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Library Construction (library + construction)
Selected AbstractsEvolution of a chlorobenzene degradative pathway among bacteria in a contaminated groundwater mediated by a genomic island in RalstoniaENVIRONMENTAL MICROBIOLOGY, Issue 3 2003Tina Andrea Müller Summary The genetic structure of two Ralstonia spp., strain JS705 and strain JS745, isolated from the same groundwater aquifer, was characterized with respect to the degradation capacities for toluene and chlorobenzene degradation. Cosmid library construction, cloning, DNA sequencing and mating experiments indicated that the genes for chlorobenzene degradation in strain JS705 were a mosaic of the clc genes, previously described for Pseudomonas sp. strain B13, and a 5 kb fragment identical to strain JS745. The 5 kb fragment identical to both JS705 and JS745 was flanked in JS705 by one complete and one incomplete insertion (IS) element. This suggested involvement of the IS element in mobilizing the genes from JS745 to JS705, although insertional activity of the IS element in its present configuration could not be demonstrated. The complete genetic structure for chlorobenzene degradation in strain JS705 resided on a genomic island very similar to the clc element (Ravatn, R., Studer, S., Springael, D., Zehnder, A.J., van der Meer, J.R. 1998. Chromosomal integration, tandem amplification, and deamplification in Pseudomonas putida F1 of a 105-kilobase genetic element containing the chlorocatechol degradative genes from Pseudomonas sp. strain B13. J Bacteriol 180: 4360,4369). The unique reconstruction of formation of a metabolic pathway through the activity of IS elements and a genomic island in the chlorobenzene-degrading strain JS705 demonstrated how pathway evolution can occur under natural conditions in a few ,steps'. [source] One-Pot Three-Step Synthesis of Naphtho[2,3- a]carbazole- 5,13-diones using a Tandem Radical Alkylation,Cyclization, Aromatization Reaction SequenceADVANCED SYNTHESIS & CATALYSIS (PREVIOUSLY: JOURNAL FUER PRAKTISCHE CHEMIE), Issue 5 2010Chunyong Ding Abstract A three-step, one-pot tandem reaction including radical nucleophilic alkylation/cyclization/aromatization was developed using 0.3 equivalents of silver(I) acetate (AgOAc) as the catalyst and 2 equivalents of ammonium persulfate [(NH4)2S2O8] as the oxidant. This strategy is highly efficient for the assembly of pentacyclic complex carbazoles from aryl-fused bromobenzoquinones and indol-3-ylpropanoic acid acids in 52,72% overall yields (three steps). This new approach provides a significant improvement over the previously reported methods and would greatly facilitate analog library construction of pentacyclic complex carbazoles and benefit further biological evaluation of these compounds. [source] Progress in the Study of Molecular Genetic Improvements of Poplar in ChinaJOURNAL OF INTEGRATIVE PLANT BIOLOGY, Issue 9 2006Shan-Zhi Lin Abstract The poplar is one of the most economically important and intensively studied tree species owing to its wide application in the timber industry and as a model material for the study of woody plants. The natural resource of poplars in China is replete. Over the past 10 years, the application of molecular biological techniques to genetic improvements in poplar species has been widely studied in China. Recent advances in molecular genetic improvements of poplar, including cDNA library construction, gene cloning and identification, genetic engineering, gene expression, genetic linkage map construction, mapping of quantitative trait loci (QTL) and molecular-assisted selection, are reviewed in the present paper. In addition, the application of modern biotechnology to molecular improvements in the genetic traits of the poplar and some unsolved problems are discussed. (Managing editor: Li-Hui Zhao) [source] The MAGi RNA extraction method: a highly efficient and simple procedure for fresh and dry plant tissuesJOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE, Issue 1 2009e Gül Ince Abstract BACKGROUND: Samples from different plant species, different organs or tissues at different times of the year, usually show great differences in their cell compositions, pH, and the endogenous RNase activities, decreasing the RNA yield and quality. RESULTS: In this study we describe a reagent and a simple total RNA isolation method for plant organs, tissues and dry seeds. The RNA extraction reagent (MAGi) is non-toxic and can be stored at room temperature for several months to years. The principle of the total RNA extraction is that tissues are lysed in extraction solution with the aid of mortar homogenization,maceration, and cellular proteins, polysaccharides and DNA are removed from the RNA. We tested the reported method on more than 16 different types of plant seed and 15 different tissues and organs of pepper. CONCLUSION: The RNA extraction procedure reported in the present study greatly reduces the time required to isolate dry seed total RNA and other tissues by more than half as compared with the previously reported methods. The range of typical RNA yield and quality represents a significant improvement over existing protocols. The quality is high enough to be considered as suitable method for RT-PCR, cDNA