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Root Samples (root + sample)

Distribution by Scientific Domains

Life Sciences	58%
Medical Sciences	25%
Chemistry	16%

Selected Abstracts

Biogeography of wetland rice methanotrophs

ENVIRONMENTAL MICROBIOLOGY, Issue 4 2010
Claudia Lüke
Summary We focused on the functional guild of methane oxidizing bacteria (MOB) as model organisms to get deeper insights into microbial biogeography. The pmoA gene was used as a functional and phylogenetic marker for MOB in two approaches: (i) a pmoA database (> 4000 sequences) was evaluated to obtain insights into MOB diversity in Italian rice paddies, and paddy fields worldwide. The results show a wide geographical distribution of pmoA genotypes that seem to be specifically adapted to paddy fields (e.g. Rice Paddy Cluster 1 and Rice Paddy Cluster 2). (ii) On the smaller geographical scale, we designed a factorial experiment including three different locations, two rice varieties and two habitats (soil and roots) within each of three rice fields. Multivariate analysis of terminal restriction fragment analysis profiles revealed different community patterns at the three field sites, located 10,20 km apart. Root samples were characterized by high abundance of type I MOB whereas the rice variety had no effect. With the agronomical practice being nearly identical, historical contingencies might be responsible for the field site differences. Considering a large reservoir of viable yet inactive MOB cells acting as a microbial seed bank, environmental conditions might have selected and activated a different subset at a time thereby shaping the community. [source]

Surveys for Beet Necrotic Yellow Vein Virus (the Cause of Rhizomania), other Viruses, and Soil-borne Fungi Infecting Sugar Beet in Syria

JOURNAL OF PHYTOPATHOLOGY, Issue 11-12 2002
A. M. Mouhanna
Abstract Production of sugar beet, the most important source of sugar in Syria, has suffered from many problems in the past, especially from diseases. No previous surveys have been made in Syria for viral diseases and soil-borne fungi of sugar beet. In 1998, samples were collected from plants showing symptoms of virus infection (yellowing, wilting, necrosis and mosaic). Root samples (341) were collected from crops of autumn-sown seed from 115 localities in seven provinces, 173 root samples from spring-sown crops and 39 leaf samples were collected during both seasons. The root samples were tested for the presence of viruses by double antibody sandwich-enzyme-linked immunosorbent assay (ELISA) and triple antibody sandwich-ELISA, and for soil-borne fungi by red plate (Rose Bengal) dishes. We have shown for the first time the presence of Beet necrotic yellow vein virus, Beet soil-borne virus, Beet yellows virus and Beet mild yellowing virus in Syrian sugar beet fields in which Rhizoctonia sp. and Fusarium sp. were also widely distributed. [source]

Activity and composition of methanotrophic bacterial communities in planted rice soil studied by flux measurements, analyses of pmoA gene and stable isotope probing of phospholipid fatty acids

ENVIRONMENTAL MICROBIOLOGY, Issue 2 2008
Minita Shrestha
Summary Methanotrophs in the rhizosphere of rice field ecosystems attenuate the emissions of CH4 into the atmosphere and thus play an important role for the global cycle of this greenhouse gas. Therefore, we measured the activity and composition of the methanotrophic community in the rhizosphere of rice microcosms. Methane oxidation was determined by measuring the CH4 flux in the presence and absence of difluoromethane as a specific inhibitor for methane oxidation. Methane oxidation started on day 24 and reached the maximum on day 32 after transplantation. The total methanotrophic community was analysed by terminal restriction fragment length polymorphism (T-RFLP) and cloning/sequencing of the pmoA gene, which encodes a subunit of particulate methane monooxygenase. The metabolically active methanotrophic community was analysed by stable isotope probing of microbial phospholipid fatty acids (PLFA-SIP) using 13C-labelled CH4 directly added to the rhizospheric region. Rhizospheric soil and root samples were collected after exposure to 13CH4 for 8 and 18 days. Both T-RFLP/cloning and PLFA-SIP approaches showed that type I and type II methanotrophic populations changed over time with respect to activity and population size in the rhizospheric soil and on the rice roots. However, type I methanotrophs were more active than type II methanotrophs at both time points indicating they were of particular importance in the rhizosphere. PLFA-SIP showed that the active methanotrophic populations exhibit a pronounced spatial and temporal variation in rice microcosms. [source]

