, which should lead to a better understanding of the identity of these channels and provide clues about their roles in plant nutrition and cell signalling.

  17. The ethylene signal transduction pathway in Arabidopsis

    NASA Technical Reports Server (NTRS)

    Kieber, J. J.; Evans, M. L. (Principal Investigator)

    1997-01-01

    The gaseous hormone ethylene is an important regulator of plant growth and development. Using a simple response of etiolated seedlings to ethylene as a genetic screen, genes involved in ethylene signal transduction have been identified in Arabidopsis. Analysis of two of these genes that have been cloned reveals that ethylene signalling involves a combination of a protein (ETR1) with similarity to bacterial histidine kinases and a protein (CTR1) with similarity to Raf-1, a protein kinase involved in multiple signalling cascades in eukaryotic cells. Several lines of investigation provide compelling evidence that ETR1 encodes an ethylene receptor. For the first time there is a glimpse of the molecular circuitry underlying the signal transduction pathway for a plant hormone.

  18. Crystal structure of Arabidopsis thaliana cytokinin dehydrogenase

    SciTech Connect

    Bae, Euiyoung; Bingman, Craig A.; Bitto, Eduard; Aceti, David J.; Phillips, Jr., George N.

    2008-08-13

    Since first discovered in Zea mays, cytokinin dehydrogenase (CKX) genes have been identified in many plants including rice and Arabidopsis thaliana, which possesses CKX homologues (AtCKX1-AtCKX7). So far, the three-dimensional structure of only Z. mays CKX (ZmCKX1) has been determined. The crystal structures of ZmCKX1 have been solved in the native state and in complex with reaction products and a slowly reacting substrate. The structures revealed four glycosylated asparagine residues and a histidine residue covalently linked to FAD. Combined with the structural information, recent biochemical analyses of ZmCKX1 concluded that the final products of the reaction, adenine and a side chain aldehyde, are formed by nonenzymatic hydrolytic cleavage of cytokinin imine products resulting directly from CKX catalysis. Here, we report the crystal structure of AtCKX7 (gene locus At5g21482.1, UniProt code Q9FUJ1).

  19. The ethylene response pathway in Arabidopsis

    NASA Technical Reports Server (NTRS)

    Kieber, J. J.; Evans, M. L. (Principal Investigator)

    1997-01-01

    The simple gas ethylene influences a diverse array of plant growth and developmental processes including germination, senescence, cell elongation, and fruit ripening. This review focuses on recent molecular genetic studies, principally in Arabidopsis, in which components of the ethylene response pathway have been identified. The isolation and characterization of two of these genes has revealed that ethylene sensing involves a protein kinase cascade. One of these genes encodes a protein with similarity to the ubiquitous Raf family of Ser/Thr protein kinases. A second gene shows similarity to the prokaryotic two-component histidine kinases and most likely encodes an ethylene receptor. Additional elements involved in ethylene signaling have only been identified genetically. The characterization of these genes and mutants will be discussed.

  20. Metabolic fingerprinting of Arabidopsis thaliana accessions

    PubMed Central

    Sotelo-Silveira, Mariana; Chauvin, Anne-Laure; Marsch-Martínez, Nayelli; Winkler, Robert; de Folter, Stefan

    2015-01-01

    In the post-genomic era much effort has been put on the discovery of gene function using functional genomics. Despite the advances achieved by these technologies in the understanding of gene function at the genomic and proteomic level, there is still a big genotype-phenotype gap. Metabolic profiling has been used to analyze organisms that have already been characterized genetically. However, there is a small number of studies comparing the metabolic profile of different tissues of distinct accessions. Here, we report the detection of over 14,000 and 17,000 features in inflorescences and leaves, respectively, in two widely used Arabidopsis thaliana accessions. A predictive Random Forest Model was developed, which was able to reliably classify tissue type and accession of samples based on LC-MS profile. Thereby we demonstrate that the morphological differences among A. thaliana accessions are reflected also as distinct metabolic phenotypes within leaves and inflorescences. PMID:26074932

  1. Catabolism of Glutathione Conjugates in Arabidopsis thaliana

    PubMed Central

    Brazier-Hicks, Melissa; Evans, Kathryn M.; Cunningham, Oliver D.; Hodgson, David R. W.; Steel, Patrick G.; Edwards, Robert

    2008-01-01

    The safener fenclorim (4,6-dichloro-2-phenylpyrimidine) increases tolerance to chloroacetanilide herbicides in rice by enhancing the expression of detoxifying glutathione S-transferases (GSTs). Fenclorim also enhances GSTs in Arabidopsis thaliana, and while investigating the functional significance of this induction in suspension cultures, we determined that these enzymes glutathionylated the safener. The resulting S-(fenclorim)-glutathione conjugate was sequentially processed to S-(fenclorim)-γ-glutamyl-cysteine and S-(fenclorim)-cysteine (FC), the latter accumulating in both the cells and the medium. FC was then either catabolized to 4-chloro-6-(methylthio)-phenylpyrimidine (CMTP) or N-acylated with malonic acid. These cysteine derivatives had distinct fates, with the enzymes responsible for their formation being induced by fenclorim and FC. Fenclorim-N-malonylcysteine was formed from FC by the action of a malonyl-CoA-dependent N-malonyltransferase. A small proportion of the fenclorim-N-malonylcysteine then underwent decarboxylation to yield a putative S-fenclorim-N-acetylcysteine intermediate, which underwent a second round of GST-mediated S-glutathionylation and subsequent proteolytic processing. The formation of CMTP was catalyzed by the concerted action of a cysteine conjugate β-lyase and an S-methyltransferase, with the two activities being coordinately regulated. Although the fenclorim conjugates tested showed little GST-inducing activity in Arabidopsis, the formation of CMTP resulted in metabolic reactivation, with the product showing good enhancing activity. In addition, CMTP induced GSTs and herbicide-safening activity in rice. The bioactivated CMTP was in turn glutathione-conjugated and processed to a malonyl cysteine derivative. These results reveal the surprisingly complex set of competing catabolic reactions acting on xenobiotics entering the S-glutathionylation pathway in plants, which can result in both detoxification and bioactivation. PMID

  2. Powerful Partners: Arabidopsis and Chemical Genomics

    PubMed Central

    Robert, Stéphanie; Raikhel, Natasha V.; Hicks, Glenn R.

    2009-01-01

    Chemical genomics (i.e. genomics scale chemical genetics) approaches capitalize on the ability of low molecular mass molecules to modify biological processes. Such molecules are used to modify the activity of a protein or a pathway in a manner that it is tunable and reversible. Bioactive chemicals resulting from forward or reverse chemical screens can be useful in understanding and dissecting complex biological processes due to the essentially limitless variation in structure and activities inherent in chemical space. A major advantage of this approach as a powerful addition to conventional plant genetics is the fact that chemical genomics can address loss-of-function lethality and redundancy. Furthermore, the ability of chemicals to be added at will and to act quickly can permit the study of processes that are highly dynamic such as endomembrane trafficking. An important aspect of utilizing small molecules effectively is to characterize bioactive chemicals in detail including an understanding of structure-activity relationships and the identification of active and inactive analogs. Bioactive chemicals can be useful as reagents to probe biological pathways directly. However, the identification of cognate targets and their pathways is also informative and can be achieved by screens for genetic resistance or hypersensitivity in Arabidopsis thaliana or other organisms from which the results can be translated to plants. In addition, there are approaches utilizing “tagged” chemical libraries that possess reactive moieties permitting the immobilization of active compounds. This opens the possibility for biochemical purification of putative cognate targets. We will review approaches to screen for bioactive chemicals that affect biological processes in Arabidopsis and provide several examples of the power and challenges inherent in this new approach in plant biology. PMID:22303245

  3. Photomorphogenesis in Arabidopsis thaliana (L.) Heynh

    PubMed Central

    Brown, J. A. M.; Klein, W. H.

