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Sample records for t-rflp aflp risa

  1. RAPD, RFLP, T-RFLP, AFLP, RISA

    International Nuclear Information System (INIS)

    Denman, S.E.; McSweeney, C.S.; Makoto Mitsumori

    2005-01-01

    Traditional methods of identifying microorganisms through culturing and microscopy techniques can be somewhat tedious and time consuming. A faster and more accurate method for identifying microorganisms is through the sequencing of its ribosomal gene. Classification of microorganisms by ribosomal gene sequencing has become widely accepted within the scientific community. Although this method is quite definitive in its ability to identify the microorganism being studied, it usually involves a pure culture and then the cloning and sequencing of its ribosomal gene. In order to look at complex communities and uncultured microorganisms, many researches have removed the culturing step and moved towards the generation of 16S clone libraries. Data generated from numerous 16S clone libraries from countless environments have produced databases full of ribosomal sequences that may have never been gathered if culturing of the microorganism had been a prerequisite. Ribosomal clone libraries are still quite time consuming, especially if one is interested in detecting differences between complex community structures under varying conditions, such as the effect, diet can impose on the rumen microbial community. Rapid screening methods that allow for the presentation of phylogenetic ribosomal diversity patterns from complex communities in an easy-to-interpret and reproducible manner have all benefited from the knowledge gained from ribosomal clone libraries. Restriction fragment length polymorphism (RFLP) and terminal restriction fragment length polymorphism (T-RFLP) are two such techniques that will be described in this chapter. Other methods such as ribosomal intergenic spacer analysis (RISA), which determines diversity through differences, found in the transcribed spacer region between the highly conserved ribosomal genes can also be employed. RISA is a particularly powerful tool for attempting to discriminate between closely related species and strains. Two methods that do not

  2. Semi-automated genetic analyses of soil microbial communities: comparison of T-RFLP and RISA based on descriptive and discriminative statistical approaches.

    Science.gov (United States)

    Hartmann, Martin; Frey, Beat; Kölliker, Roland; Widmer, Franco

    2005-06-01

    Cultivation independent analyses of soil microbial community structures are frequently used to describe microbiological soil characteristics. This approach is based on direct extraction of total soil DNA followed by PCR amplification of selected marker genes and subsequent genetic fingerprint analyses. Semi-automated genetic fingerprinting techniques such as terminal restriction fragment length polymorphism (T-RFLP) and ribosomal intergenic spacer analysis (RISA) yield high-resolution patterns of highly diverse soil microbial communities and hold great potential for use in routine soil quality monitoring, when rapid high throughput screening for differences or changes is more important than phylogenetic identification of organisms affected. Our objective was to perform profound statistical analysis to evaluate the cultivation independent approach and the consistency of results from T-RFLP and RISA. As a model system, we used two different heavy metal treated soils from an open top chamber experiment. Bacterial T-RFLP and RISA profiles of 16S rDNA were converted into numeric data matrices in order to allow for detailed statistical analyses with cluster analysis, Mantel test statistics, Monte Carlo permutation tests and ANOVA. Analyses revealed that soil DNA-contents were significantly correlated with soil microbial biomass in our system. T-RFLP and RISA yielded highly consistent and correlating results and both allowed to distinguish the four treatments with equal significance. While RISA represents a fast and general fingerprinting method of moderate cost and labor intensity, T-RFLP is technically more demanding but offers the advantage of phylogenetic identification of detected soil microorganisms. Therefore, selection of either of these methods should be based on the specific research question under investigation.

  3. AFLP

    African Journals Online (AJOL)

    AJL

    2012-05-29

    May 29, 2012 ... 3Institute of Medicinal Plants (IMP), Tehran, Iran. 4Agricultural Biotechnology Research Institute, ... Hyoscyamus sp. is one of the most important medicinal plants belonging to the Solanaceae family. ..... et al., 2006) and Matricaria chamomilla (Solouki et al.,. 2008). In conclusion, AFLP and retro/AFLP data ...

  4. Tools for T-RFLP data analysis using Excel.

    Science.gov (United States)

    Fredriksson, Nils Johan; Hermansson, Malte; Wilén, Britt-Marie

    2014-11-08

    Terminal restriction fragment length polymorphism (T-RFLP) analysis is a DNA-fingerprinting method that can be used for comparisons of the microbial community composition in a large number of samples. There is no consensus on how T-RFLP data should be treated and analyzed before comparisons between samples are made, and several different approaches have been proposed in the literature. The analysis of T-RFLP data can be cumbersome and time-consuming, and for large datasets manual data analysis is not feasible. The currently available tools for automated T-RFLP analysis, although valuable, offer little flexibility, and few, if any, options regarding what methods to use. To enable comparisons and combinations of different data treatment methods an analysis template and an extensive collection of macros for T-RFLP data analysis using Microsoft Excel were developed. The Tools for T-RFLP data analysis template provides procedures for the analysis of large T-RFLP datasets including application of a noise baseline threshold and setting of the analysis range, normalization and alignment of replicate profiles, generation of consensus profiles, normalization and alignment of consensus profiles and final analysis of the samples including calculation of association coefficients and diversity index. The procedures are designed so that in all analysis steps, from the initial preparation of the data to the final comparison of the samples, there are various different options available. The parameters regarding analysis range, noise baseline, T-RF alignment and generation of consensus profiles are all given by the user and several different methods are available for normalization of the T-RF profiles. In each step, the user can also choose to base the calculations on either peak height data or peak area data. The Tools for T-RFLP data analysis template enables an objective and flexible analysis of large T-RFLP datasets in a widely used spreadsheet application.

  5. Using terminal restriction fragment length polymorphism (T-RFLP) to identify mycorrhizal fungi: a methods review.

    Science.gov (United States)

    Dickie, I A; FitzJohn, R G

    2007-06-01

    Terminal restriction fragment length polymorphism (T-RFLP) is an increasingly widely used technique in mycorrhizal ecology. In this paper, we review the technique as it is used to identify species of mycorrhizal fungi and distinguish two different versions of the technique: peak-profile T-RFLP (the original version) and database T-RFLP. We define database T-RFLP as the use of T-RFLP to identify individual species within samples by comparison of unknown data with a database of known T-RFLP patterns. This application of T-RFLP avoids some of the pitfalls of peak-profile T-RFLP and allows T-RFLP to be applied to polyphyletic functional groups such as ectomycorrhizal fungi. The identification of species using database T-RFLP is subject to several sources of potential error, including (1) random erroneous matches of peaks to species, (2) shared T-RFLP profiles across species, and (3) multiple T-RFLP profiles within a species. A mathematical approximation of the risk of the first type of error as a function of experimental parameters is discussed. Although potentially less accurate than some other methods such as clone libraries, the high throughput of database T-RFLP permits much greater replication and may, therefore, be preferable for many ecological questions, particularly when combined with other techniques such as cloning.

  6. Conditioners and significance of t-RFLP profile of the assemblage of ...

    African Journals Online (AJOL)

    Following an increased interest in management practices designed to reduce posed phytotoxicity during phytoremediation experiments, crude oil polluted soil and variants from conditioners-aided phytoremediation experiment were subjected to terminal restriction fragment polymorphism (t-RFLP) to evalute the biodiversity ...

  7. Impact of T-RFLP data analysis choices on assessments of microbial community structure and dynamics.

    Science.gov (United States)

    Fredriksson, Nils Johan; Hermansson, Malte; Wilén, Britt-Marie

    2014-11-08

    Terminal restriction fragment length polymorphism (T-RFLP) analysis is a common DNA-fingerprinting technique used for comparisons of complex microbial communities. Although the technique is well established there is no consensus on how to treat T-RFLP data to achieve the highest possible accuracy and reproducibility. This study focused on two critical steps in the T-RFLP data treatment: the alignment of the terminal restriction fragments (T-RFs), which enables comparisons of samples, and the normalization of T-RF profiles, which adjusts for differences in signal strength, total fluorescence, between samples. Variations in the estimation of T-RF sizes were observed and these variations were found to affect the alignment of the T-RFs. A novel method was developed which improved the alignment by adjusting for systematic shifts in the T-RF size estimations between the T-RF profiles. Differences in total fluorescence were shown to be caused by differences in sample concentration and by the gel loading. Five normalization methods were evaluated and the total fluorescence normalization procedure based on peak height data was found to increase the similarity between replicate profiles the most. A high peak detection threshold, alignment correction, normalization and the use of consensus profiles instead of single profiles increased the similarity of replicate T-RF profiles, i.e. lead to an increased reproducibility. The impact of different treatment methods on the outcome of subsequent analyses of T-RFLP data was evaluated using a dataset from a longitudinal study of the bacterial community in an activated sludge wastewater treatment plant. Whether the alignment was corrected or not and if and how the T-RF profiles were normalized had a substantial impact on ordination analyses, assessments of bacterial dynamics and analyses of correlations with environmental parameters. A novel method for the evaluation and correction of the alignment of T-RF profiles was shown to reduce

  8. The influence of the cage system and colonisation of Salmonella Enteritidis on the microbial gut flora of laying hens studied by T-RFLP and 454 pyrosequencing

    DEFF Research Database (Denmark)

    Nordentoft, Steen; Mølbak, Lars; Bjerrum, Lotte Bjerrum

    2011-01-01

    , furnished cage or aviary), were compared using Terminal Restriction Fragment Length Polymorphism (T-RFLP). The distribution of genera in the microbiota in caecum was furthermore described by next generation sequencing of 16S rDNA libraries. RESULTS: Hens in the same cage type developed similar T-RFLP...