Chemical speciation and cellular deposition of lead in Sesbania drummondii

ENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 9 2004
Nilesh C. Sharma
Abstract The internalized speciation of lead in roots and leaves of Sesbania drummondii, a lead hyperaccumulator, grown in lead nitrate solution was studied using x-ray absorption near-edge structure and extended x-ray absorption fine structure. Lead was predominantly present as lead acetate in both plant tissues. The other dominant forms of accumulation were lead,sulfur compounds. Whereas lead sulfate and sulfide were found in leaves, only lead sulfide was detected in root samples. These observations indicate that S. drummondii is able to biotransform lead nitrate in the nutrient solution to lead acetate and sulfate in its tissues. Complexation with acetate and sulfate may be a lead detoxification strategy in this plant. Transmission-electron microscopy revealed the pattern of lead distribution in and around the cells. Dense distributions of lead grains were detected in root cell walls and plasma membranes, whereas evidence for vacuolar transport of lead was noticed in the stem cells. [source]

Phylogenetic diversity of non-nodulating Rhizobium associated with pine ectomycorrhizae

FEMS MICROBIOLOGY ECOLOGY, Issue 3 2009
Megumi Tanaka
Abstract Most Rhizobium species described are symbionts that form nodules on legume roots; however, non-nodulating strains of Rhizobium are also widespread in nature. Unfortunately, knowledge of non-nodulating Rhizobium is quite limited compared with nodulating Rhizobium. Here, we studied the phylogenetic diversity of Rhizobium species that inhabit Japanese red pine roots (Pinus densiflora). Because fine roots of pine trees are usually colonized by ectomycorrhizal fungi in nature, we mainly used ectomycorrhizal root tips for bacterial isolation. Out of 1195 bacteria isolated from 75 independent root samples from the field and greenhouse experiments, 102 isolates were confirmed to be Rhizobium following partial 16S rRNA gene analysis. Rhizobium species were occasionally dominant in culturable bacterial communities, whereas no Rhizobium species were isolated from the soil itself. Molecular phylogenetic analyses using 16S rRNA, atpD, and recA gene sequences revealed that isolated Rhizobium strains were phylogenetically diverse and that several were distantly related to known Rhizobium species. Considering that a single species of pine is associated with unique and phylogenetically diverse Rhizobium populations, we should pay more attention to non-nodulating strains to better understand the diversity, ecology, and evolution of the genus Rhizobium and plant,Rhizobium associations. [source]

Morphology, chemical structure and diffusion processes of root surface after Er:YAG and Nd:YAG laser irradiation