    1971-01-01

    Arabidopsis seeds were germinated on sterile mineral agar supplemented with 1% glucose and cultured under continuous light regimes. With 4-hour incandescent plus 20-hour monochromatic illumination in the region from 400 to 485 nanometers there was effective floral induction at an intensity of 100 microwatts per square centimeter. Exclusion of far red wave lengths from the 4-hour incandescent period sharply reduced the effectiveness of subsequent monochromatic blue light in promoting floral induction. Delayed floral induction occurred under continuous incandescent light lacking far red and was attributable to the blue wave lengths. Continuous 485 nanometer (100 microwatts per square centimeter) exposure without any white light treatment during the postgermination growth period was ineffective in floral induction and meristem development. Light at 730 nanometers under the same conditions was partially effective, whereas energy between 500 and 700 nanometers was completely ineffective. When continuous monochromatic light at a 3-fold higher energy level was administered, all photomorphogenic responses were accomplished with 485 nanometer light, including germination and 100% floral induction without any white light treatment at any time during the experiment. Almost equal quantum effectiveness was calculated when equivalent quantum flux densities in the region from 710 to 740 nanometers or at 485 nanometers were used. It is postulated that floral induction in Arabidopsis may be the result of a continuous excitation of a stable form of far red-absorbing phytochrome localized in or on a membrane, and that excitation can be either by direct absorption of energy by far red-absorbing phytochrome or by transfer from an accessory pigment. Images PMID:16657629

  4. Formation of the Arabidopsis pentatricopeptide repeat family.

    PubMed

    Rivals, Eric; Bruyère, Clémence; Toffano-Nioche, Claire; Lecharny, Alain

    2006-07-01

    In Arabidopsis (Arabidopsis thaliana) the 466 pentatricopeptide repeat (PPR) proteins are putative RNA-binding proteins with essential roles in organelles. Roughly half of the PPR proteins form the plant combinatorial and modular protein (PCMP) subfamily, which is land-plant specific. PCMPs exhibit a large and variable tandem repeat of a standard pattern of three PPR variant motifs. The association or not of this repeat with three non-PPR motifs at their C terminus defines four distinct classes of PCMPs. The highly structured arrangement of these motifs and the similar repartition of these arrangements in the four classes suggest precise relationships between motif organization and substrate specificity. This study is an attempt to reconstruct an evolutionary scenario of the PCMP family. We developed an innovative approach based on comparisons of the proteins at two levels: namely the succession of motifs along the protein and the amino acid sequence of the motifs. It enabled us to infer evolutionary relationships between proteins as well as between the inter- and intraprotein repeats. First, we observed a polarized elongation of the repeat from the C terminus toward the N-terminal region, suggesting local recombinations of motifs. Second, the most N-terminal PPR triple motif proved to evolve under different constraints than the remaining repeat. Altogether, the evidence indicates different evolution for the PPR region and the C-terminal one in PCMPs, which points to distinct functions for these regions. Moreover, local sequence homogeneity observed across PCMP classes may be due to interclass shuffling of motifs, or to deletions/insertions of non-PPR motifs at the C terminus.

  5. Gene expression in response to cryoprotectant and liquid nitrogen exposure in Arabidopsis shoot tips

    USDA-ARS?s Scientific Manuscript database

    Arabidopsis thaliana serves as an ideal model system to study cryopreservation at the molecular level. We have developed reliable cryopreservation methods for Arabidopsis shoot tips using Plant Vitrification Solution 2, Plant Vitrification Solution 3 and polyethylene glycol-glucose-dimethylsulfoxid...

  6. Comprehensive analysis of CLE polypeptide signaling gene expression and overexpression activity in Arabidopsis

    USDA-ARS?s Scientific Manuscript database

    Technical Abstract: Intercellular signaling is essential for the coordination of growth and development in higher plants. Although hundreds of putative receptors have been identified in Arabidopsis (Arabidopsis thaliana), only a few families of extracellular signaling molecules have been discovered...

  7. Effect of drying history on swelling properties and cell attachment to oligo(poly(ethylene glycol) fumarate) hydrogels for guided tissue regeneration applications.

    PubMed

    Temenoff, Johnna S; Steinbis, Emily S; Mikos, Antonios G

    2003-01-01

    In these experiments, the effects of the drying history of hydrogels made from a novel polymer, oligo(poly(ethylene glycol) fumarate) (OPF) with two different poly(ethylene glycol) (PEG) molecular weights (approximately 920 (1K) and 9110 (10K) g/mol), were investigated. The hydrogels were either formed, dried and then swelled, representing what may occur in the case of a pre-formed membrane for guided tissue regeneration, or were formed and swelled immediately, as may occur with an injectable material for such applications. Subsequently, swelling properties, sol fraction and polymer network structure (as indicated by differential scanning calorimetry), as well as attachment of human dermal fibroblasts to these hydrogels at 4 and 24 h was examined. It was found that drying before swelling caused a significant reduction in final fold swelling of OPF hydrogels, regardless of OPF formulation or method of drying (air-dried or vacuum-dried) (e.g. PEG 10K swollen first: 13.94 +/- 0.35 vs. vacuum first: 6.53 +/- 0.12; PEG 1K swollen first: 8.99 +/- 0.47 vs. vacuum first: 2.26 +/- 0.08). This decreased swelling correlated to significantly higher cell attachment (% seeded) to these hydrogels at 24 h (PEG 10K vacuum first: 21.1 +/- 4.7% vs. swollen first: 7.1 +/- 5.5%; PEG 1K vacuum first: 58.2 +/- 2% vs. swollen first: 7.4 +/- 2.2%). LIVE/DEAD staining followed by microscopic analysis revealed attached cells were viable, yet rounded, and that, in the case of the PEG 1K dried-first samples, undulations in the surface visible in the hydrated state may have affected cell adhesion. Regardless of treatment, all hydrogels showed significantly less cell attachment than the tissue culture polystyrene control after 24 h (104.9 +/- 4.4%). These results suggest that, by altering the PEG molecular weight used in synthesis, OPF hydrogels may be tailored to produce desired swelling properties and reduce non-specific cell adhesion for either injectable or pre-formed applications, thus

  8. A High Fiber and Vegetable Protein Diet is Associated with Low Lumbar Bone Mineral Density in Young Oligo-amenorrheic Athletes

    PubMed Central

    Barron, Elizabeth; Sokoloff, Natalia Cano; Maffazioli, Giovana D. N.; Ackerman, Kathryn E.; Woolley, Ryan; Holmes, Tara M.; Anderson, Ellen J.; Misra, Madhusmita

    2015-01-01

    Background Associations of bone mineral density (BMD) with specific food components, including dietary fiber and isoflavones (that have a negative association with serum estrogen), are unclear and need to be determined, particularly in a population more likely to consume large amounts of these nutrients (such as young athletes). Objective To determine dietary intake of specific food components in oligo-amenorrheic athletes (OA) compared to eumenorrheic athletes (EA) and non-athletes (NA), and associations of the dietary intake of these nutrients with lumbar spine BMD. Design and Subjects This cross-sectional study evaluated 68 OA, 24 EA, and 26 NA 14–23 years old. Measurements included four-day food records (assessed using Nutrient Data System for Research software), a DXA scan evaluating lumbar spine BMD and body composition, and hormone levels. Multivariate analysis was used to estimate associations of nutrients with lumbar spine BMD. Results Compared with EA and NA, OA had higher intake of fiber, phytic acid, and vegetable protein (p<0.0001 for all). Intake of isoflavones, genistein and daidzein, was higher in OA than NA (p=0.003 and 0.0002 respectively). OA had lower consumption of energy from saturated fatty acids (%SFA) than NA (p=0.002). After controlling for confounders such as body weight, menstrual status (indicative of estrogen status), calcium intake, and serum vitamin D (known BMD determinants), lumbar spine BMD Z-scores were inversely associated with dietary fiber [β coefficient (β)= −0.30; p=0.01], vegetable protein (β = −0.28, p=0.02), phytic acid (β = −0.27, p=0.02), genistein (β = −0.25, p=0.01), and daidzein (β = −0.24, p=0.01), and positively with %SFA (β =0.32, p=0.0006)]. Conclusions Compared to EA and NA, OA had a higher dietary intake of fiber, vegetable protein and phytic acid, which were inversely associated with lumbar spine BMD Z-scores. Further studies are needed to assess dietary recommendations for OA to optimize

  9. Prebiotic effects of diet supplemented with the cultivated red seaweed Chondrus crispus or with fructo-oligo-saccharide on host immunity, colonic microbiota and gut microbial metabolites.

    PubMed

    Liu, Jinghua; Kandasamy, Saveetha; Zhang, Junzeng; Kirby, Christopher W; Karakach, Tobias; Hafting, Jeff; Critchley, Alan T; Evans, Franklin; Prithiviraj, Balakrishnan

    2015-08-14

    Gastrointestinal microbial communities are diverse and are composed of both beneficial and pathogenic groups. Prebiotics, such as digestion-resistant fibers, influence the composition of gut microbiota, and can contribute to the improvement of host health. The red seaweed Chondrus crispus is rich in dietary fiber and oligosaccharides, however its prebiotic potential has not been studied to date. Prebiotic effects were investigated with weaning rats fed a cultivated C. crispus-supplemented diet. Comparison standards included a fructo-oligo-saccharide (FOS) diet and a basal diet. The colonic microbiome was profiled with a 16S rRNA sequencing-based Phylochip array. Concentrations of short chain fatty acids (SCFAs) in the feacal samples were determined by gas chromatography with a flame ionization detector (GC-FID) analysis. Immunoglobulin levels in the blood plasma were analyzed with an enzyme-linked immunosorbent assay (ELISA). Histo-morphological parameters of the proximal colon tissue were characterized by hematoxylin and eosin (H&E) staining. Phylochip array analysis indicated differing microbiome composition among the diet-supplemented and the control groups, with the C. crispus group (2.5% supplementation) showing larger separation from the control than other treatment groups. In the 2.5% C. crispus group, the population of beneficial bacteria such as Bifidobacterium breve increased (4.9-fold, p=0.001), and the abundance of pathogenic species such as Clostridium septicum and Streptococcus pneumonia decreased. Higher concentrations of short chain fatty acids (i.e., gut microbial metabolites), including acetic, propionic and butyric acids, were found in faecal samples of the C. crispus-fed rats. Furthermore, both C. crispus and FOS supplemented rats showed significant improvements in proximal colon histo-morphology. Higher faecal moisture was noted in the 2.5% C. crispus group, and elevated plasma immunoglobulin (IgA and IgG) levels were observed in the 0.5% C

  10. Efficient Cellular Knockdown Mediated by siRNA Nanovectors of Gemini Cationic Lipids Having Delocalizable Headgroups and Oligo-Oxyethylene Spacers.