  9. Community analysis of preservative-treated southern pine (Pinus spp.) using terminal restriction fragment length polymorphism (T-RFLP) analysis

    Science.gov (United States)

    Grant T. Kirker; M. Lynn Prewitt; Walter J. Diehl; Susan V. Diehl

    2012-01-01

    The effects of wood preservatives on the bacterial community in southern yellow pine were assessed by the molecular method ‘terminal restriction fragment length polymorphism’ (T-RFLP). Stakes, treated with 0.25 % and 0.37 % ammoniacal copper quat (ACQ-C), 0.1 % and 0.25 % chlorothalonil (CTN), 0.1 % and 0.25 % CTN with 2 % butylated hydroxytoluene (BHT), and 2 % BHT...

  10. Relative diversity and community structure analysis of rumen protozoa according to T-RFLP and microscopic methods.

    Science.gov (United States)

    Tymensen, Lisa; Barkley, Cindy; McAllister, Tim A

    2012-01-01

    Protozoa are common inhabitants of the rumen where they play roles in host nutrition and methanogenesis. Knowledge of how changes in the composition of protozoa communities affect these processes is limited in part due to a lack of efficient methods for protozoa community analysis. In this study, a terminal-restriction fragment length polymorphism (T-RFLP) assay targeting the 18S rRNA gene was developed for comparative analysis of rumen protozoa communities. Comparison of diversity and structure of protozoa communities from hay-fed versus silage/grain-fed cattle via T-RFLP analysis yielded similar overall results to microscopy analysis. According to both methods, Entodinium spp. were more abundant in the silage/grain-fed cattle and protozoa diversity (as calculated using the Shannon index) was higher for the hay-fed cattle due to greater species evenness. Type B protozoa were more prevalent in the hay-fed cattle, whereas Type A protozoa were more prevalent in the silage/grain-fed cattle. Analysis of similarity (ANOSIM) indicated that the protozoa communities from hay-fed and silage/grain-fed cattle were different, and multivariate analysis indicated that pen mates (i.e., cattle fed the same diet and housed together) tended to have similar protozoa communities types. In summary, we present a T-RFLP method for analyzing rumen protozoa communities which complements traditional microscopy approaches but has the advantage of being amenable to high-throughput. Copyright © 2011. Published by Elsevier B.V.

  11. De la risa y la sonrisa

    Directory of Open Access Journals (Sweden)

    Ernesto Cortés Ahumada

    1963-01-01

    Full Text Available Nada anda tan incierto en el juicio de las gentes como lo que pretende ser más cierto. Obsérvese, por ejemplo, la seguridad, la certeza casi religiosa con que se habla de cuanto al hombre se refiere: inteligencia, lógica, memoria, intuición, sentimiento, risa, sonrisa, etc.

  12. Using Terminal Restriction Fragment Length Polymorphism (T-RFLP) Analysis to Assess Microbial Community Structure in Compost Systems

    Science.gov (United States)

    Tiquia, Sonia M.

    Terminal restriction fragment length polymorphism (T-RFLP) analysis of PCR-amplified genes is a widely used fingerprinting technique in composting systems. This analysis is based on the restriction endonuclease digestion of fluorescently end-labeled PCR products. The digested product is mixed with a DNA size standard, itself labeled with a distinct fluorescent dye, and the fragments are then separated by capillary or gel electrophoresis using an automated sequencer. Upon analysis, only the terminal end-labeled restriction fragments are detected. An electropherogram is produced, which shows a profile of compost microbial community as a series of peaks of varying height. This technique has also been effectively used in the exploration of complex microbial environments and in the study of bacterial, archaeal, and eukaryal populations in natural habitats.

  13. RISA: Remote Interface for Science Analysis

    Science.gov (United States)

    Gabriel, C.; Ibarra, A.; de La Calle, I.; Salgado, J.; Osuna, P.; Tapiador, D.

    2008-08-01

    The Scientific Analysis System (SAS) is the package for interactive and pipeline data reduction of all XMM-Newton data. Freely distributed by ESA to run under many different operating systems, the SAS has been used by almost every one of the 1600 refereed scientific publications obtained so far from the mission. We are developing RISA, the Remote Interface for Science Analysis, which makes it possible to run SAS through fully configurable web service workflows, enabling observers to access and analyse data making use of all of the existing SAS functionalities, without any installation/download of software/data. The workflows run primarily but not exclusively on the ESAC Grid, which offers scalable processing resources, directly connected to the XMM-Newton Science Archive. A first project internal version of RISA was issued in May 2007, a public release is expected already within this year.

  14. Solving the Software Legacy Problem with RISA

    Science.gov (United States)

    Ibarra, A.; Gabriel, C.

    2012-09-01

    Nowadays hardware and system infrastructure evolve on time scales much shorter than the typical duration of space astronomy missions. Data processing software capabilities have to evolve to preserve the scientific return during the entire experiment life time. Software preservation is a key issue that has to be tackled before the end of the project to keep the data usable over many years. We present RISA (Remote Interface to Science Analysis) as a solution to decouple data processing software and infrastructure life-cycles, using JAVA applications and web-services wrappers to existing software. This architecture employs embedded SAS in virtual machines assuring a homogeneous job execution environment. We will also present the first studies to reactivate the data processing software of the EXOSAT mission, the first ESA X-ray astronomy mission launched in 1983, using the generic RISA approach.

  15. Towards the molecular characterisation of parasitic nematode assemblages: an evaluation of terminal-restriction fragment length polymorphism (T-RFLP) analysis.

    Science.gov (United States)

    Lott, M J; Hose, G C; Power, M L

    2014-09-01

    Identifying factors which regulate temporal and regional structuring within parasite assemblages requires the development of non-invasive techniques which facilitate both the rapid discrimination of individual parasites and the capacity to monitor entire parasite communities across time and space. To this end, we have developed and evaluated a rapid fluorescence-based method, terminal restriction fragment length polymorphism (T-RFLP) analysis, for the characterisation of parasitic nematode assemblages in macropodid marsupials. The accuracy with which T-RFLP was capable of distinguishing between the constituent taxa of a parasite community was assessed by comparing sequence data from two loci (the ITS+ region of nuclear ribosomal DNA and the mitochondrial CO1) across ∼20 species of nematodes (suborder Strongylida). Our results demonstrate that with fluorescent labelling of the forward and reverse terminal restriction fragments (T-RFs) of the ITS+ region, the restriction enzyme Hinf1 was capable of generating species specific T-RFLP profiles. A notable exception was within the genus Cloacina, in which closely related species often shared identical T-RFs. This may be a consequence of the group's comparatively recent evolutionary radiation. While the CO1 displayed higher sequence diversity than the ITS+, the subsequent T-RFLP profiles were taxonomically inconsistent and could not be used to further differentiate species within Cloacina. Additionally, several of the ITS+ derived T-RFLP profiles exhibited unexpected secondary peaks, possibly as a consequence of the restriction enzymes inability to cleave partially single stranded amplicons. These data suggest that the question of T-RFLPs utility in monitoring parasite communities cannot be addressed without considering the ecology and unique evolutionary history of the constituent taxa. Copyright © 2014 Elsevier Inc. All rights reserved.

  16. Alkane-degrading bacteria at the soil-litter interface: comparing isolates with T-RFLP-based community profiles.

    Science.gov (United States)

    Giebler, Julia; Wick, Lukas Y; Chatzinotas, Antonis; Harms, Hauke

    2013-10-01

    Alkane-degrading bacteria were isolated from uncontaminated soil microcosms, which had been incubated with maize litter as natural alkane source. The isolates served to understand spatio-temporal community changes at the soil-litter interface, which had been detected using alkB as a functional marker gene for bacterial alkane degraders. To obtain a large spectrum of isolates, liquid subcultivation was combined with a matrix-assisted enrichment (Teflon membranes, litter). Elevated cell numbers of alkane degraders were detected by most probable number counting indicating enhanced alkane degradation potential in soil in response to litter treatment. Partial 16S rRNA gene sequencing of 395 isolates revealed forty different phylogenetic groups [operational taxonomic units (OTUs)] and spatio-temporal shifts in community composition. Ten OTUs comprised so far unknown alkane degraders, and five OTUs represented putative new bacterial genera. The combination of enrichment methods yielded a higher diversity of isolates than liquid subcultivation alone. Comparison of 16S rRNA gene T-RFLP profiles indicated that many alkane degraders present in the enrichments were not detectable in the DNA extracts from soil microcosms. These possibly rare specialists might represent a seed bank for the alkane degradation capacity in uncontaminated soil. This relevant ecosystem function can be fostered by the formation of the soil-litter interface. © 2013 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  17. Community analysis of preservative-treated southern pine (Pinus spp.) using terminal restriction fragment length polymorphism (T-RFLP) analysis. Part 1: Fungal field study

    Science.gov (United States)

    Grant T. Kirker; M. Lynn Prewitt; Tor P. Schultz; Susan V. Dieh

    2012-01-01

    The effects of chlorothalonil (CTN), butylated hydroxytoluene (BHT), and ammoniacal copper quat (ACQ-C) on the fungal community on southern yellow pine (SYP) were assessed using terminal restriction fragment length polymorphism (T-RFLP) analysis over 15 months. Field stakes, treated with 0.25 and 0.37 % ACQ-C, 0.1 and 0.25 % CTN, 2 % BHT alone, 0.1 and 0.25 % CTN...