library construction and microarray gene expression studies. Copyright © 2008 Society of Chemical Industry [source] SMILIB: Rapid Assembly of Combinatorial Libraries in SMILES NotationMOLECULAR INFORMATICS, Issue 7 2003Andreas Schüller Abstract A software tool was developed for fast combinatorial library enumeration (SMILIB). Its particular features are its simplicity to use, high flexibility in constructing combinatorial libraries and high speed of library construction. SMILIB offers the possibility to construct very large combinatorial libraries using the flexible and portable SMILES format. Libraries are generated at rates of approximately 30,000 molecules per minute. Combinatorial building blocks are attached to scaffolds by means of linkers rather than to concatenate them directly. This allows for creation of easily customized libraries using linkers of different size and chemical nature. A web interface for a limited web-based version of the software is available at URL: www.modlab.de. An unlimited binary version of SMILIB for command line execution on Linux systems is available from this URL. [source] Isolation of high-quality RNA from white spruce tissue using a three-stage purification method and subsequent cloning of a transcript from the PR-10 gene familyPHYTOCHEMICAL ANALYSIS, Issue 4 2003Nathalie Mattheus Abstract Isolation of PinmIII cDNA homologues from white spruce tissues required a rigorous RNA extraction protocol developed following assessment of three previously reported conifer RNA extraction protocols. Total RNA was extracted via several purification steps designed to minimize binding of phenolics to nucleic acids and was then subjected to caesium chloride ultra-centrifugation. This procedure produced consistently high-quality, intact RNA from both needles and roots with spectrophotometric ratios of approximately 2.0 for both 260/280,nm and 260/230,nm. Total RNA was obtained from the roots of cold-hardened white spruce seedlings for cDNA library construction. More than 2 million recombinant phage particles were generated from 5,µg of a poly(A)+RNA fraction, and ca. 1.3 million cDNA particles were amplified for storage. Approximately 500,000 primary recombinant clones were screened with an heterologous PinmIII cDNA sequence yielding a unique clone, picg1, that was very similar to members of the PR10 gene family. Copyright © 2003 John Wiley & Sons, Ltd. [source] Molecular Evidence that Phylogenetically Diverged Ciliates Are Active in Microbial Mats of Deep-Sea Cold-Seep SedimentTHE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 1 2010KIYOTAKA TAKISHITA ABSTRACT. Cold seeps are areas of the seafloor where hydrogen sulfide- and methane-rich fluid seepage occurs, often sustaining chemosynthetic ecosystems. It is well known that both archaea and bacteria oxidize sulfides and methane to produce chemical energy and that several endemic animals use this energy to thrive in cold seeps. On the other hand, there is little knowledge regarding diversity and ecology of microbial eukaryotes in this ecosystem. In this study we isolated environmental RNA and DNA from microbial mats of cold-seep sediment in Sagami Bay, Japan, and retrieved eukaryotic small-subunit ribosomal RNA sequences with polymerase chain reaction methods followed by clone library construction. Most RNA-derived clones obtained were from ciliates, although DNA-derived clones were mainly from the fungus Cryptococcus curvatus, suggesting that ciliates are active in the environment. The ciliate sequences were phylogenetically diverse, and represented eight known class lineages as well as undesignated lineages. Because most ciliates are bacterivorous, it is highly likely that the ciliates for which sequences were recovered play a role in the food web of this ecosystem as grazers of microbial mats. In addition, given that the environment studied is under highly reduced (anoxic) conditions, based on the prokaryotic community structure deduced from T-RFLP profiles, the ciliates detected may be obligatory or facultative anaerobes. [source] Broad host range vectors for stable genomic library constructionBIOTECHNOLOGY & BIOENGINEERING, Issue 1 2006Michael D. Lynch Abstract We describe the construction of 36 stable vectors for genomic library construction in gram-negative species. These vectors contain the pBBR1 replicon that has been shown to stably replicate in every gram-negative species tested. The plasmids also contain bidirectional, rho-independent transcriptional terminators flanking the multiple cloning site, which allows for greater insert stability, and thus, greater genomic representation. Each vector varies in its antibiotic resistance cassette, mobilization function, and promoter used to express insert sequences. These vectors should prove useful in the screening of highly representational genomic libraries in a broad variety of gram-negative species. © 2006 Wiley Periodicals, Inc. [source] ChemInform Abstract: Organocatalyzed Enantioselective One-Pot Three-Component Access to Indoloquinolizidines by a Michael Addition,Pictet,Spengler Sequence.CHEMINFORM, Issue 36 2010Xiaoyu Wu Abstract The title method is potentially useful in combinatorial library construction and the synthesis of natural alkaloids. [source] | |||||||||||||