    PubMed

    Martínez-Negro, María; Kumar, Krishan; Barrán-Berdón, Ana L; Datta, Sougata; Kondaiah, Paturu; Junquera, Elena; Bhattacharya, Santanu; Aicart, Emilio

    2016-08-31

    The use of small interfering RNAs (siRNAs) to silence specific genes is one of the most promising approaches in gene therapy, but it requires efficient nanovectors for successful cellular delivery. Recently, we reported liposomal gene carriers derived from a gemini cationic lipid (GCL) of the 1,2-bis(hexadecyl dimethyl imidazolium) oligo-oxyethylene series ((C16Im)2(C2H4O)nC2H4 with n = 1, 2, or 3) and 1,2-dioleyol phosphatidylethanolamine as highly efficient cytofectins for pDNA. On the basis of the satisfactory outcomes of the previous study, the present work focuses on the utility of coliposomes of these gemini lipids with the biocompatible neutral lipid mono oleoyl glycerol (MOG) as highly potent vectors for siRNA cellular transport in the presence of serum. The (C16Im)2(C2H4O)nC2H4/MOG-siRNA lipoplexes were characterized through (i) a physicochemical study (zeta potential, cryo-transmission electron microscopy, small-angle X-ray scattering, and fluorescence anisotropy) to establish the relationship between size, structure, fluidity, and the interaction between siRNA and the GCL/MOG gene vectors and (ii) a biological analysis (flow cytometry, fluorescence microscopy, and cell viability) to report the anti-GFP siRNA transfections in HEK 293T, HeLa, and H1299 cancer cell lines. The in vitro biological analysis confirms the cellular uptake and indicates that a short spacer, a very low molar fraction of GCL in the mixed lipid, and a moderate effective charge ratio of the lipoplex yielded maximum silencing efficacy. At these experimental conditions, the siRNA used in this work is compacted by the GCL/MOG nanovectors by forming two cubic structures (Ia3d and Pm3n) that are correlated with excellent silencing activity. These liposomal nanocarriers possess high silencing activity with a negligible cytotoxicity, which strongly supports their practical use for in vivo knockdown studies.

  11. Transforming growth factor-beta 1 release from oligo(poly(ethylene glycol) fumarate) hydrogels in conditions that model the cartilage wound healing environment.

    PubMed

    Holland, Theresa A; Tessmar, Joerg K V; Tabata, Yasuhiko; Mikos, Antonios G

    2004-01-08

    This research demonstrates that controlled material degradation and transforming growth factor-beta1 (TGF-beta1) release can be achieved by encapsulation of TGF-beta1-loaded gelatin microparticles within the biodegradable polymer oligo(poly(ethylene glycol) fumarate) (OPF), so that these microparticles function as both a digestible porogen and a delivery vehicle. Release studies performed with non-encapsulated microparticles confirmed that at normal physiological pH, TGF-beta1 complexes with acidic gelatin, resulting in slow release rates. At pH 4.0, this complexation no longer persists, and TGF-beta1 release is enhanced. However, by encapsulating TGF-beta1-loaded microparticles in a network of OPF, release at either pH can be diffusionally controlled. For instance, after 28 days of incubation at pH 4.0, final cumulative release from non-encapsulated microparticles crosslinked in 10 and 40 mM glutaraldehyde (GA) was 75.4+/-1.6% and 76.6+/-1.1%, respectively. However, when either microparticle formulation was encapsulated in an OPF hydrogel (noted as OPF-10 mM and OPF-40 mM, respectively), these values were reduced to 44.7+/-14.6% and 47.4+/-4.7%. More interestingly, release studies, in conditions that model the expected collagenase concentration of injured cartilage, demonstrated that by altering the microparticle crosslinking extent and loading within OPF hydrogels, TGF-beta1 release, composite swelling, and polymer loss could be systematically altered. Composites encapsulating less crosslinked microparticles (OPF-10 mM) exhibited 100% release after only 18 days and were completely degraded by day 24 in collagenase-containing phosphate-buffered saline (PBS). Hydrogels encapsulating 40 mM GA microparticles did not exhibit 100% release or polymer loss until day 28. Hydrogels with no microparticle component demonstrated only 79.3+/-9.2% release and 89.2+/-3.4% polymer loss after 28 days in enzyme-containing PBS. Accordingly, these studies confirm that the rate of TGF

  12. Cononsolvency-induced micellization of pyrene end-labeled diblock copolymers of N-isopropylacrylamide and oligo(ethylene glycol) methyl ether methacrylate.

    PubMed

    Rao, Jingyi; Xu, Jian; Luo, Shizhong; Liu, Shiyong

    2007-11-06

    Pyrene end-labeled double hydrophilic diblock copolymers, poly(N-isopropylacrylamide)-b-poly(oligo(ethylene glycol) methyl ether methacrylate) (Py-PNIPAM-b-POEGMA), were synthesized via consecutive reversible addition-fragmentation chain transfer polymerization using a pyrene-containing dithioester as the chain transfer agent. These diblock copolymers molecularly dissolve in pure methanol and water, but form well-defined and nearly monodisperse PNIPAM-core micelles in an appropriate mixture of them due to the cononsolvency of PNIPAM block. 1H NMR, laser light scattering, fluorescence spectroscopy, and transmission electron microscopy were employed to characterize the cononsolvency-induced PNIPAM-core micelles. When the volume fraction of water, phi water, in the methanol/water mixture is in the range of 0.5-0.8, the sizes of micelles are in the range of 20-30 nm in radius for Py-PNIPAM50-b- POEGMA18. At phi water = 0.5, the formed micelles possess the highest overall micelle density and the largest molar mass. The effects of varying the block lengths of Py-PNIPAM-b-POEGMA diblock copolymers on the structural parameters of PNIPAM-core micelles have also been explored. Although we can observe the immediate appearance of bluish tinge upon mixing the diblock copolymer solution in methanol with equal volume of water (phi water = 0.5), which is characteristic of the formation of micellar aggregates, the whole micellization process apparently takes a relatively long time to complete, as revealed by monitoring the time dependence of fluorescence emission spectra. The excimer/monomer fluorescence intensity ratios, IE/IM, continuously decrease with time and then reach a plateau value after approximately 20 min. The decrease of IE/IM after the initial formation of pseudo-equilibrium micelles should be ascribed to the structural rearrangement and further packing of PNIPAM segments within the micelle core, restricting the mobility of pyrene end groups and decreasing the

  13. Genes encoding calmodulin-binding proteins in the Arabidopsis genome

    NASA Technical Reports Server (NTRS)

    Reddy, Vaka S.; Ali, Gul S.; Reddy, Anireddy S N.

    2002-01-01

    Analysis of the recently completed Arabidopsis genome sequence indicates that approximately 31% of the predicted genes could not be assigned to functional categories, as they do not show any sequence similarity with proteins of known function from other organisms. Calmodulin (CaM), a ubiquitous and multifunctional Ca(2+) sensor, interacts with a wide variety of cellular proteins and modulates their activity/function in regulating diverse cellular processes. However, the primary amino acid sequence of the CaM-binding domain in different CaM-binding proteins (CBPs) is not conserved. One way to identify most of the CBPs in the Arabidopsis genome is by protein-protein interaction-based screening of expression libraries with CaM. Here, using a mixture of radiolabeled CaM isoforms from Arabidopsis, we screened several expression libraries prepared from flower meristem, seedlings, or tissues treated with hormones, an elicitor, or a pathogen. Sequence analysis of 77 positive clones that interact with CaM in a Ca(2+)-dependent manner revealed 20 CBPs, including 14 previously unknown CBPs. In addition, by searching the Arabidopsis genome sequence with the newly identified and known plant or animal CBPs, we identified a total of 27 CBPs. Among these, 16 CBPs are represented by families with 2-20 members in each family. Gene expression analysis revealed that CBPs and CBP paralogs are expressed differentially. Our data suggest that Arabidopsis has a large number of CBPs including several plant-specific ones. Although CaM is highly conserved between plants and animals, only a few CBPs are common to both plants and animals. Analysis of Arabidopsis CBPs revealed the presence of a variety of interesting domains. Our analyses identified several hypothetical proteins in the Arabidopsis genome as CaM targets, suggesting their involvement in Ca(2+)-mediated signaling networks.