  18. Quantitative analysis of Terminal Restriction Fragment Length Polymorphism (T-RFLP microbial community profiles: peak height data showed to be more reproducible than peak area Análise quantitativa de perfis de T-RFLP de comunidades microbianas: dados de altura de picos mostraram-se mais reprodutíveis do que os de área

    Directory of Open Access Journals (Sweden)

    Roberto A. Caffaro-Filho

    2007-12-01

    Full Text Available Terminal Restriction Fragment Length Polymorphism (T-RFLP is a culture-independent fingerprinting method for microbial community analysis. Profiles generated by an automated electrophoresis system can be analysed quantitatively using either peak height or peak area data. Statistical testing demontrated that peak height data showed to be more reproducible than peak area data.Terminal Restriction Fragment Length Polymorphism (T-RFLP é um método molecular, independente de cultivo, para análise de comunidades microbianas. Perfis gerados por um sistema automatizado de eletroforese podem ser analisados quantitativamente usando dados de altura ou área dos picos. Os dados de altura mostraram-se mais reprodutíveis do que os de área.

  19. The multifaceted RisA regulon of Bordetella pertussis.

    Science.gov (United States)

    Coutte, Loïc; Huot, Ludovic; Antoine, Rudy; Slupek, Stephanie; Merkel, Tod J; Chen, Qing; Stibitz, Scott; Hot, David; Locht, Camille

    2016-09-13

    The whooping cough agent Bordetella pertussis regulates the production of its virulence factors by the BvgA/S system. Phosphorylated BvgA activates the virulence-activated genes (vags) and represses the expression of the virulence-repressed genes (vrgs) via the activation of the bvgR gene. In modulating conditions, with MgSO4, the BvgA/S system is inactive, and the vrgs are expressed. Here, we show that the expression of almost all vrgs depends on RisA, another transcriptional regulator. We also show that some vags are surprisingly no longer modulated by MgSO4 in the risA(-) background. RisA also regulates the expression of other genes, including chemotaxis and flagellar operons, iron-regulated genes, and genes of unknown function, which may or may not be controlled by BvgA/S. We identified RisK as the likely cognate RisA kinase and found that it is important for expression of most, but not all RisA-regulated genes. This was confirmed using the phosphoablative RisAD(60)N and the phosphomimetic RisAD(60)E analogues. Thus the RisA regulon adds a new layer of complexity to B. pertussis virulence gene regulation.

  20. Phylogenetic Signal in AFLP Data Sets

    NARCIS (Netherlands)

    Koopman, W.J.M.

    2005-01-01

    AFLP markers provide a potential source of phylogenetic information for molecular systematic studies. However, there are properties of restriction fragment data that limit phylogenetic interpretation of AFLPs. These are (a) possible nonindependence of fragments, (b) problems of homology assignment

  1. Down-regulation of Risa improves insulin sensitivity by enhancing autophagy.

    Science.gov (United States)

    Wang, Yuangao; Hu, Yanan; Sun, Chenxia; Zhuo, Shu; He, Zhishui; Wang, Hui; Yan, Menghong; Liu, Jun; Luan, Yi; Dai, Changgui; Yang, Yonggang; Huang, Rui; Zhou, Ben; Zhang, Fang; Zhai, Qiwei

    2016-09-01

    It has been reported that some small noncoding RNAs are involved in the regulation of insulin sensitivity. However, whether long noncoding RNAs also participate in the regulation of insulin sensitivity is still largely unknown. We identified and characterized a long noncoding RNA, regulator of insulin sensitivity and autophagy (Risa), which is a poly(A)(+) cytoplasmic RNA. Overexpression of Risa in mouse primary hepatocytes or C2C12 myotubes attenuated insulin-stimulated phosphorylation of insulin receptor, Akt, and Gsk3β, and knockdown of Risa alleviated insulin resistance. Further studies showed that overexpression of Risa in hepatocytes or myotubes decreased autophagy, and knockdown of Risa up-regulated autophagy. Moreover, knockdown of Atg7 or -5 significantly inhibited the effect of knockdown of Risa on insulin resistance, suggesting that knockdown of Risa alleviated insulin resistance via enhancing autophagy. In addition, tail vein injection of adenovirus to knock down Risa enhanced insulin sensitivity and hepatic autophagy in both C57BL/6 and ob/ob mice. Taken together, the data demonstrate that Risa regulates insulin sensitivity by affecting autophagy and suggest that Risa is a potential target for treating insulin-resistance-related diseases.-Wang, Y., Hu, Y., Sun, C., Zhuo, S., He, Z., Wang, H., Yan, M., Liu, J., Luan, Y., Dai, C., Yang, Y., Huang, R., Zhou, B., Zhang, F., Zhai, Q. Down-regulation of Risa improves insulin sensitivity by enhancing autophagy. © FASEB.

  2. Applying Data Mining to Classify Age by Intestinal Microbiota in 92 Healthy Men Using a Combination of Several Restriction Enzymes for T-RFLP Experiments.

    Science.gov (United States)

    Kobayashi, Toshio; Osaki, Takako; Oikawa, Shinya

    2014-01-01

    The composition of the intestinal microbiota was measured following consumption of identical meals for 3 days in 92 Japanese men, and terminal restriction fragment length polymorphism (T-RFLP) was used to analyze their feces. The obtained operational taxonomic units (OTUs) and the subjects' ages were classified by using Data mining (DM) software that compared these data with continuous data and for 5 partitions for age divided at 5 years intervals between the ages of 30 and 50. The DM provided Decision trees in which the selected OTUs were closely related to the ages of the subjects. DM was also used to compare the OTUs from the T-RFLP data with seven restriction enzymes (two enzymes of 516f-BslI and 516f-HaeIII, two enzymes of 27f-MspI and 27f-AluI, three enzymes of 35f-HhaI, 35f-MspI and 35f-AluI) and their various combinations. The OTUs delivered from the five enzyme-digested partitions were analyzed to classify their age clusters. For use in future DM processing, we discussed the enzymes that were effective for accurate classification. We selected two OTUs (HA624 and HA995) that were useful for classifying the subject's ages. Depending on the 16S rRNA sequences of the OTUs, Ruminicoccus obeum clones 1-4 were present in 18 of 36 bacterial candidates in the older age group-related OTU (HA624). On the other hand, Ruminicoccus obeum clones 1-33 were present in 65 of 269 candidates in the younger age group-related OUT (HA995).

  3. Analysis of the airway microbiota of healthy individuals and patients with chronic obstructive pulmonary disease by T-RFLP and clone sequencing.

    Science.gov (United States)

    Zakharkina, Tetyana; Heinzel, Elke; Koczulla, Rembert A; Greulich, Timm; Rentz, Katharina; Pauling, Josch K; Baumbach, Jan; Herrmann, Mathias; Grünewald, Christiane; Dienemann, Hendrik; von Müller, Lutz; Bals, Robert

    2013-01-01

    Chronic obstructive pulmonary disease (COPD) is a progressive, inflammatory lung disease that affects a large number of patients and has significant impact. One hallmark of the disease is the presence of bacteria in the lower airways. The aim of this study was to analyze the detailed structure of microbial communities found in the lungs of healthy individuals and patients with COPD. Nine COPD patients as compared and 9 healthy individuals underwent flexible bronchoscopy and BAL was performed. Bacterial nucleic acids were subjected to terminal restriction fragment (TRF) length polymorphism and clone library analysis. Overall, we identified 326 T-RFLP band, 159 in patients and 167 in healthy controls. The results of the TRF analysis correlated partly with the data obtained from clone sequencing. Although the results of the sequencing showed high diversity, the genera Prevotella, Sphingomonas, Pseudomonas, Acinetobacter, Fusobacterium, Megasphaera, Veillonella, Staphylococcus, and Streptococcus constituted the major part of the core microbiome found in both groups. A TRF band possibly representing Pseudomonas sp. monoinfection was associated with a reduction of the microbial diversity. Non-cultural methods reveal the complexity of the pulmonary microbiome in healthy individuals and in patients with COPD. Alterations of the microbiome in pulmonary diseases are correlated with disease.

  4. SSU rDNA sequence diversity and seasonally differentiated distribution of nanoplanktonic ciliates in neritic Bohai and Yellow Seas as revealed by T-RFLP.

    Directory of Open Access Journals (Sweden)

    Jun Dong

    Full Text Available Nanociliates have been frequently found to be important players in the marine microbial loop, however, little is known about their diversity and distribution in coastal ecosystems. We investigated the molecular diversity and distribution patterns of nanoplanktonic oligotrich and choreotrich (OC ciliates in surface water of three neritic basins of northern China, the South Yellow Sea (SYS, North Yellow Sea (NYS, and Bohai Sea (BS in June and November 2011. SSU rRNA gene clone libraries generated from three summertime samples (sites B38, B4 and H8 were analyzed and revealed a large novel ribotype diversity, of which many were low-abundant phylotypes belonging to the subclass Oligotrichia, but divergent from described morphospecies. Based on the data of terminal-restriction fragment length polymorphism (T-RFLP analysis of all 35 samples, we found that the T-RF richness was generally higher in the SYS than in the BS, and negatively correlated with the molar ratio of P to Si. Overall, multidimensional scaling and permutational multivariate analysis of variance of the community turnover demonstrated a distinct seasonal pattern but no basin-to-basin differentiation across all samples. Nevertheless, significant community differences among basins were recognized in the winter dataset. Mantel tests showed that the environmental factors, P:Si ratio, water temperature and concentration of dissolved oxygen (DO, determined the community across all samples. However, both biogeographic distance and environment shaped the community in winter, with DO being the most important physicochemical factor. Our results indicate that the stoichiometric ratio of P:Si is a key factor, through which the phytoplankton community may be shaped, resulting in a cascade effect on the diversity and community composition of OC nanociliates in the N-rich, Si-limited coastal surface waters, and that the Yellow Sea Warm Current drives the nanociliate community, and possibly the

  5. SSU rDNA sequence diversity and seasonally differentiated distribution of nanoplanktonic ciliates in neritic Bohai and Yellow Seas as revealed by T-RFLP.