JOURNAL OF CLINICAL PERIODONTOLOGY, Issue 6 2001
B. Ga
Abstract Objectives: The aim of this in vitro study was to evaluate the effects of Er:YAG and Nd:YAG lasers on morphology, chemical structure and diffusion processes of the root surface. Material and methods: 60 root samples were irradiated for 1 min each either with 60 mJ/p, 80mJ/p and 100mJ/p using Er:YAG laser or with 0.5W, 1.0W and 1.5W using Nd:YAG laser. Scanning electron microscopy (SEM) was used to determine the morphology, infrared (IR) spectroscopy to assess the alterations in chemical structure and one dimensional electron paramagnetic resonance imaging (1-D EPRI) was used to estimate the diffusion coefficients in dental root samples. Results: Er:YAG laser treatment resulted in deep crater formation with exposed dentin. Morphological alterations of root surface after Nd:YAG laser irradiation included cracks, crater formation, meltdown of the root mineral and resolidified porous globules formation. Er:YAG laser failed to alter the intensity of Amide peaks I, II or III. In contrast, treatment with Nd:YAG laser, using the highest power setting of 1.5W, reduced the intensity of Amide peak II and III in comparison to the control. The diffusion coefficients were increased significantly in all Er:YAG and Nd:YAG treated root samples. Conclusion: This study demonstrated that Er:YAG laser influences only on morphology and diffusion processes of root surfaces, while Nd:YAG laser also alters the chemical structure of root proteins. Zusammenfassung Ziele: Das Ziel dieser in vitro Studie war es, die Wirkung von Er:YAG- und Nd:YAG-Laser auf die Morphologie, chemische Struktur und die Diffusionsprozesse zu evaluieren. Material und Methoden: 60 Proben von Wurzeln wurden für eine Minute entweder mit einem Er:YAG-Laser und 60 mJ/p, 80 mJ/p und 100 mJ/p oder einem Nd:YAGLaser und 0.5 W, 1.0 W und 1.5 W bestrahlt. Die Rasterelektronenmikroskopie (REM) wurde verwendet um die Morphologie zu bestimmen, Infrarotspektroskopie (IR) zur Messung der Veränderung in der chemischen Struktur und die eindimensionale paramagnetische Elektronenresonanz-Bildgebung (1-D EPRI) wurde verwendet um die Diffusions-Koeffizienten in den dentalen Wurzelproben abzuschätzen. Ergebnisse: Die Behandlung mit dem Er: YAG-Laser resultierte in der Ausbildung tiefer Krater mit exponiertem Dentin. Die morphologischen Veränderungen der Wurzeloberfläche nach Bestrahlung mit dem Nd: YAG-Laser waren Brüche, Kraterbildung, Aufschmelzen des Wurzelminerals und Bildung wiederverfestigter poröser Globuli. Mit dem Er:YAG-Laser gelang es nicht die Intensität der Amid-peaks I, II oder III zu verändern. Im Gegensatz dazu reduzierte die Behandlung mit dem Nd:YAG-Laser im Vergleich mit der Kontrolle bei der höchsten Leistungseinstellung von 1.5 W die Intensität der Amid-Peaks II und III. In allen mit Er: YAG und Nd:YAG behandelten Wurzelproben waren die Wurzeldiffusionskoeffizienten signifikant erhöht. Schlussfolgerung: Diese Studie demonstrierte, dass der Er:YAG-Laser nur die Morphologie und die Diffusionsprozesse der Wurzeloberfläche beeinflusst, während der Nd: YAG-Laser auch die chemische Struktur der Wurzelproteine verändert. Résumé Morphologie, structure chimique et processus de diffusion de surfaces radiculaires après irradiation au lasers Er:YAG et Nd:YAG But: Le but de cette étude in vitro était d'évaluer les effets des lasers Er:YAG et Nd:YAG sur la morphologie, la structure chimique et les processus de diffusion des surfaces radiculaires. Matériaux et méthodes: 60 échantillons de racines furent irradiés pendant 1 min chacun par 60 mJ/p, 80 mJ/p et 100 mJ/p avec le laser Er:YAG ou par 0.5 W, 1.0 W et 1.5 W avec le laser Nd:YAG. La microscopie électronique à balayage (SEM) a été utilisée pour déterminer la morphologie, la spectroscopie infra rouge pour mettre en évidence les altérations de la structure chimique et l'imagerie en une dimension par résonnance magnétique électronique (1-DEPRI) fut utilisée pour estimer les coefficients de diffusion dans les échantillons de racines dentaires. Résultats: Le traitement au laser Er:YAG entrainait la formation de cratères profonds avec de la detine exposée. Les altérations morphologiques de la surface radiculaire après irradiation au laser Nd:YAG prenaient la forme de félures, de cratères, fusion du minéral radiculaire et formation de globules poreux resolidifiés. Le laser Er:YAG n'arrivait pas à altérer l'intensité des pics Amide I, II our III. Au contraire, le traitement au laser Nd:YAG, en utilisant la plus haute puissance de 1.5 W, réduisait l'intensité des pics Amide II et III, par rapport au contrôle. Les coefficients de diffusion étaient significativement augmentés pour toutes les racines traitées par les lasers Er:YAG et Nd:YAG. Conclusions: Cette étude démontre que le laser Er:YAG a une influence sur seulement la morphologie et les processus de diffusion des surfaces radiculaires alors que le laser Nd:YAG modifie également la structure chinique des protéines radiculaires. [source]

Surveys for Beet Necrotic Yellow Vein Virus (the Cause of Rhizomania), other Viruses, and Soil-borne Fungi Infecting Sugar Beet in Syria

Mapping the intake of different elements in vegetal tissues by dual-energy X-ray imaging at Da,ne synchrotron light source

MICROSCOPY RESEARCH AND TECHNIQUE, Issue 3 2008
L. Reale
Abstract This article reports on the first utilization of the soft X-ray beamline at the Da,ne synchrotron light source for mapping the intake of different elements in plant tissues. As a test, the method of dual-energy X-ray microradiography was applied to the investigation of the natural sulfur content in dried leaf and root samples. Our ultimate goal was to monitor the pollutant lead and its intake, which was added in controlled doses to the hydroponic medium of laboratory-controlled samples of vegetal species. The results obtained by the nondestructive X-ray radiographic analysis are compared to the values of concentrations determined by a standard chemical analysis utilizing atomic absorption spectroscopy. From this comparison the validity of the X-ray detection of heavy metals in biological samples has been confirmed. The superposition of the dual energy results on the simple planar radiography shows the representation of the pollutant intake directly on the sample structures. It should be pointed out that this method, developed here for plant root and leaves could be applied to any biological sample of interest, but the preparation and observation conditions necessitate different strategies according to the type of sample under analysis. Microsc. Res. Tech., 2008. © 2007 Wiley-Liss, Inc. [source]