  14. Genes encoding calmodulin-binding proteins in the Arabidopsis genome

    NASA Technical Reports Server (NTRS)

    Reddy, Vaka S.; Ali, Gul S.; Reddy, Anireddy S N.

    2002-01-01

    Analysis of the recently completed Arabidopsis genome sequence indicates that approximately 31% of the predicted genes could not be assigned to functional categories, as they do not show any sequence similarity with proteins of known function from other organisms. Calmodulin (CaM), a ubiquitous and multifunctional Ca(2+) sensor, interacts with a wide variety of cellular proteins and modulates their activity/function in regulating diverse cellular processes. However, the primary amino acid sequence of the CaM-binding domain in different CaM-binding proteins (CBPs) is not conserved. One way to identify most of the CBPs in the Arabidopsis genome is by protein-protein interaction-based screening of expression libraries with CaM. Here, using a mixture of radiolabeled CaM isoforms from Arabidopsis, we screened several expression libraries prepared from flower meristem, seedlings, or tissues treated with hormones, an elicitor, or a pathogen. Sequence analysis of 77 positive clones that interact with CaM in a Ca(2+)-dependent manner revealed 20 CBPs, including 14 previously unknown CBPs. In addition, by searching the Arabidopsis genome sequence with the newly identified and known plant or animal CBPs, we identified a total of 27 CBPs. Among these, 16 CBPs are represented by families with 2-20 members in each family. Gene expression analysis revealed that CBPs and CBP paralogs are expressed differentially. Our data suggest that Arabidopsis has a large number of CBPs including several plant-specific ones. Although CaM is highly conserved between plants and animals, only a few CBPs are common to both plants and animals. Analysis of Arabidopsis CBPs revealed the presence of a variety of interesting domains. Our analyses identified several hypothetical proteins in the Arabidopsis genome as CaM targets, suggesting their involvement in Ca(2+)-mediated signaling networks.

  15. Genes encoding calmodulin-binding proteins in the Arabidopsis genome.

    PubMed

    Reddy, Vaka S; Ali, Gul S; Reddy, Anireddy S N

    2002-03-22

    Analysis of the recently completed Arabidopsis genome sequence indicates that approximately 31% of the predicted genes could not be assigned to functional categories, as they do not show any sequence similarity with proteins of known function from other organisms. Calmodulin (CaM), a ubiquitous and multifunctional Ca(2+) sensor, interacts with a wide variety of cellular proteins and modulates their activity/function in regulating diverse cellular processes. However, the primary amino acid sequence of the CaM-binding domain in different CaM-binding proteins (CBPs) is not conserved. One way to identify most of the CBPs in the Arabidopsis genome is by protein-protein interaction-based screening of expression libraries with CaM. Here, using a mixture of radiolabeled CaM isoforms from Arabidopsis, we screened several expression libraries prepared from flower meristem, seedlings, or tissues treated with hormones, an elicitor, or a pathogen. Sequence analysis of 77 positive clones that interact with CaM in a Ca(2+)-dependent manner revealed 20 CBPs, including 14 previously unknown CBPs. In addition, by searching the Arabidopsis genome sequence with the newly identified and known plant or animal CBPs, we identified a total of 27 CBPs. Among these, 16 CBPs are represented by families with 2-20 members in each family. Gene expression analysis revealed that CBPs and CBP paralogs are expressed differentially. Our data suggest that Arabidopsis has a large number of CBPs including several plant-specific ones. Although CaM is highly conserved between plants and animals, only a few CBPs are common to both plants and animals. Analysis of Arabidopsis CBPs revealed the presence of a variety of interesting domains. Our analyses identified several hypothetical proteins in the Arabidopsis genome as CaM targets, suggesting their involvement in Ca(2+)-mediated signaling networks.

  16. AtCCX3 is an Arabidopsis endomembrane H(+)-dependent K(+) transporter

    USDA-ARS?s Scientific Manuscript database

    The Arabidopsis ("Arabidopsis thaliana") cation calcium exchangers (CCXs) were recently identified as a subfamily of cation transporters; however, no plant "CCXs" have been functionally characterized. Here, we show that Arabidopsis AtCCX3 (At3g14070) and AtCCX4 (At1g54115) can suppress yeast mutants...

  17. Similar Pathogen Targets in Arabidopsis thaliana and Homo sapiens Protein Networks

    DTIC Science & Technology

    2012-09-21

    Similar Pathogen Targets in Arabidopsis thaliana and Homo sapiens Protein Networks Paulo Shakarian1*, J. Kenneth Wickiser2 1 Paulo Shakarian...pathogens on host protein networks for humans and Arabidopsis - noting striking similarities. Specifically, we preform k-shell decomposition analysis on...significantly attacked. Citation: Shakarian P, Wickiser JK (2012) Similar Pathogen Targets in Arabidopsis thaliana and Homo sapiens Protein Networks

  18. Arabidopsis cell-free extract, ACE, a new in vitro translation system derived from Arabidopsis callus cultures.

    PubMed

    Murota, Katsunori; Hagiwara-Komoda, Yuka; Komoda, Keisuke; Onouchi, Hitoshi; Ishikawa, Masayuki; Naito, Satoshi

    2011-08-01

    The analysis of post-transcriptional regulatory mechanisms in plants has benefited greatly from the use of cell-free extract systems. Arabidopsis as a model system provides extensive genetic resources; however, to date a suitable cell-free translation system from Arabidopsis has not been available. In this study, we devised an Arabidopsis cell-free extract (ACE) to be used for in vitro translation studies. Protoplasts were prepared from callus cultures derived from Arabidopsis seedlings, and cell-free extracts were prepared after evacuolation of the protoplasts by Percoll gradient centrifugation. The new ACE system exhibits translation activity comparable with that of the wheat germ extract system. We demonstrated that ACE prepared from the 5'-3' exoribonuclease-deficient mutant of Arabidopsis, xrn4-5, exhibited increased stability of an uncapped mRNA as compared with that from wild-type Arabidopsis. We applied the ACE system to study post-transcriptional regulation of AtCGS1. AtCGS1 codes for cystathionine γ-synthase (CGS) that catalyzes the first committed step of methionine and S-adenosyl-l-methionine (AdoMet) biosynthesis in plants, and is feedback regulated by mRNA degradation coupled with translation elongation arrest. The ACE system was capable of reproducing translation elongation arrest and subsequent AtCGS1 mRNA degradation that are induced by AdoMet. The ACE system described here can be prepared in a month after seed sowing and will make it possible to study post-transcriptional regulation of plant genes while taking advantage of the genetics of Arabidopsis.

  19. Stomatal development in Arabidopsis and grasses: differences and commonalities.

    PubMed

    Serna, Laura

    2011-01-01

    Stomata, found on the epidermis of all terrestrial plants, consist of two specialized cells called guard cells, which surround a tiny pore. Major advances have been made in our understanding of the genetic control of stomatal development in Arabidopsis and grasses. In Arabidopsis, three basic-helix-loop-helix (bHLH) genes control the successive steps that lead to stomatal formation. SPEECHLESS (SPCH) drives the cell division that initiates the stomatal cell lineage, MUTE induces the formation of the immediate stomatal precursor cell, and FAMA causes the stomatal precursor cell to divide into the two guard cells. Recent results demonstrate that these genes share functions with their grass homologs, and that MUTE is expressed later in development than its grass counterparts. Other differences in stomatal development between these two plant groups are exemplified by the PANGLOSS1 (PAN1) gene of maize. PAN1, which encodes a leucine-rich repeat receptor-like kinase with an inactive kinase domain, promotes polarization of the subsidiary mother cell and orients its cell division plane. Because such events do not exist in Arabidopsis, it is likely that the PAN1-like genes of Arabidopsis and PAN1 are paralogs. Together, these results indicate that distinctions in the regulation of gene expression and protein function are both responsible for the divergence of stomatal development between Arabidopsis and grasses.

  20. Arsenic uptake and speciation in Arabidopsis thaliana under hydroponic conditions.

    PubMed

    Park, Jin Hee; Han, Young-Soo; Seong, Hye Jin; Ahn, Joo Sung; Nam, In-Hyun

    2016-07-01

    Arsenic (As) uptake and species in Arabidopsis thaliana were evaluated under hydroponic conditions. Plant nutrient solutions were treated with arsenite [As(III)] or arsenate [As(V)], and aqueous As speciation was conducted using a solid phase extraction (SPE) cartridge. Arabidopsis reduced As(V) to As(III) in the nutrient solution, possibly due to root exudates such as organic acids or the efflux of As(III) from plant roots after in vivo reduction of As(V) to As(III). Arsenic uptake by Arabidopsis was associated with increased levels of Ca and Fe, and decreased levels of K in plant tissues. Arsenic in Arabidopsis mainly occurred as As(III), which was coordinated with oxygen and sulfur based on XANES and EXAFS results. The existence of As(III)O and As(III)S in EXAFS indicates partial biotransformation of As(III)O to a sulfur-coordinated form because of limited amount of glutathione in plants. Further understanding the mechanism of As biotransformation in Arabidopsis may help to develop measures that can mitigate As toxicity via genetic engineering.