    Science.gov (United States)

    Dong, Jun; Shi, Fei; Li, Han; Zhang, Xiaoming; Hu, Xiaozhong; Gong, Jun

    2014-01-01

    Nanociliates have been frequently found to be important players in the marine microbial loop, however, little is known about their diversity and distribution in coastal ecosystems. We investigated the molecular diversity and distribution patterns of nanoplanktonic oligotrich and choreotrich (OC) ciliates in surface water of three neritic basins of northern China, the South Yellow Sea (SYS), North Yellow Sea (NYS), and Bohai Sea (BS) in June and November 2011. SSU rRNA gene clone libraries generated from three summertime samples (sites B38, B4 and H8) were analyzed and revealed a large novel ribotype diversity, of which many were low-abundant phylotypes belonging to the subclass Oligotrichia, but divergent from described morphospecies. Based on the data of terminal-restriction fragment length polymorphism (T-RFLP) analysis of all 35 samples, we found that the T-RF richness was generally higher in the SYS than in the BS, and negatively correlated with the molar ratio of P to Si. Overall, multidimensional scaling and permutational multivariate analysis of variance of the community turnover demonstrated a distinct seasonal pattern but no basin-to-basin differentiation across all samples. Nevertheless, significant community differences among basins were recognized in the winter dataset. Mantel tests showed that the environmental factors, P:Si ratio, water temperature and concentration of dissolved oxygen (DO), determined the community across all samples. However, both biogeographic distance and environment shaped the community in winter, with DO being the most important physicochemical factor. Our results indicate that the stoichiometric ratio of P:Si is a key factor, through which the phytoplankton community may be shaped, resulting in a cascade effect on the diversity and community composition of OC nanociliates in the N-rich, Si-limited coastal surface waters, and that the Yellow Sea Warm Current drives the nanociliate community, and possibly the microbial food webs

  6. Multiplex T-RFLP allows for increased target number and specificity: detection of Salmonella enterica and six species of Listeria in a single test.

    Directory of Open Access Journals (Sweden)

    Geoffrey N Elliott

    Full Text Available A multiplex T-RFLP test was developed to detect and identify Salmonella enterica and all six species of Listeria inoculated into milk at minimal levels. Extensive in silico analysis was used to design a fifteen-primer, six-amplimer methodology and in vitro application showed target organism DNA, when amplified individually, yielded the predicted terminal restriction fragments (TRFs following digestion. Non-target organisms were either not-amplified or yielded TRFs which did not interfere with target identification. Multiple target DNA analysis gave over 86% detection of total TRFs predicted, and this was improved to over 90% detection of total TRFs predicted when only two target DNA extracts were combined analysed. Co-inoculation of milk with five strains each of the target species of S. enterica and L. monocytogenes, along with five strains of the non-target species E. coli was followed by enrichment in SEL medium for M-TRFLP analysis. This allowed for detection of both target species in all samples, with detection of one S. enterica and two Listeria TRFs in all cases, and detection of a second S. enterica TRF in 91% of cases. This was from an initial inoculum of <5 cfu per 25 ml milk with a background of competing E. coli present, and gave a result from sampling of under 20 hours. The ability to increase target species number without loss of sensitivity means that extensive screening can be performed at reduced cost due to a reduction in the number of tests required.

  7. RIKEN Integrated Sequence Analysis (RISA) System—384-Format Sequencing Pipeline with 384 Multicapillary Sequencer

    Science.gov (United States)

    Shibata, Kazuhiro; Itoh, Masayoshi; Aizawa, Katsunori; Nagaoka, Sumiharu; Sasaki, Nobuya; Carninci, Piero; Konno, Hideaki; Akiyama, Junichi; Nishi, Katsuo; Kitsunai, Tokuji; Tashiro, Hideo; Itoh, Mari; Sumi, Noriko; Ishii, Yoshiyuki; Nakamura, Shin; Hazama, Makoto; Nishine, Tsutomu; Harada, Akira; Yamamoto, Rintaro; Matsumoto, Hiroyuki; Sakaguchi, Sumito; Ikegami, Takashi; Kashiwagi, Katsuya; Fujiwake, Syuji; Inoue, Kouji; Togawa, Yoshiyuki; Izawa, Masaki; Ohara, Eiji; Watahiki, Masanori; Yoneda, Yuko; Ishikawa, Tomokazu; Ozawa, Kaori; Tanaka, Takumi; Matsuura, Shuji; Kawai, Jun; Okazaki, Yasushi; Muramatsu, Masami; Inoue, Yorinao; Kira, Akira; Hayashizaki, Yoshihide

    2000-01-01

    The RIKEN high-throughput 384-format sequencing pipeline (RISA system) including a 384-multicapillary sequencer (the so-called RISA sequencer) was developed for the RIKEN mouse encyclopedia project. The RISA system consists of colony picking, template preparation, sequencing reaction, and the sequencing process. A novel high-throughput 384-format capillary sequencer system (RISA sequencer system) was developed for the sequencing process. This system consists of a 384-multicapillary auto sequencer (RISA sequencer), a 384-multicapillary array assembler (CAS), and a 384-multicapillary casting device. The RISA sequencer can simultaneously analyze 384 independent sequencing products. The optical system is a scanning system chosen after careful comparison with an image detection system for the simultaneous detection of the 384-capillary array. This scanning system can be used with any fluorescent-labeled sequencing reaction (chain termination reaction), including transcriptional sequencing based on RNA polymerase, which was originally developed by us, and cycle sequencing based on thermostable DNA polymerase. For long-read sequencing, 380 out of 384 sequences (99.2%) were successfully analyzed and the average read length, with more than 99% accuracy, was 654.4 bp. A single RISA sequencer can analyze 216 kb with >99% accuracy in 2.7 h (90 kb/h). For short-read sequencing to cluster the 3′ end and 5′ end sequencing by reading 350 bp, 384 samples can be analyzed in 1.5 h. We have also developed a RISA inoculator, RISA filtrator and densitometer, RISA plasmid preparator which can handle throughput of 40,000 samples in 17.5 h, and a high-throughput RISA thermal cycler which has four 384-well sites. The combination of these technologies allowed us to construct the RISA system consisting of 16 RISA sequencers, which can process 50,000 DNA samples per day. One haploid genome shotgun sequence of a higher organism, such as human, mouse, rat, domestic animals, and plants, can

  8. RIKEN integrated sequence analysis (RISA) system--384-format sequencing pipeline with 384 multicapillary sequencer.

    Science.gov (United States)

    Shibata, K; Itoh, M; Aizawa, K; Nagaoka, S; Sasaki, N; Carninci, P; Konno, H; Akiyama, J; Nishi, K; Kitsunai, T; Tashiro, H; Itoh, M; Sumi, N; Ishii, Y; Nakamura, S; Hazama, M; Nishine, T; Harada, A; Yamamoto, R; Matsumoto, H; Sakaguchi, S; Ikegami, T; Kashiwagi, K; Fujiwake, S; Inoue, K; Togawa, Y

    2000-11-01

    The RIKEN high-throughput 384-format sequencing pipeline (RISA system) including a 384-multicapillary sequencer (the so-called RISA sequencer) was developed for the RIKEN mouse encyclopedia project. The RISA system consists of colony picking, template preparation, sequencing reaction, and the sequencing process. A novel high-throughput 384-format capillary sequencer system (RISA sequencer system) was developed for the sequencing process. This system consists of a 384-multicapillary auto sequencer (RISA sequencer), a 384-multicapillary array assembler (CAS), and a 384-multicapillary casting device. The RISA sequencer can simultaneously analyze 384 independent sequencing products. The optical system is a scanning system chosen after careful comparison with an image detection system for the simultaneous detection of the 384-capillary array. This scanning system can be used with any fluorescent-labeled sequencing reaction (chain termination reaction), including transcriptional sequencing based on RNA polymerase, which was originally developed by us, and cycle sequencing based on thermostable DNA polymerase. For long-read sequencing, 380 out of 384 sequences (99.2%) were successfully analyzed and the average read length, with more than 99% accuracy, was 654.4 bp. A single RISA sequencer can analyze 216 kb with >99% accuracy in 2.7 h (90 kb/h). For short-read sequencing to cluster the 3' end and 5' end sequencing by reading 350 bp, 384 samples can be analyzed in 1.5 h. We have also developed a RISA inoculator, RISA filtrator and densitometer, RISA plasmid preparator which can handle throughput of 40,000 samples in 17.5 h, and a high-throughput RISA thermal cycler which has four 384-well sites. The combination of these technologies allowed us to construct the RISA system consisting of 16 RISA sequencers, which can process 50,000 DNA samples per day. One haploid genome shotgun sequence of a higher organism, such as human, mouse, rat, domestic animals, and plants, can be

  9. Observation of high seasonal variation in community structure of denitrifying bacteria in arable soil receiving artificial fertilizer and cattle manure by determining T-RFLP of nir gene fragments

    DEFF Research Database (Denmark)

    Priemé, Anders; Wolsing, Martin

    2004-01-01

    Temporal and spatial variation of communities of soil denitrifying bacteria at sites receiving mineral fertilizer (60 and 120 kg N ha-1 year-1) and cattle manure (75 and 150 kg N ha-1 year-1) were explored using terminal restriction fragment length polymorphism (T-RFLP) analyses of PCR amplified...... nitrite reductase (nirK and nirS) gene fragments. The analyses were done three times during the year: in March, July and October. nirK gene fragments could be amplified in all three months, whereas nirS gene fragments could be amplified only in March. Analysis of similarities in T-RFLP patterns revealed...... a significant seasonal shift in the community structure of nirK-containing bacteria. Also, sites treated with mineral fertilizer or cattle manure showed different communities of nirK-containing denitrifying bacteria, since the T-RFLP patterns of soils treated with these fertilizers were significantly different...