Genetic diversity of the arbuscular mycorrhizal fungus Glomus intraradices as determined by mitochondrial large subunit rRNA gene sequences is considerably higher than previously expected

NEW PHYTOLOGIST, Issue 2 2008
Boris Börstler
Summary ,,Glomus intraradices is a widespread arbuscular mycorrhizal fungus (AMF), which has been found in an extremely broad range of habitats, indicating a high tolerance for environmental factors and a generalist life history strategy. Despite this ecological versatility, not much is known about the genetic diversity of this fungal species across different habitats or over large geographic scales. ,,A nested polymerase chain reaction (PCR) approach for the mitochondrial rRNA large subunit gene (mtLSU), distinguished different haplotypes among cultivated isolates of G. intraradices and within mycorrhizal root samples from the field. ,,From analysis of 16 isolates of this species originating from five continents, 12 mitochondrial haplotypes were distinguished. Five additional mtLSU haplotypes were detected in field-collected mycorrhizal roots. Some introns in the mtLSU region appear to be stable over years of cultivation and are ancestral to the G. intraradices clade. ,,Genetic diversity within G. intraradices is substantially higher than previously thought, although some mtLSU haplotypes are widespread. A restriction fragment length polymorphism approach also was developed to distinguish mtLSU haplotypes without sequencing. Using this molecular tool, intraspecific genetic variation of an AMF species can be studied directly in field plants. [source]

Polyphenolic composition of roots and petioles of Rheum rhaponticum L.

PHYTOCHEMICAL ANALYSIS, Issue 2 2009
Tõnu Püssa
Abstract Introduction Various species of the genus Rheum (Polygonaceae) are known for their high content of medicinally important hydroxyanthraquinones. However, little information is available concerning the polyphenolic composition of garden or dietary rhubarb Rheum rhaponticum L. (R. rhaponticum). Objective Determination of further polyphenols in the roots and petioles of R. rhaponticum. Methodology The dried plant material was extracted with 10-fold excess (v/w) of methanol and subsequently diluted five times with methanol,water (1:1) and analysed by reversed-phase liquid chromatography using tandem UV-photodiode array and mass selective detection (RP-HPLC-UV-ESI/MS2). Polyphenols were identified using either HPLC-ESI/MS2 data obtained for respective commercial standards or by comparison of a parent ion fragmentation picture with the respective MS2 spectrum from the literature. Results The roots of R. rhaponticum were very rich in various hydroxystilbenes and contained four main substance groups ,derivatives of trans -piceatannol, trans -resveratrol, trans -rhapontigenin and trans -deoxyrhapontigenin. Additionally, pterostilbene acetylglucosides and a number of hydroxyanthraquinones and their glycosides were identified in the root samples. The profile of polyphenols in the petioles of R. rhaponticum was similar to that of the roots but the content of individual substances was remarkably lower. The petioles of the R. rhaponticum additionally contained significant amounts of derivatives of flavonol quercetin, which is a good antioxidant. Conclusion The study has shown that roots of R. rhaponticum contain a wide variety of hydroxystilbenes and deserve further consideration as a source of medicinally interesting compounds. Copyright © 2008 John Wiley & Sons, Ltd. [source]

Study on the enantiomeric ratio of the pharmaceutical substances alkannin and shikonin

BIOMEDICAL CHROMATOGRAPHY, Issue 10 2004
A. N. Assimopoulou
Abstract The chiral pair alkannin and shikonin (A/S) are potent pharmaceutical substances with a wide spectrum of biological activity; their enantiomeric ratio does not in,uence the major biological activity studied hitherto. Nevertheless, in pharmaceutical development and approval of chiral drugs from the Health and Regulatory Authorities, full documentation of methods of analysis of enantiomeric drugs, is required in order to evaluate the enantiomeric purity of starting materials and ,nal products and to control the stability of enantiomers in pharmaceutical formulations under several experimental conditions. In the present study, the enantiomeric ratio of A/S was determined in several commercial samples of alkannin and shikonin and also the proportion of A/S derivatives in several Alkanna root samples, which are all used as active ingredients in pharmaceuticals. Light and air proved not to in,uence the enantiomeric ratio of A/S on a shikonin commercial sample, and temperature also did not alter the A/S ratio on shikonin and alkannin commercial samples. Microencapsulation of alkannin and shikonin commercial samples in ethylcellulose microspheres and also molecular inclusion of a shikonin commercial sample in , -hydroxypropyl-cyclodextrin, which are used as drug delivery systems, did not alter the A/S enantiomeric ratio. Copyright © 2004 John Wiley & Sons, Ltd. [source]