  1. 50 years of Arabidopsis research: highlights and future directions.

    PubMed

    Provart, Nicholas J; Alonso, Jose; Assmann, Sarah M; Bergmann, Dominique; Brady, Siobhan M; Brkljacic, Jelena; Browse, John; Chapple, Clint; Colot, Vincent; Cutler, Sean; Dangl, Jeff; Ehrhardt, David; Friesner, Joanna D; Frommer, Wolf B; Grotewold, Erich; Meyerowitz, Elliot; Nemhauser, Jennifer; Nordborg, Magnus; Pikaard, Craig; Shanklin, John; Somerville, Chris; Stitt, Mark; Torii, Keiko U; Waese, Jamie; Wagner, Doris; McCourt, Peter

    2016-02-01

    922 I. 922 II. 922 III. 925 IV. 925 V. 926 VI. 927 VII. 928 VIII. 929 IX. 930 X. 931 XI. 932 XII. 933 XIII. Natural variation and genome-wide association studies 934 XIV. 934 XV. 935 XVI. 936 XVII. 937 937 References 937 SUMMARY: The year 2014 marked the 25(th) International Conference on Arabidopsis Research. In the 50 yr since the first International Conference on Arabidopsis Research, held in 1965 in Göttingen, Germany, > 54 000 papers that mention Arabidopsis thaliana in the title, abstract or keywords have been published. We present herein a citational network analysis of these papers, and touch on some of the important discoveries in plant biology that have been made in this powerful model system, and highlight how these discoveries have then had an impact in crop species. We also look to the future, highlighting some outstanding questions that can be readily addressed in Arabidopsis. Topics that are discussed include Arabidopsis reverse genetic resources, stock centers, databases and online tools, cell biology, development, hormones, plant immunity, signaling in response to abiotic stress, transporters, biosynthesis of cells walls and macromolecules such as starch and lipids, epigenetics and epigenomics, genome-wide association studies and natural variation, gene regulatory networks, modeling and systems biology, and synthetic biology.

  2. Ethylene signaling in rice and Arabidopsis: conserved and diverged aspects.

    PubMed

    Yang, Chao; Lu, Xiang; Ma, Biao; Chen, Shou-Yi; Zhang, Jin-Song

    2015-04-01

    Ethylene as a gas phytohormone plays significant roles in the whole life cycle of plants, ranging from growth and development to stress responses. A linear ethylene signaling pathway has been established in the dicotyledonous model plant Arabidopsis. However, the ethylene signaling mechanism in monocotyledonous plants such as rice is largely unclear. In this review, we compare the ethylene response phenotypes of dark-grown seedlings of Arabidopsis, rice, and other monocotyledonous plants (maize, wheat, sorghum, and Brachypodium distachyon) and pinpoint that rice has a distinct phenotype of root inhibition but coleoptile promotion in etiolated seedlings upon ethylene treatment. We further summarize the homologous genes of Arabidopsis ethylene signaling components in these monocotyledonous plants and discuss recent progress. Although conserved in most aspects, ethylene signaling in rice has evolved new features compared with that in Arabidopsis. These analyses provide novel insights into the understanding of ethylene signaling in the dicotyledonous Arabidopsis and monocotyledonous plants, particularly rice. Further characterization of rice ethylene-responsive mutants and their corresponding genes will help us better understand the whole picture of ethylene signaling mechanisms in plants.

  3. The Alphabet of Galactolipids in Arabidopsis thaliana

    PubMed Central

    Ibrahim, Amina; Schütz, Anna-Lena; Galano, Jean-Marie; Herrfurth, Cornelia; Feussner, Kirstin; Durand, Thierry; Brodhun, Florian; Feussner, Ivo

    2011-01-01

    Galactolipids constitute the major lipid class in plants. In recent years oxygenated derivatives of galactolipids have been detected. They are discussed as signal molecules during leaf damage, since they accumulate in wounded leaves in high levels. Using different analytical methods such as nuclear magnetic resonance, infra-red spectroscopy, and high performance liquid chromatography/mass spectrometry (HPLC/MS) earlier reports focused on the analysis of either oxidized or non-oxidized species and needed high levels of analytes. Here, we report on the analysis of the galactolipid subfraction of the Arabidopsis leaf lipidome by an improved HPLC/MS2-based method that is fast, robust, and comparatively simple in its performance. Due to a combination of phase partitioning, solid phase fractionation, liquid chromatography, and MS2 experiments this method has high detection sensitivity and requires only low amounts of plant material. With this method 167 galactolipid species were detected in leaves of Arabidopsis thaliana. Out of these 79 being newly described species. From all species the head group and acyl side chains were identified via MS2 experiments. Moreover, the structural identification was supported by HPLC/time-of-flight (TOF)-MS and gas chromatography (GC)/MS analysis. The quantification of different galactolipid species that accumulated 30 min after a mechanical wounding in A. thaliana leaves showed that the oxidized acyl side chains in galactolipids are divided into 65% cyclopentenones, 27% methyl-branched ketols, 3.8% hydroperoxides/straight-chain ketols, 2.0% hydroxides, and 2.6% phytoprostanes. In comparison to the free cyclopentenone derivatives, the esterified forms occur in a 149-fold excess supporting the hypothesis that galactolipids might function as storage compounds for cyclopentenones. Additional analysis of the ratio of non-oxidized to oxidized galactolipid species in leaves of wounded plants was performed resulting in a ratio of 2.0 in case

  4. Transformation of beta-lycopene cyclase genes from Salicornia europaea and Arabidopsis conferred salt tolerance in Arabidopsis and tobacco.

    PubMed

    Chen, Xianyang; Han, Heping; Jiang, Ping; Nie, Lingling; Bao, Hexigeduleng; Fan, Pengxiang; Lv, Sulian; Feng, Juanjuan; Li, Yinxin

    2011-05-01

    Inhibition of lycopene cyclization decreased the salt tolerance of the euhalophyte Salicornia europaea L. We isolated a β-lycopene cyclase gene SeLCY from S. europaea and transformed it into Arabidopsis with stable expression. Transgenic Arabidopsis on post-germination exhibited enhanced tolerance to oxidative and salt stress. After 8 and 21 d recovery from 200 mM NaCl treatment, transgenic lines had a higher survival ratio than wild-type (WT) plants. Three-week-old transgenic plants treated with 200 mM NaCl showed better growth than the WT with higher photosystem activity and less H(2)O(2) accumulation. Determination of endogenous pigments of Arabidopsis treated with 200 mM NaCl for 0, 2 or 4 d demonstrated that the transgenic plants retained higher contents of carotenoids than the WT. Furthermore, to compare the difference between SeLCY and AtLCY from Arabidopsis, we used viral vector mediating ectopic expression of SeLCY and AtLCY in Nicotiana benthamiana. Although LCY genes transformation increased the salt tolerance in tobacco, there is no significant difference between SeLCY- and AtLCY-transformed plants. These findings indicate that SeLCY transgenic Arabidopsis improved salt tolerance by increasing synthesis of carotenoids, which impairs reactive oxygen species and protects the photosynthesis system under salt stress, and as a single gene, SeLCY functionally showed no advantage for salt tolerance improvement compared with AtLCY.

  5. Identification of Pseudomonas syringae pathogens of Arabidopsis and a bacterial locus determining avirulence on both Arabidopsis and soybean.

    PubMed Central

    Whalen, M C; Innes, R W; Bent, A F; Staskawicz, B J

    1991-01-01

    To develop a model system for molecular genetic analysis of plant-pathogen interactions, we studied the interaction between Arabidopsis thaliana and the bacterial pathogen Pseudomonas syringae pv tomato (Pst). Pst strains were found to be virulent or avirulent on specific Arabidopsis ecotypes, and single ecotypes were resistant to some Pst strains and susceptible to others. In many plant-pathogen interactions, disease resistance is controlled by the simultaneous presence of single plant resistance genes and single pathogen avirulence genes. Therefore, we tested whether avirulence genes in Pst controlled induction of resistance in Arabidopsis. Cosmids that determine avirulence were isolated from Pst genomic libraries, and the Pst avirulence locus avrRpt2 was defined. This allowed us to construct pathogens that differed only by the presence or absence of a single putative avirulence gene. We found that Arabidopsis ecotype Col-0 was susceptible to Pst strain DC3000 but resistant to the same strain carrying avrRpt2, suggesting that a single locus in Col-0 determines resistance. As a first step toward genetically mapping the postulated resistance locus, an ecotype susceptible to infection by DC3000 carrying avrRpt2 was identified. The avrRpt2 locus from Pst was also moved into virulent strains of the soybean pathogen P. syringae pv glycinea to test whether this locus could determine avirulence on soybean. The resulting strains induced a resistant response in a cultivar-specific manner, suggesting that similar resistance mechanisms may function in Arabidopsis and soybean. PMID:1824334

  6. Inflorescence abnormalities occur with overexpression of Arabidopsis lyrata FT in the fwa mutant of Arabidopsis thaliana.