  10. Identification of amplified fragment length polymorphism (AFLP ...

    African Journals Online (AJOL)

    Identification of amplified fragment length polymorphism (AFLP) fragments linked to soybean mosaic virus resistance gene in Glycine soja and conversion to a sequence characterized amplified regions (SCAR) marker for rapid selection.

  11. Codominant scoring of AFLP in association panels

    NARCIS (Netherlands)

    Gort, G.; Eeuwijk, van F.A.

    2010-01-01

    A study on the codominant scoring of AFLP markers in association panels without prior knowledge on genotype probabilities is described. Bands are scored codominantly by fitting normal mixture models to band intensities, illustrating and optimizing existing methodology, which employs the

  12. RISA cisternography in the option of ventriculocisternal shunt for infantile non-tumoural aqueductal stenosis.

    Science.gov (United States)

    Palma, L; Mariottini, A; D'Addetta, R; Mastronardi, L

    1988-01-01

    Twenty cases of infantile triventricular hydrocephalus from non-tumoural aqueductal stenosis were treated by ventriculocisternal shunt following RISA cisternography. In 11 cases RISA cisternography showed a normal pattern of CSF circulation. One patient was lost to follow-up. Two had their intrathecal shunt converted into an extrathecal one because of postoperative meningeal infection. Of the remaining 8 patients, 7 had good and 1 fair long term results. In 9 cases RISA cisternography presented an abnormal pattern without indicating a definite impairment of CSF absorption. Slow flow of the tracer leading to its complete disappearance from 36 to 48 hours and 48 to 72 hours was observed respectively in 7 and 2 patients. In both the latter as well in two of the other seven an extrathecal shunt had to be employed (44%). A retrospective analysis to assess the predictive value of CSF absorption test by RISA in the selection of this kind of intrathecal shunt is made.

  13. RISA-HPLC analysis of lung bacterial colonizers of cystic fibrosis children.

    Science.gov (United States)

    Nazaret, S; Assade, F; Brothier, E; Freydière, A-M; Bellon, G; Cournoyer, B

    2009-01-01

    Microbiological analysis of sputum samples, from children affected by cystic fibrosis (CF) and showing signs of acute or chronic infections, is routinely performed by culture-dependent approaches involving selective media and biochemical tests. These identification schemes are time-consuming, and may lead to false negative results. The aim of this work was to evaluate the efficacy of a Ribosomal Intergenic Spacer Analysis (RISA) coupled to high performance liquid chromatography (HPLC) for the detection and monitoring of CF lung microbial colonizers including Staphylococcus aureus, Haemophilus influenzae, Pseudomonas aeruginosa, the Burkholderia cepacia complex, Stenotrophomonas maltophilia, and Achromobacter xylosoxidans. These RISA-HPLC analyses were performed over a 10-months period on infants (below 18 months) and children that were or were not yet known to be colonised by P. aeruginosa. The RISA-HPLC profiles were found specific of the patients' microbial communities. A specific P. aeruginosa RISA-HPLC peak corresponding to 550 bp PCR products was recorded, and used to investigate P. aeruginosa persistence through time and after various therapeutic treatments. The RISA-HPLC profiles showed the CF children to be colonized by few bacterial species, and sometimes revealed peaks corresponding to bacterial species that were not detected by the selective plating approaches. Significant RISA-HPLC infra-specific variations were observed for most bacterial colonizers of CF lungs except P. aeruginosa. These species could yield as much as 5 distinct RISA-HPLC peaks, with some of these profiles being strain-specific. RISA-HPLC shows a great potential for revealing colonization by novel emerging pathogens, and for evaluating the efficacy of therapeutic treatments on the global bacterial community of CF lungs.

  14. Quality control procedures for iodinated radiopharmaceuticals 131I-Hippuran and 131I-Risa

    International Nuclear Information System (INIS)

    Toledo e Souza, I.T. de; Pereira, N.P.S. de; Silva, C.P.G. da.

    1986-02-01

    A rapid miniaturized chromatography system was developed for fast determination of the proportion of inorganic radioactive iodide from radiopharmaceutical 131 I-Hippuran and 131 I-Risa. The technical parameters associated with miniaturized chromatography system were evaluated. One of the problems found in this system was the movement of the 131 I-Risa from the origin with consequent overestimation of the inorganic iodide. A correct spot placement eliminated this problem. (Author) [pt

  15. AFLP variation in 25 Avena species.

    Science.gov (United States)

    Fu, Yong-Bi; Williams, David J

    2008-08-01

    Current molecular characterization of ex situ plant germplasm has placed more emphasis on cultivated gene pools and less on exotic gene pools representing wild relative species. This study attempted to characterize a selected set of germplasm accessions representing various Avena species with the hope to establish a reference set of exotic oat germplasm for oat breeding and research. The amplified fragment length polymorphism (AFLP) technique was applied to screen 163 accessions of 25 Avena species with diverse geographic origins. For each accession, 413 AFLP polymorphic bands detected by five AFLP primer pairs were scored. The frequencies of polymorphic bands ranged from 0.006 to 0.994 and averaged 0.468. Analysis of molecular variance revealed 59.5% of the total AFLP variation resided among 25 oat species, 45.9% among six assessed sections of the genus, 36.1% among three existing ploidy levels, and 50.8% among eight defined genome types. All the species were clustered together according to their ploidy levels. The C genome diploids appeared to be the most distinct, followed by the Ac genome diploid A. canariensis. The Ac genome seemed to be the oldest in all the A genomes, followed by the As, Al and Ad genomes. The AC genome tetraploids were more related to the ACD genome hexaploids than the AB genome tetraploids. Analysis of AFLP similarity suggested that the AC genome tetraploid A. maroccana was likely derived from the Cp genome diploid A. eriantha and the As genome diploid A. wiestii, and might be the progenitor of the ACD genome hexaploids. These AFLP patterns are significant for our understanding of the evolutionary pathways of Avena species and genomes, for establishing reference sets of exotic oat germplasm, and for exploring new exotic sources of genes for oat improvement.

  16. Activation of the vrg6 promoter of Bordetella pertussis by RisA.

    Science.gov (United States)

    Cróinín, Tadhg O; Grippe, Vanessa K; Merkel, Tod J

    2005-03-01

    The BvgAS two-component system positively regulates the expression of the virulence genes of Bordetella pertussis and negatively regulates a second set of genes whose function is unknown. The BvgAS-mediated regulation of the bvg-repressed genes is accomplished through the activation of expression of the negative regulator, BvgR. A second two-component regulatory system, RisAS, is required for expression of the bvg-repressed surface antigens VraA and VraB. We examined the roles of BvgR and RisA in the regulation of four bvg-repressed genes in B. pertussis. Our analyses demonstrated that all four genes are repressed by the product of the bvgR locus and are activated by the product of the risA locus. Deletion analysis of the vrg6 promoter identified the upstream and downstream boundaries of the promoter and, in contrast to previously published results, demonstrated that sequences downstream of the start of transcription are not required for the regulation of expression of vrg6. Gel mobility-shift experiments demonstrated sequence-specific binding of RisA to the vrg6 and vrg18 promoters, and led to the identification of two putative RisA binding sites. Finally, transcriptional analysis and Western blot analysis demonstrated that BvgR regulates neither the expression nor the stability of RisA.

  17. Climate Dynamics and Experimental Prediction (CDEP) and Regional Integrated Science Assessments (RISA) Programs at NOAA Office of Global Programs

    Science.gov (United States)

    Bamzai, A.

    2003-04-01

    This talk will highlight science and application activities of the CDEP and RISA programs at NOAA OGP. CDEP, through a set of Applied Research Centers (ARCs), supports NOAA's program of quantitative assessments and predictions of global climate variability and its regional implications on time scales of seasons to centuries. The RISA program consolidates results from ongoing disciplinary process research under an integrative framework. Examples of joint CDEP-RISA activities will be presented. Future directions and programmatic challenges will also be discussed.

  18. Amplified fragment length polymorphism (AFLP) and genealogy ...

    African Journals Online (AJOL)

    STORAGESEVER

    2010-06-07

    Jun 7, 2010 ... Pang CY, Du XM, Ma ZY (2006). Evaluation of the introgressed lines and screening for elite germplasm in Gossypium, Chin. Sci. Bull. 51(1):. 304-312. Pieter V, Rene H, Marjo B (1995). AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res. 23(21): 4407-4414. Qian SY, Huang JQ, Zhou BL, Peng ...

  19. Characterization of a three bacteria mixed culture in a chemostat: evaluation and application of a quantitative terminal-restriction fragment length polymorphism (T-RFLP) analysis for absolute and species specific cell enumeration.

    Science.gov (United States)

    Schmidt, Julia K; König, Brigitte; Reichl, Udo

    2007-03-01

    Growth dynamics of Pseudomonas aeruginosa, Burkholderia cepacia, and Staphylococcus aureus in a batch and chemostat, were investigated as a laboratory model system for persistent infections in cystic fibrosis. Most species-specific enumeration methods for mixed cultures are laborious or only qualitative, and therefore impede generation of quantitative data required for validation of mathematical models. Here, a quantitative T-RFLP method was evaluated and applied for specific and absolute cell number enumerations. The method was tested to be unbiased by quantitative sample composition and allowed reproducible enumerations of mixed cultures. For assay validation, samples of defined concentration containing one, two or three species were quantified. Logarithmically transformed absolute cell numbers of single-species dilutions were linear within a lower working range of 10(4)-10(6) cfu/mL (species-dependent) and an upper working range of 10(10) cfu/mL. Quantifications of single species (10(6)-10(10) cfu/mL) spiked with one or two other species agreed well with single species controls. Differences between slopes of first order linear regression of spiked and pure dilution series were insignificant. Coefficient of variation of defined mixed replicates was maximum 4.39%, of a three-species chemostat it was maximum 1.76%. T-RFLP monitoring of pure cultures in parallel shake flasks and of a three-species mixed chemostat gave very consistent results. Coexistence of at least two species after a time period equivalent to more than 33 volume exchanges was found. This result was not predicted from pure cultures clearly indicating the need for quantitative mixed culture experiments to better understand microbial growth dynamics and for mathematical model validation.

  20. RISA progress in the development of drought indicators to support decision making

    Science.gov (United States)

    Close, S.; Simpson, C.

    2015-12-01

    Communities around the country are increasingly recognizing the need to plan for water shortages and long-term drought. To build preparedness and help communities manage risk, researchers funded by NOAA's National Integrated Drought Information System (NIDIS) Coping with Drought initiative through the Regional Integrated Sciences and Assessments (RISA) program are working to better understand these impacts across the country and work with communities and resource managers to develop adaptation strategies that meet their needs. The Coping with Drought initiative supports research involving the use of climate predictions and forecast information in decision-making across a range of sectors including agriculture, natural and water resources management, and public health. As a component of this initiative, the RISA program supported research and engagement to develop indicators of drought designed to be of most use to managers and planners grappling with severe and in some cases ongoing drought in their regions. Indicators are being developed for coastal ecosystems in the Carolinas, water management in California, and native communities in Arizona. For instance, the California Nevada Applications Program (CNAP) RISA developed a percentile-based indicator system for analyzing historic droughts and characterizing the ongoing California drought. And in the Southwest, the Climate Assessment for the Southwest (CLIMAS) RISA has been working with the Hopi community on drought monitoring and planning to develop the first-ever Hopi Quarterly Drought Status Report which integrates scientific and local knowledge about drought. This presentation will discuss RISA's role in developing drought indicators based on engagement with decision makers and how this work fits into the larger role that RISAs are playing in the development of the NIDIS Regional Drought Early Warning Systems across the U.S.

  1. Bordetella pertussis risA, but not risS, is required for maximal expression of Bvg-repressed genes.

    Science.gov (United States)

    Stenson, Trevor H; Allen, Andrew G; Al-Meer, Jehan A; Maskell, Duncan; Peppler, Mark S

    2005-09-01

    Expression of virulence determinants by Bordetella pertussis, the primary etiological agent of whooping cough, is regulated by the BvgAS two-component regulatory system. The role of a second two-component regulatory system, encoded by risAS, in this process is not defined. Here, we show that mutation of B. pertussis risA does not affect Bvg-activated genes or proteins. However, mutation of risA resulted in greatly diminished expression of Bvg-repressed antigens and decreased transcription of Bvg-repressed genes. In contrast, mutation of risS had no effect on the expression of Bvg-regulated molecules. Mutation of risA also resulted in decreased bacterial invasion in a HeLa cell model. However, decreased invasion could not be attributed to the decreased expression of Bvg-repressed products, suggesting that mutation of risA may affect the expression of a variety of genes. Unlike the risAS operons in B. parapertussis and B. bronchiseptica, B. pertussis risS is a pseudogene that encodes a truncated RisS sensor. Deletion of the intact part of the B. pertussis risS gene does not affect the expression of risA-dependent, Bvg-repressed genes. These observations suggest that RisA activation occurs through cross-regulation by a heterologous system.

  2. Evaluation of interspecific DNA variability in poplars using AFLP and ...

    African Journals Online (AJOL)

    The objective of this paper was to examine interspecific DNA variation in poplars using AFLP and SSR markers. The AFLP and SSR markers polymorphism and its power of discrimination were determined within 13 genotypes of different genetic background (clones, cultivars, hybrids) of two sections (Aigeiros and ...

  3. Molecular phylogeny of Fusarium species by AFLP fingerprint ...

    African Journals Online (AJOL)

    The high-resolution genotyping method of amplified fragment length polymorphism (AFLP) analysis was used to study the genetic relationships within and between natural populations of five Fusarium spp. AFLP templates were prepared by the digestion of Fusarium DNA with EcoRI and MseI restriction endonucleases and ...

  4. Review and simulation of homoplasy and collision in AFLP

    NARCIS (Netherlands)

    Gort, G.; Eeuwijk, van F.A.

    2012-01-01

    In this paper we give a short review of the problems of homoplasy and collision in AFLP, and describe a software tool that we developed to illustrate these problems. AFLP is a DNA fingerprinting technique, producing profiles of bands, the result of the separation of DNA fragments by length on a gel

  5. Fragment Length Distributions and Collision Probabilities for AFLP Markers

    NARCIS (Netherlands)

    Gort, G.; Koopman, W.J.M.; Stein, A.

    2006-01-01

    AFLP is a DNA fingerprinting technique frequently used in plant and animal sciences. A drawback of the technique is the occurrence of multiple DNA fragments of the same length in a single AFLP lane, which we name a collision. In this article we quantify the problem. The well-known birthday problem

  6. Amplified fragment length polymorphism (AFLP) studies on Indian ...

    African Journals Online (AJOL)

    Jane

    2011-07-11

    Jul 11, 2011 ... Due to high degree of reproducibility, AFLP is now increasingly used in the determination of genetic diversity of a large number of wild plant species. In previous studies, AFLP has been used successfully for the reconstruction of the phylogeny of closely related species as well as in the studies of population ...

  7. Papel de la risa y el humor en la enseñanza y aprendizaje: Explicaciones neurofisiológicas

    OpenAIRE

    Madrid Valdiviezo, Jazmin; Psicóloga. Magíster en Ciencias de la Familia y diplomado en Neuropedagogía. Se ha desempeñado como docente de cursos de Psicología Cognitiva y Dinámica de Grupos de la Universidad Peruana Unión. Asimismo ha participado en la implementación de programas psicoeducativos para el desarrollo de habilidades metacognitivas y socioemocionales con estudiantes talentosos. Actualmente se desempeña en el área de Formación y Desarrollo de Capacidades del Programa Nacional Cuna Más (Lima, Perú)

    2015-01-01

    En esta revisión se recoge información acerca del uso de la risa y el humor en el proceso de enseñanza-aprendizaje de los estudiantes en el contexto del aula y bajo el enfoque de las neurociencias. Se definen los conceptos de risa y humor, se dan explicaciones neurofisiológicas, se identifican las principales teorías y finalmente, se revisan investigaciones sobre el uso de la risa y el humor en el aula. También se incluyen reflexiones que atribuyen una influencia positiva al uso del humor en ...

  8. Preparation and purification of DNA from insects for AFLP analysis.

    Science.gov (United States)

    Reineke, A; Karlovsky, P; Zebitz, C P

    1998-02-01

    Analysis of amplified fragment length polymorphism (AFLP) has the potential to become a powerful new DNA fingerprinting technique for studying genetic relationships and genetic diversity in arthropods. Since DNA of high quality is a crucial prerequisite for AFLP analysis we evaluated the applicability of six protocols (one fast and four complex methods with phenol-chloroform treatments as well as one CTAB-based method) for extracting DNA from insect material and three additional DNA purification steps. The most rapid DNA isolation method did not produce DNA suitable for AFLP analysis. Among four complex methods tested, two protocols resulted in comparatively low yields of DNA that was therefore not used as template for AFLP analysis. The other two complex methods with phenol treatments and a CTAB-based DNA extraction protocol provided DNA suitable for AFLP assay. An additional purification of the DNA using spermine precipitation revealed a few extra bands in an AFLP gel that were masked in unpurified DNA. Therefore spermine precipitation is recommended for AFLP templates.

  9. Using of AFLP to evaluate gamma-irradiated amaranth mutants

    Directory of Open Access Journals (Sweden)

    Labajová Mária

    2013-01-01

    Full Text Available To determine which of several gamma-irradiated mutants of amaranth Ficha cultivar and K-433 hybrid are most genetically similar to their non-irradiated control genotypes, we performed amplified fragment length polymorphism (AFLP based analysis. A total of 40 selective primer combinations were used in reported analyses. First analyses of gamma-irradiated amaranth mutant lines were done used the AFLP. In the study, primers with the differentiation ability for all analysed mutant lines are reported. The very specific changes in the mutant lines´ non-coding regions based on AFLP length polymorphism were analysed. Mutant lines of the Ficha cultivar (C15, C26, C27, C82, C236 shared a genetic dissimilarity of 0,11 and their ISSR profiles are more similar to the Ficha than those of K-433 hybrid mutant lines. The K-433 mutant lines (D54, D279, D282 shared genetic dissimilarity of 0,534 but are more distinct to their control plant as a whole, as those of the Ficha mutant lines. Different AFLP fingerprints patters of the mutant lines when compared to the Ficha cultivar and K-433 hybrid AFLP profiles may be a consequence of the complex response of the intergenic space of mutant lines to the gamma-radiance. Although a genetic polymorphism was detected within accessions, the AFLP markers successfully identified all the accessions. The AFLP results are discussed by a combination of biochemical characteristics of mutant lines and their control genotypes.