    PubMed

    Kawanabe, Takahiro; Fujimoto, Ryo

    2011-10-01

    Arabidopsis thaliana is a quantitative long-day plant with the timing of the floral transition being regulated by both endogenous signals and multiple environmental factors. fwa is a late-flowering mutant, and this phenotype is due to ectopic FWA expression caused by hypomethylation at the FWA locus. The floral transition results in the activation of the floral development process, the key regulators being the floral meristem identity genes, AP1 (APETALA1) and LFY (LEAFY). In this study, we describe inflorescence abnormalities in plants overexpressing the Arabidopsis lyrata FT (AlFT) and A. thaliana FWA (AtFWA) genes simultaneously. The inflorescence abnormality phenotype was present in only a proportion of plants. All plants overexpressing both AlFT and AtFWA flowered earlier than fwa, suggesting that the inflorescence abnormality and earlier flowering time are caused independently. The inflorescence abnormality phenotype was similar to that of the double mutant of ap1 and lfy, and AP1 and LFY genes were down-regulated in the abnormal inflorescences. From these results, we suggest that not only does ectopic AtFWA expression inhibit AtFT/AlFT function to delay flowering but that overexpression of AtFWA and AlFT together inhibits AP1 and LFY function to produce abnormal inflorescences. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

  7. Arabidopsis Hormone Database: a comprehensive genetic and phenotypic information database for plant hormone research in Arabidopsis

    PubMed Central

    Peng, Zhi-yu; Zhou, Xin; Li, Linchuan; Yu, Xiangchun; Li, Hongjiang; Jiang, Zhiqiang; Cao, Guangyu; Bai, Mingyi; Wang, Xingchun; Jiang, Caifu; Lu, Haibin; Hou, Xianhui; Qu, Lijia; Wang, Zhiyong; Zuo, Jianru; Fu, Xiangdong; Su, Zhen; Li, Songgang; Guo, Hongwei

    2009-01-01

    Plant hormones are small organic molecules that influence almost every aspect of plant growth and development. Genetic and molecular studies have revealed a large number of genes that are involved in responses to numerous plant hormones, including auxin, gibberellin, cytokinin, abscisic acid, ethylene, jasmonic acid, salicylic acid, and brassinosteroid. Here, we develop an Arabidopsis hormone database, which aims to provide a systematic and comprehensive view of genes participating in plant hormonal regulation, as well as morphological phenotypes controlled by plant hormones. Based on data from mutant studies, transgenic analysis and gene ontology (GO) annotation, we have identified a total of 1026 genes in the Arabidopsis genome that participate in plant hormone functions. Meanwhile, a phenotype ontology is developed to precisely describe myriad hormone-regulated morphological processes with standardized vocabularies. A web interface (http://ahd.cbi.pku.edu.cn) would allow users to quickly get access to information about these hormone-related genes, including sequences, functional category, mutant information, phenotypic description, microarray data and linked publications. Several applications of this database in studying plant hormonal regulation and hormone cross-talk will be presented and discussed. PMID:19015126

  8. Arabidopsis Hormone Database: a comprehensive genetic and phenotypic information database for plant hormone research in Arabidopsis.

    PubMed

    Peng, Zhi-yu; Zhou, Xin; Li, Linchuan; Yu, Xiangchun; Li, Hongjiang; Jiang, Zhiqiang; Cao, Guangyu; Bai, Mingyi; Wang, Xingchun; Jiang, Caifu; Lu, Haibin; Hou, Xianhui; Qu, Lijia; Wang, Zhiyong; Zuo, Jianru; Fu, Xiangdong; Su, Zhen; Li, Songgang; Guo, Hongwei

    2009-01-01

    Plant hormones are small organic molecules that influence almost every aspect of plant growth and development. Genetic and molecular studies have revealed a large number of genes that are involved in responses to numerous plant hormones, including auxin, gibberellin, cytokinin, abscisic acid, ethylene, jasmonic acid, salicylic acid, and brassinosteroid. Here, we develop an Arabidopsis hormone database, which aims to provide a systematic and comprehensive view of genes participating in plant hormonal regulation, as well as morphological phenotypes controlled by plant hormones. Based on data from mutant studies, transgenic analysis and gene ontology (GO) annotation, we have identified a total of 1026 genes in the Arabidopsis genome that participate in plant hormone functions. Meanwhile, a phenotype ontology is developed to precisely describe myriad hormone-regulated morphological processes with standardized vocabularies. A web interface (http://ahd.cbi.pku.edu.cn) would allow users to quickly get access to information about these hormone-related genes, including sequences, functional category, mutant information, phenotypic description, microarray data and linked publications. Several applications of this database in studying plant hormonal regulation and hormone cross-talk will be presented and discussed.

  9. Arabidopsis cpSRP54 regulates carotenoid accumulation in Arabidopsis and Brassica napus

    PubMed Central

    Gruber, Margaret Y.; Hannoufa, Abdelali

    2012-01-01

    An Arabidopsis thaliana mutant, cbd (carotenoid biosynthesis deficient), was recovered from a mutant population based on its yellow cotyledons, yellow-first true leaves, and stunted growth. Seven-day-old seedlings and mature seeds of this mutant had lower chlorophyll and total carotenoids than the wild type (WT). Genetic and molecular characterization revealed that cbd was a recessive mutant caused by a T-DNA insertion in the gene cpSRP54 encoding the 54kDa subunit of the chloroplast signal recognition particle. Transcript levels of most of the main carotenoid biosynthetic genes in cbd were unchanged relative to WT, but expression increased in carotenoid and abscisic acid catabolic genes. The chloroplasts of cbd also had developmental defects that contributed to decreased carotenoid and chlorophyll contents. Transcription of AtGLK1 (Golden 2-like 1), AtGLK2, and GUN4 appeared to be disrupted in the cbd mutant suggesting that the plastid-to-nucleus retrograde signal may be affected, regulating the changes in chloroplast functional and developmental states and carotenoid content flux. Transformation of A. thaliana and Brassica napus with a gDNA encoding the Arabidopsis cpSRP54 showed the utility of this gene in enhancing levels of seed carotenoids without affecting growth or seed yield. PMID:22791829

  10. Structure, Wettability, and Thermal Stability of Organic Thin-Films on Gold Generated from the Molecular Self-Assembly of Unsymmetrical Oligo(ethylene glycol) Spiroalkanedithiols.

    PubMed

    Chinwangso, Pawilai; Lee, Han Ju; Jamison, Andrew C; Marquez, Maria D; Park, Chul Soon; Lee, T Randall

    2017-02-28

    Organic thin-films on gold were prepared from a set of new, custom-designed bidentate alkanethiols possessing a mixture of normal alkane and methoxy-terminated tri(ethylene glycol) chains. The new unsymmetrical spiroalkanedithiol adsorbates were of the form [CH3O(CH2CH2O)3(CH2)5]-[CH3(CH2)n+1]C[CH2SH]2 where n = 3 and 14; designated EG3C7-C7 and EG3C7-C18, respectively. Their corresponding self-assembled monolayers (SAMs) on gold were characterized and compared with monothiol SAMs derived from an analogous normal alkanethiol (C18SH) and an alkanethiol terminated with an oligo(ethylene glycol) (OEG) moiety (i.e., EG3C7SH). Ellipsometric data revealed reduced film thicknesses for the double-chained dithiolate SAMs, which perhaps arose from the phase-incompatible merger of a hydrocarbon chain with an OEG moiety, contributing to disorder in the films and/or an increase in chain tilt. The comparable wettabilities of the SAMs derived from EG3C7SH and EG3C7-C7, using water as the contacting liquid, are consistent with exposure of the OEG moieties at both interfaces, whereas the lower wettability of the SAM derived from EG3C7-C18 is consistent with exposure of hydrocarbon chains at the interface. The data collected by X-ray photoelectron spectroscopy confirmed the formation of the new OEG-terminated dithiolate SAMs, and also revealed them as less densely packed monolayers due in part to the large molecular cross section of the OEG moieties and to their double-chained structure with dual surface bonds. Mixed SAMs formed from pairs of monothiols having chain compositions analogous to those of the chains of the new dithiols showed that an EG3C7SH/heptanethiol-mixed SAM and the EG3C7-C7 SAM produced almost identical characterization data, revealing the favorable film formation dynamics for adsorbate structures where the alkyl chains can assemble beneath the phase-incompatible OEG termini. For the mixed SAM formed from EG3C7SH/C18SH, the data indicate that the EG3C7SH component