  10. Eukaryotic transcriptomics in silico: Optimizing cDNA-AFLP efficiency

    Directory of Open Access Journals (Sweden)

    Wüst Christian

    2009-11-01

    Full Text Available Abstract Background Complementary-DNA based amplified fragment length polymorphism (cDNA-AFLP is a commonly used tool for assessing the genetic regulation of traits through the correlation of trait expression with cDNA expression profiles. In spite of the frequent application of this method, studies on the optimization of the cDNA-AFLP assay design are rare and have typically been taxonomically restricted. Here, we model cDNA-AFLPs on all 92 eukaryotic species for which cDNA pools are currently available, using all combinations of eight restriction enzymes standard in cDNA-AFLP screens. Results In silco simulations reveal that cDNA pool coverage is largely determined by the choice of individual restriction enzymes and that, through the choice of optimal enzyme combinations, coverage can be increased from Conclusion The insights gained from in silico screening of cDNA-AFLPs from a broad sampling of eukaryotes provide a set of guidelines that should help to substantially increase the efficiency of future cDNA-AFLP experiments in eukaryotes. In silico simulations also suggest a novel use of cDNA-AFLP screens to determine the number of transcripts expressed in a target tissue, an application that should be invaluable as next-generation sequencing technologies are adapted for differential display.

  11. The Risa R/Bioconductor package: integrative data analysis from experimental metadata and back again.

    Science.gov (United States)

    González-Beltrán, Alejandra; Neumann, Steffen; Maguire, Eamonn; Sansone, Susanna-Assunta; Rocca-Serra, Philippe

    2014-01-01

    The ISA-Tab format and software suite have been developed to break the silo effect induced by technology-specific formats for a variety of data types and to better support experimental metadata tracking. Experimentalists seldom use a single technique to monitor biological signals. Providing a multi-purpose, pragmatic and accessible format that abstracts away common constructs for describing Investigations, Studies and Assays, ISA is increasingly popular. To attract further interest towards the format and extend support to ensure reproducible research and reusable data, we present the Risa package, which delivers a central component to support the ISA format by enabling effortless integration with R, the popular, open source data crunching environment. The Risa package bridges the gap between the metadata collection and curation in an ISA-compliant way and the data analysis using the widely used statistical computing environment R. The package offers functionality for: i) parsing ISA-Tab datasets into R objects, ii) augmenting annotation with extra metadata not explicitly stated in the ISA syntax; iii) interfacing with domain specific R packages iv) suggesting potentially useful R packages available in Bioconductor for subsequent processing of the experimental data described in the ISA format; and finally v) saving back to ISA-Tab files augmented with analysis specific metadata from R. We demonstrate these features by presenting use cases for mass spectrometry data and DNA microarray data. The Risa package is open source (with LGPL license) and freely available through Bioconductor. By making Risa available, we aim to facilitate the task of processing experimental data, encouraging a uniform representation of experimental information and results while delivering tools for ensuring traceability and provenance tracking. The Risa package is available since Bioconductor 2.11 (version 1.0.0) and version 1.2.1 appeared in Bioconductor 2.12, both along with documentation

  12. AFLP and MS-AFLP analysis of the variation within saffron crocus (Crocus sativus L. germplasm.

    Directory of Open Access Journals (Sweden)

    Matteo Busconi

    Full Text Available The presence and extent of genetic variation in saffron crocus are still debated, as testified by several contradictory articles providing contrasting results about the monomorphism or less of the species. Remarkably, phenotypic variations have been frequently observed in the field, such variations are usually unstable and can change from one growing season to another. Considering that gene expression can be influenced both by genetic and epigenetic changes, epigenetics could be a plausible cause of the alternative phenotypes. In order to obtain new insights into this issue, we carried out a molecular marker analysis of 112 accessions from the World Saffron and Crocus Collection. The accessions were grown for at least three years in the same open field conditions. The same samples were analysed using Amplified Fragment Length Polymorphism (AFLP and Methyl Sensitive AFLP in order to search for variation at the genetic (DNA sequence and epigenetic (cytosine methylation level. While the genetic variability was low (4.23% polymorphic peaks and twelve (12 effective different genotypes, the methyl sensitive analysis showed the presence of high epigenetic variability (33.57% polymorphic peaks and twenty eight (28 different effective epigenotypes. The pattern obtained by Factorial Correspondence Analysis of AFLP and, in particular, of MS-AFLP data was consistent with the geographical provenance of the accessions. Very interestingly, by focusing on Spanish accessions, it was observed that the distribution of the accessions in the Factorial Correspondence Analysis is not random but tends to reflect the geographical origin. Two clearly defined clusters grouping accessions from the West (Toledo and Ciudad Real and accessions from the East (Cuenca and Teruel were clearly recognised.

  13. RiSA: A Science Festival for the Bilingual and Bicultural Rio Grande Valley

    Science.gov (United States)

    Key, Joey Shapiro; Torres, Cristina; Stone, Robert

    2014-03-01

    The Rio Grande Science and Arts (RiSA) Festival organized by the Center for Gravitational Wave Astronomy (CGWA) at the University of Texas at Brownsville (UTB) will use a wide variety of artforms to bring physics and science topics to the bilingual and bicultural population of the Rio Grande Valley of South Texas. The science and art faculty at UTB will partner with art and education professionals to create an annual community event celebrating science though art. Music, dance, poetry, and visual arts will headline the festival activities. Festival events and products will be produced in both English and Spanish to attract and inform the bilingual local community. The RiSA Festival is supported by the Science Festival Alliance and the Sloan Foundation. Supported by the Science Festival Alliance and the Sloan Foundation.

  14. F-RISA fungal clones as potential bioindicators of organic and metal contamination in soil.

    Science.gov (United States)

    Hong, J W; Fomina, M; Gadd, G M

    2010-08-01

    This work has examined the effects of a polycyclic aromatic hydrocarbon and selected toxic metals on fungal populations in a soil microcosm. By using fungal ribosomal intergenic spacer analysis (F-RISA) in combination with real-time PCR quantification, four fungi (D63P2-1, D63C2-1, D21Cu1-1 and D63Pb2-2) with specific primer pairs to each were successfully evaluated for their potential as bioindicators in response to pyrene, copper (Cu) and lead (Pb), supplied singly and in combination. F-RISA coupled with real-time PCR is a useful approach for the identification of microorganisms with potential as bioindicators of organic and toxic metal contamination. These bioindicators could be monitored for their population changes that may indicate pollutant-induced perturbations in a given system.

  15. Use of AFLPs to differentiate between Fusarium species causing ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-09-15

    Fusarium spp. and. Helmintosporium sativum) diseases are common. The aim of this study was to use the AFLP technique to determine variation and genetic relationships between Syrian Fusarium isolates; and compare them.

  16. Activation of Bvg-Repressed Genes in Bordetella pertussis by RisA Requires Cross Talk from Noncooperonic Histidine Kinase RisK.

    Science.gov (United States)

    Chen, Qing; Ng, Victoria; Warfel, Jason M; Merkel, Tod J; Stibitz, Scott

    2017-11-15

    The two-component response regulator RisA, encoded by open reading frame BP3554 in the Bordetella pertussis Tohama I genomic sequence, is a known activator of vrg genes, a set of genes whose expression is increased under the same environmental conditions (known as modulation) that result in repression of the bvgAS virulence regulon. Here we demonstrate that RisA is phosphorylated in vivo and that RisA phosphorylation is required for activation of vrg genes. An adjacent histidine kinase gene, risS , is truncated by frameshift mutation in B. pertussis but not in Bordetella bronchiseptica or Bordetella parapertussis Neither deletion of risS ' or bvgAS nor phenotypic modulation with MgSO 4 affected levels of phosphorylated RisA (RisA∼P) in B. pertussis However, RisA phosphorylation did require the histidine kinase encoded by BP3223, here named RisK (cognate histidine kinase of RisA). RisK was also required for expression of the vrg genes. This requirement could be obviated by the introduction of the phosphorylation-mimicking RisA D60E mutant, indicating that an active conformation of RisA, but not phosphorylation per se , is crucial for vrg activation. Interestingly, expression of vrg genes is still modulated by MgSO 4 in cells harboring the RisA D60E mutation, suggesting that the activated RisA senses additional signals to control vrg expression in response to environmental stimuli. IMPORTANCE In B. pertussis , the BvgAS two-component system activates the expression of virulence genes by binding of BvgA∼P to their promoters. Expression of the reciprocally regulated vrg genes requires RisA and is also repressed by the Bvg-activated BvgR. RisA is an OmpR-like response regulator, but RisA phosphorylation was not expected because the gene for its presumed, cooperonic, histidine kinase is inactivated by mutation. In this study, we demonstrate phosphorylation of RisA in vivo by a noncooperonic histidine kinase. We also show that RisA phosphorylation is necessary but not

  17. Expression of bvg-repressed genes in Bordetella pertussis is controlled by RisA through a novel c-di-GMP signaling pathway

    Science.gov (United States)

    The BvgAS two component system of Bordetella pertussis controls virulence factor expression. In addition, BvgAS controls expression of the bvg-repressed genes through the action of the repressor, BvgR. The transcription factor RisA is inhibited by BvgR, and when BvgR is not expressed RisA induces th...

  18. Genetic relationships among Arachis species based on AFLP

    Directory of Open Access Journals (Sweden)

    Gimenes Marcos A.

    2002-01-01

    Full Text Available Amplified Fragment Length Polymorphism (AFLP was used to establish the genetic relationships among 20 species from seven of the nine sections of genus Arachis. The level of polymorphism among nine accessions of the cultivated peanut, A. hypogaea L., was also evaluated. Three combinations of primers were used to amplify the AFLPs. The fragments were separated in 6% denaturing acrylamide gels. A total of 408 fragments were analyzed. An average of 135.3 fragments per primer combination were scored, and the largest number of fragments was 169 using primer combination Eco RI - ACC / Mse I - CTG, while the lowest was 108, with Eco RI - ACT / Mse I - CTT. In general, the genetic relationships established using AFLPs agreed with the classification established using morphology and crossability data. The results indicated that AFLPs are good markers for establishing the relationships among Arachis species. The polymorphism detected in A. hypogaea by this method was higher than the one found with other markers, like RAPDs and RFLPs. However, our data suggest that the polymorphism detected be using AFLP with only three primer combinations is still too low to be used for any kind of genetic study in this species.