  11. Building an efficient curation workflow for the Arabidopsis literature corpus

    PubMed Central

    Li, Donghui; Berardini, Tanya Z.; Muller, Robert J.; Huala, Eva

    2012-01-01

    TAIR (The Arabidopsis Information Resource) is the model organism database (MOD) for Arabidopsis thaliana, a model plant with a literature corpus of about 39 000 articles in PubMed, with over 4300 new articles added in 2011. We have developed a literature curation workflow incorporating both automated and manual elements to cope with this flood of new research articles. The current workflow can be divided into two phases: article selection and curation. Structured controlled vocabularies, such as the Gene Ontology and Plant Ontology are used to capture free text information in the literature as succinct ontology-based annotations suitable for the application of computational analysis methods. We also describe our curation platform and the use of text mining tools in our workflow. Database URL: www.arabidopsis.org PMID:23221298

  12. A petal breakstrength meter for Arabidopsis abscission studies

    PubMed Central

    Lease, Kevin A; Cho, Sung Ki; Walker, John C

    2006-01-01

    Background Abscission is the regulated dropping of plant organs, such as leaves or flower petals. This process involves a break down of the cell wall between layers of cells in the abscission zone, causing the organ to become detached. The model plant Arabidopsis thaliana undergoes floral organ abscission. Various experimental methods have been used to study Arabidopsis floral organ abscission, including measuring the petal breakstrength, or the amount of force required to pull a petal from the receptacle. Petal breakstrength provides a quantitative insight into the physical integrity of the petal abscission zone. Results We developed a petal breakstrength meter that allows rapid data acquisition on a personal computer. We present the design of the device and show its utility in measuring Arabidopsis petal breakstrength for abscission studies. Conclusion This petal breakstrength meter should enable researchers to perform the petal breakstrength assay as a routine part of the characterization of environmental and genetic factors affecting abscission. PMID:16483376

  13. Cryptochrome blue-light photoreceptors of Arabidopsis implicated in phototropism.

    PubMed

    Ahmad, M; Jarillo, J A; Smirnova, O; Cashmore, A R

    1998-04-16

    Phototropism-bending towards the light-is one of the best known plant tropic responses. Despite being reported by Darwin and others over a century ago to be specifically under the control of blue light, the photoreceptors mediating phototropism have remained unknown. We have characterized a blue-light photoreceptor from Arabidopsis, named CRY1 for cryptochrome 1; this photoreceptor is a flavoprotein that mediates numerous blue-light-dependent responses. In Arabidopsis, HY4 (the gene encoding CRY1) is a member of a small gene family that also encodes a related photoreceptor, CRY2, which shares considerable functional overlap with CRY1. Here we report that mutant plants lacking both the CRY1 and the CRY2 blue-light photoreceptors are deficient in the phototropic response. Transgenic Arabidopsis plants overexpressing CRY1 or CRY2 show enhanced phototropic curvature. We conclude that cryptochrome is one of the photoreceptors mediating phototropism in plants.

  14. Abiotic stresses induce different localizations of anthocyanins in Arabidopsis

    PubMed Central

    Kovinich, Nik; Kayanja, Gilbert; Chanoca, Alexandra; Otegui, Marisa S; Grotewold, Erich

    2015-01-01

    Anthocyanins are induced in plants in response to abiotic stresses such as drought, high salinity, excess light, and cold, where they often correlate with enhanced stress tolerance. Numerous roles have been proposed for anthocyanins induced during abiotic stresses including functioning as ROS scavengers, photoprotectants, and stress signals. We have recently found different profiles of anthocyanins in Arabidopsis (Arabidopsis thaliana) plants exposed to different abiotic stresses, suggesting that not all anthocyanins have the same function. Here, we discuss these findings in the context of other studies and show that anthocyanins induced in Arabidopsis in response to various abiotic stresses have different localizations at the organ and tissue levels. These studies provide a basis to clarify the role of particular anthocyanin species during abiotic stress. PMID:26179363

  15. Building an efficient curation workflow for the Arabidopsis literature corpus.

    PubMed

    Li, Donghui; Berardini, Tanya Z; Muller, Robert J; Huala, Eva

    2012-01-01

    TAIR (The Arabidopsis Information Resource) is the model organism database (MOD) for Arabidopsis thaliana, a model plant with a literature corpus of about 39 000 articles in PubMed, with over 4300 new articles added in 2011. We have developed a literature curation workflow incorporating both automated and manual elements to cope with this flood of new research articles. The current workflow can be divided into two phases: article selection and curation. Structured controlled vocabularies, such as the Gene Ontology and Plant Ontology are used to capture free text information in the literature as succinct ontology-based annotations suitable for the application of computational analysis methods. We also describe our curation platform and the use of text mining tools in our workflow. Database URL: www.arabidopsis.org

  16. Lateral root development in Arabidopsis: fifty shades of auxin.

    PubMed

    Lavenus, Julien; Goh, Tatsuaki; Roberts, Ianto; Guyomarc'h, Soazig; Lucas, Mikaël; De Smet, Ive; Fukaki, Hidehiro; Beeckman, Tom; Bennett, Malcolm; Laplaze, Laurent

    2013-08-01

    The developmental plasticity of the root system represents a key adaptive trait enabling plants to cope with abiotic stresses such as drought and is therefore important in the current context of global changes. Root branching through lateral root formation is an important component of the adaptability of the root system to its environment. Our understanding of the mechanisms controlling lateral root development has progressed tremendously in recent years through research in the model plant Arabidopsis thaliana (Arabidopsis). These studies have revealed that the phytohormone auxin acts as a common integrator to many endogenous and environmental signals regulating lateral root formation. Here, we review what has been learnt about the myriad roles of auxin during lateral root formation in Arabidopsis.

  17. Using Arabidopsis to understand centromere function: progress and prospects.

    PubMed

    Copenhaver, Gregory P

    2003-01-01

    Arabidopsis thaliana has emerged in recent years as a leading model for understanding the structure and function of higher eukaryotic centromeres. Arabidopsis centromeres, like those of virtually all higher eukaryotes, encompass large DNA domains consisting of a complex combination of unique, dispersed middle repetitive and highly repetitive DNA. For this reason, they have required creative analysis using molecular, genetic, cytological and genomic techniques. This synergy of approaches, reinforced by rapid progress in understanding how proteins interact with the centromere DNA to form a complete functional unit, has made Arabidopsis one the best understood centromere systems. Yet major problems remain to be solved: gaining a complete structural definition of the centromere has been surprisingly difficult, and developing synthetic mini-chromosomes in plants has been even more challenging.

  18. Study of cis-cinnamic acid in Arabidopsis thaliana.

    PubMed

    Wong, Wai Shing; Guo, Di; Wang, Xiao Li; Yin, Zhi Qi; Xia, Bing; Li, Ning

    2005-01-01

    Trans-cinnamic acid (CA) can be isomerized to cis-CA in Arabidopsis thaliana extract under sunlight. Piperonylic acid treatment of Arabidopsis under ultraviolet (UV) light increased the level of cis-CA in these treated tissues. Similarly, cis-CA was also detected from Oryza sativa seedlings grown under sunlight. These results suggest that cis-CA may occur in planta. Application of cis-CA to seedlings of both wild type Arabidopsis and auxin-insensitive mutants, aux1 and axr2, resulted in nearly identical dose response curves in root growth, indicating that the mode of action by which cis-CA affects plant growth is different from that of auxins. According to root growth inhibition assay, cis-CA is nearly 10 times more active than trans-CA. These results suggest that cis-CA is a unique plant growth regulator but its in vivo function remains to be elucidated.

  19. Chromatin associations in Arabidopsis interphase nuclei.

    PubMed

    Schubert, Veit; Rudnik, Radoslaw; Schubert, Ingo

    2014-01-01

    The arrangement of chromatin within interphase nuclei seems to be caused by topological constraints and related to gene expression depending on tissue and developmental stage. In yeast and animals it was found that homologous and heterologous chromatin association are required to realize faithful expression and DNA repair. To test whether such associations are present in plants we analyzed Arabidopsis thaliana interphase nuclei by FISH using probes from different chromosomes. We found that chromatin fiber movement and variable associations, although in general relatively seldom, may occur between euchromatin segments along chromosomes, sometimes even over large distances. The combination of euchromatin segments bearing high or low co-expressing genes did not reveal different association frequencies probably due to adjacent genes of deviating expression patterns. Based on previous data and on FISH analyses presented here, we conclude that the global interphase chromatin organization in A. thaliana is relatively stable, due to the location of its 10 centromeres at the nuclear periphery and of the telomeres mainly at the centrally localized nucleolus. Nevertheless, chromatin movement enables a flexible spatial genome arrangement in plant nuclei.

  20. Shotgun proteomic analysis of Arabidopsis thaliana leaves.

    PubMed

    Lee, Joohyun; Garrett, Wesley M; Cooper, Bret

    2007-09-01

    Two shotgun tandem MS proteomics approaches, multidimensional protein identification technology (MudPIT) and 1-D gel-LC-MS/MS, were used to identify Arabidopsis thaliana leaf proteins. These methods utilize different protein/peptide separation strategies. Detergents not compatible with MudPIT were used with 1-D gel-LC-MS/MS to help enrich for the detection of membrane-spanning and hydrophobic proteins. By combining the data from all MudPIT and 1-D gel-LC-MS/MS experiments, 2342 nonredundant proteins spanning a broad range of molecular weights and pI values were detected. With the exception of unknown proteins, the distribution of gene ontology (GO) classifications for the detected proteins was similar to that encoded by the genome, which shows that these extraction and separation procedures are useful for a broad proteomic survey of plant cells. Unknown proteins will likely have to be targeted by using additional methods, some of which should be compatible with separation strategies taken here.

  1. Alternative and effective proteomic analysis in Arabidopsis.

    PubMed

    Espagne, Christelle; Martinez, Aude; Valot, Benoît; Meinnel, Thierry; Giglione, Carmela

    2007-10-01

    Various functional genomics platforms are required to define the phenotype associated with a mutant. Global protein analyses may be included in any study. We describe here a rapid method of protein sample preparation and analysis, suitable for all laboratories and using Arabidopsis plantlets as the starting material. This reliable and reproducible method for high yield protein extraction from small amounts of material can be used on even the most recalcitrant tissues. The proteins extracted are suitable for many types of protein analysis, including nondenaturing investigations. This method was validated by a rigorous 2-DE approach, coupled with unambiguous LC-MS/MS identifications featuring strong sequence coverage (average of 26% with eight different peptides/spot protein). The reproducibility of the method was demonstrated by multiple protein identifications from identical series of spots. An interactive map (http://www.isv.cnrsgif.fr/gel2d/), including 435 protein variants showed that (i) 38% of the proteins were yet unreported, (ii) reduced subfractionation, (iii) had frequent protein modifications (average of two spots/protein entry), and (iv) underwent no major proteolytic events other than leader peptide cleavage. Finally, a simple mobility shift method for the large subunit of RuBisCo (LS) in the first dimension made it possible to characterize previously masked protein spots.

  2. Accumulation of coumarins in Arabidopsis thaliana.

    PubMed

    Kai, Kosuke; Shimizu, Bun-ichi; Mizutani, Masaharu; Watanabe, Ken; Sakata, Kanzo

    2006-02-01

    The biosynthesis of coumarins in plants is not well understood, although these metabolic pathways are often found in the plant kingdom. We report here the occurrence of coumarins in Arabidopsis thaliana ecotype Columbia. Considerably high levels of scopoletin and its beta-d-glucopyranoside, scopolin, were found in the wild-type roots. The scopolin level in the roots was approximately 1200nmol/gFW, which was approximately 180-fold of that in the aerial parts. Calli accumulated scopolin at a level of 70nmol/gFW. Scopoletin and scopolin formation were induced in shoots after treatment with either 2,4-dichlorophenoxyacetic acid (at 100microM) or a bud-cell suspension of Fusarium oxysporum. In order to gain insight into the biosynthetic pathway of coumarins in A. thaliana, we analyzed coumarins in the mutants obtained from the SALK Institute collection that carried a T-DNA insertion within the gene encoding the cytochrome P450, CYP98A3, which catalyzes 3'-hydroxylation of p-coumarate units in the phenylpropanoid pathway. The content of scopoletin and scopolin in the mutant roots greatly decreased to approximately 3% of that in the wild-type roots. This observation suggests that scopoletin and scopolin biosynthesis in A. thaliana are strongly dependent on the 3'-hydroxylation of p-coumarate units catalyzed by CYP98A3. We also found that the level of skimmin, a beta-d-glucopyranoside of umbelliferone, was slightly increased in the mutant roots.

  3. Mutants of Arabidopsis thaliana with altered phototropism

    NASA Technical Reports Server (NTRS)

    Khurana, J. P.; Poff, K. L.

    1989-01-01

    Thirty five strains of Arabidopsis thaliana (L.) Heynh. have been identified with altered phototropic responses to 450-nm light. Four of these mutants have been more thoroughly characterized. Strain JK224 shows normal gravitropism and "second positive" phototropism. However, while the amplitude for "first positive" phototropism is the same as that in the wild-type, the threshold and fluence for the maximum response in "first positive" phototropism are shifted to higher fluence by a factor of 20-30. This mutant may represent an alteration in the photoreceptor pigment for phototropism. Strain JK218 exhibits no curvature to light at any fluence from 1 micromole m-2 to 2700 micromoles m-2, but shows normal gravitropism. Strain JK345 shows no "first positive" phototropism, and reduced gravitropism and "second positive" phototropism. Strain JK229 shows no measurable "first positive" phototropism, but normal gravitropism and "second positive" phototropism. Based on these data, it is suggested that: 1. gravitropism and phototropism contain at least one common element; 2. "first positive" and "second positive" phototropism contain at least one common element; and 3. "first positive" phototropism can be substantially altered without any apparent alteration of "second positive" phototropism.

  4. G2 Checkpoint Responses in Arabidopsis

    SciTech Connect

    Britt, Anne

    2013-03-18

    This project focused on the mechanism and biological significance of the G2 arrest response to replication stress in plants. We employed both forward and reverse genetic approaches to identify genes required for this response. A total of 3 different postdocs, 5 undergraduates, and 2 graduate students participated in the project. We identified several genes required for damage response in plants, including homologs of genes previously identified in animals (ATM and ATR), novel, a plant-specific genes (SOG1) and a gene known in animals but previously thought to be missing from the Arabidopsis genome (ATRIP). We characterized the transcriptome of gamma-irradiated plants, and found that plants, unlike animals, express a robust transcriptional response to damage, involving genes that regulate the cell cycle and DNA metabolism. This response requires both ATM and the transcription factor SOG1. We found that both ATM and ATR play a role in meiosis in plants. We also found that plants have a cell-type-specific programmed cell death response to ionizing radiation and UV light, and that this response requires ATR, ATM, and SOG1. These results were published in a series of 5 papers.

  5. Metabolic fluxes in an illuminated Arabidopsis rosette.

    PubMed

    Szecowka, Marek; Heise, Robert; Tohge, Takayuki; Nunes-Nesi, Adriano; Vosloh, Daniel; Huege, Jan; Feil, Regina; Lunn, John; Nikoloski, Zoran; Stitt, Mark; Fernie, Alisdair R; Arrivault, Stéphanie

    2013-02-01

    Photosynthesis is the basis for life, and its optimization is a key biotechnological aim given the problems of population explosion and environmental deterioration. We describe a method to resolve intracellular fluxes in intact Arabidopsis thaliana rosettes based on time-dependent labeling patterns in the metabolome. Plants photosynthesizing under limiting irradiance and ambient CO2 in a custom-built chamber were transferred into a (13)CO2-enriched environment. The isotope labeling patterns of 40 metabolites were obtained using liquid or gas chromatography coupled to mass spectrometry. Labeling kinetics revealed striking differences between metabolites. At a qualitative level, they matched expectations in terms of pathway topology and stoichiometry, but some unexpected features point to the complexity of subcellular and cellular compartmentation. To achieve quantitative insights, the data set was used for estimating fluxes in the framework of kinetic flux profiling. We benchmarked flux estimates to four classically determined flux signatures of photosynthesis and assessed the robustness of the estimates with respect to different features of the underlying metabolic model and the time-resolved data set.

  6. Microgravity effects on Arabidopsis thaliana energy pool

    NASA Astrophysics Data System (ADS)

    Dobrota, C.; Piso, M. I.; Banciu, H.; Keul, A.

    The flexibility of plant bioenergetics helps plants to acclimate to environmental stresses Our work is focused on standard free energy changes for PPi and ATP hydrolysis in order to assess the relative importance of PPi versus ATP as an energy donor in the plant cytosol of Arabidopsis plants exposed to microgravity The results indicated that PPi would be particularly favored as a phosphoryl donor relative to ATP under cytosolic conditions known to accompany stresses Recent researches showed that besides its functions inside the cell ATP may be released to the extracellular milieu where it functions as the primary signaling molecule of a diverse range of physiological processes It seems that extracellular ATP is essential for maintaining plant cell viability We intend to study how the production and the release of ATP is influenced by the microgravity References begin enumerate item Chivasaa S Bongani K Ndimbab W Simonc J Lindseyc K and Slabasc A 2005 Extracellular ATP Functions as an Endogenous External Metabolite Regulating Plant Cell Viability The Plant Cell 17 3019-3034 item Palma D A Blumwald E and Plaxton W C 2000 Upregulation of vacuolar H -translocating pyrophosphatase by phosphate starvation of Brassica napus rapeseed suspension cell cultures FEBS Letters 486 155-158 item Plaxton W C 2004 Plant response to stress Biochemical adaptations to phosphate deficiency In R Goodman ed Encyclopedia of Plant and Crop Science Marcel Dekker Inc N Y end enumerate

  7. Isolation and Suborganellar Fractionation of Arabidopsis Chloroplasts.

    PubMed

    Fl