  19. ¿Cuán liviana puede ser la risa? Nietzsche y levinas frente al “fin del hombre”

    Directory of Open Access Journals (Sweden)

    Aïcha Liviana Messina

    2012-10-01

    Full Text Available El artículo parte de la siguiente lectura: en distintas ocasiones, Levinas se refiere al pensamiento de Nietzsche, a su risa, que “rechaza el lenguaje”; sorprendentemente, Levinas no sitúa a Nietzsche, a diferencia de Heidegger, como el último metafísico, sino que lo descoloca en esta historia, subrayando más bien la “extrema juventud” de la risa nietzscheana. Este artículo propone mostrar cómo la risa nietzscheana se articula con lo que Levinas llamaba una “subjetividad del sujeto inocente de conjunciones ontológicas”. Se concluye con una reflexión sobre la vergüenza y los límites del hombre.

  20. ¿CUÁN LIVIANA PUEDE SER LA RISA? NIETZSCHE Y LEVINAS FRENTE AL "FIN DEL HOMBRE"

    Directory of Open Access Journals (Sweden)

    Aïcha Liviana Messina

    2012-01-01

    Full Text Available El artículo parte de la siguiente lectura: en distintas ocasiones, Levinas se refiere al pensamiento de Nietzsche, a su risa, que "rechaza el lenguaje"; sorprendentemente, Levinas no sitúa a Nietzsche, a diferencia de Heidegger, como el último metafísico, sino que lo descoloca en esta historia, subrayando más bien la "extrema juventud" de la risa nietzscheana. Este artículo propone mostrar cómo la risa nietzscheana se articula con lo que Levinas llamaba una "subjetividad del sujeto inocente de conjunciones ontológicas". Se concluye con una reflexión sobre la vergüenza y los límites del hombre.

  1. RISAS Y SONRISAS DEL PROFESORADO. PERCEPCIONES DE ESTUDIANTES DE LA UNIVERSIDAD VERACRUZANA

    Directory of Open Access Journals (Sweden)

    Griselda Hernández Méndez

    2017-06-01

    Full Text Available Este artículo es resultado de una investigación, cuyo objetivo consistió en analizar la relación entre la percepción de los estudiantes respecto a los aspectos personales de los profesores como edad, género y elementos de comunicación no verbal (proxémica, kinésica, paralingüística y apariencia física y la efectividad de la enseñanza. En este texto se dan a conocer los resultados referidos a los elementos no verbales paralingüísticos y, en específico, las risas y sonrisas docentes. Se trabajó a partir del método hermenéutico, siguiendo algunas pautas de la etnografía, como la técnica de la entrevista a profundidad. Los resultados muestran que la presencia (con las diversas maneras de reír o ausencia de risas y sonrisas de los profesores afectan positiva o negativamente la relación entre los profesores y los estudiantes y, por ende, el proceso de enseñanza-aprendizaje.

  2. Phylogenic analysis in Acacia senegal using AFLP molecular ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-10-05

    Oct 5, 2009 ... chloroform (1:1) and chloroform/ isoamyl alcohol (24:1). Total nucleic acids were precipitated with 0.7 volume of isopropanol and vacuum dried. Finally, the pellets were re-dissolved in water and ... of the separated AFLP fingerprint were visualized after silver staining of the gels (Heukeshoven and Dernick, ...

  3. Phylogenic analysis in Acacia senegal using AFLP molecular ...

    African Journals Online (AJOL)

    Amplified fragment length polymorphism (AFLP) DNA markers were used to characterize the genetic diversity and relationships in gum Arabic tree (Acacia senegal). Twenty eight samples of Acacia senegal collected from populations distributed throughout the Gum Arabic belt were tested in comparison with samples of ...

  4. Eukaryotic transcriptomics in silico: Optimizing cDNA-AFLP efficiency

    NARCIS (Netherlands)

    Stölting, K.N.; Gort, G.; Wüst, C.; Wilson, A.B.

    2009-01-01

    Background - Complementary-DNA based amplified fragment length polymorphism (cDNA-AFLP) is a commonly used tool for assessing the genetic regulation of traits through the correlation of trait expression with cDNA expression profiles. In spite of the frequent application of this method, studies on

  5. Modified AFLP technique for rapid genetic characterization in plants.

    Science.gov (United States)

    Ranamukhaarachchi, D G; Kane, M E; Guy, C L; Li, Q B

    2000-10-01

    The standard amplified fragment-length polymorphism (AFLP) technique was modified to develop a convenient and reliable technique for rapid genetic characterization of plants. Modifications included (i) using one restriction enzyme, one adapter molecule and primer, (ii) incorporating formamide to generate more intense and uniform bands and (iii) using agarose gel electrophoresis. Sea oats (Uniola paniculata L.), pickerel-weed (Pontederia cordata L.), Bermudagrass (Cynodon dactylon L.) and Penstemon heterophyllus Lindl. were used to determine the ability to generate adequate resolution power with both self- and cross-pollinated plant species including cultivars, ecotypes and individuals within populations. Reproducibility of bands was higher in all the AFLP experiments compared to random amplified polymorphic DNA (RAPD). Formamide with or without bovine serum albumin improved band intensities compared to dimethyl sulfoxide and the standard reaction mixture with no organic solvents. Comparison between RAPD and modified AFLP using sea-oats population samples proved that modified AFLP exhibits (i) a low number of faint bands with increased specificity of amplified bands, (ii) a significantly higher number of polymorphic loci per primer, (iii) less primer screening time, (iv) easy scoring associated with fewer faint bands and (v) greatly enhanced reproducibility. The technique described here can be applied with a high degree of accuracy for plant genetic characterization.

  6. Analysis of genetic diversity in linseed using AFLP markers | Wakjira ...

    African Journals Online (AJOL)

    Linseed (Linum usitatissimum L.) is the second most important oilseed crop in the highlands of Ethiopia where it has been cultivated for its valuable seed-oil since antiquity. Sixty accessions of linseed predominantly from Ethiopia were analysed using amplified fragment length polymorphism (AFLP) markers to assess their ...

  7. AFLP analysis on genetic diversity and population structure of small ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-06-17

    Jun 17, 2009 ... However, the resource of small yellow croaker has faced to a high fishing pressure and has been now considered over-exploited (Jin and Tang, ..... four subspecies of cherry salmon (Oncorhynchus masou) inferred using AFLP. Mol. Phylogenet. Evol. 48: 776-781. Han ZQ, Li YZ, Chen GB, Gao TX (2008a).

  8. Phylogenetic relationships within Fritillaria section Petilium based on AFLP fingerprints

    NARCIS (Netherlands)

    Wietsma, W.A.; Deinum, D.; Teunissen, H.; Berg, van den R.G.

    2015-01-01

    Fritillaria sect. Petilium (Fritillaria L., Liliaceae), consists of four species: F. chitralensis, F. eduardii, F. imperialis and F. raddeana. We studied their phylogenetic relationships with AFLP’s, crossing experiments and morphological observations. The AFLP data confirm that F. eduardii is a

  9. Amplified fragment length polymorphism (AFLP) studies on Indian ...

    African Journals Online (AJOL)

    Jane

    2011-07-11

    Jul 11, 2011 ... Amplified fragment length polymorphism (AFLP) technology was used to reveal the genetic variation in six species of Cycas collected from eleven natural populations. Two sets of primer with 4-selective nucleotides were used in this study and 78% polymorphism was found. The results correlated with.

  10. Comparison of the radioiodinated serum albumin (RISA) dilution technique with direct volumetric measurements in animal models of peritoneal dialysis.

    Science.gov (United States)

    Van Biesen, Wim; De Vriese, An S; Carlsson, Ola; Van Landschoot, Mike; Dheuvaert, Tomy; Lameire, Norbert H; Devriese, An S

    2002-01-01

    Rat models of peritoneal dialysis (PD) are useful for studying the physiology of peritoneal transport and evaluating new osmotic agents. Intraperitoneal (IP) solute concentrations and their evolution over time are easy to measure, but IP volume (IPV) is not. Direct volumetric measurements are the "gold standard:" but they are expensive and do not allow for repetitive measurements in the same animal. The Indicator dilution technique is therefore used as an alternative. However, that technique is based on assumptions that are not always valid. The present study compares direct volume measurement with the Indicator dilution technique [radioiodinated serum albumin (RISA)] to determine the IPV over time curves In a rat model of PD. In series 1, 17 Sprague-Dawley rats were instilled IP with 25 mL 1.36% glucose dialysate through a Teflon catheter. In 9 animals, 0.35 mL dialysate was sampled and discarded at time points 0, 3,15, 30, 60, 180, and 240 minutes. In the other 8 animals, no sampling was performed. At 240 minutes, all 12 animals were humanely killed, and direct volumetric measurements of IPV were performed. In series 2, rats were instilled IP with 25 mL 1.36% glucose dialysate containing 18.5 kBq 1311 RISA. In 9 animals, dialysate was sampled at 0, 3, 15, 30, 60, 90, 120,180, and 240 minutes for the construction of the RISA concentration-over-time curve, and to calculate the elimination constant Ke. At 30, 60, 180, and 240 minutes, dialysate was sampled in 6 different animals (total n = 24) to calculate IPV using the RISA dilution technique. Immediately afterward, the animals were humanely killed, and direct volumetric measurements of IPV were performed. In series 1, after 240 minutes' dwell time, the IPV was lower in the sampled animals as compared with the non sampled animals (27.11 +/- 1.85 mL vs 30.75 +/- 0.59 mL, p = 0.001). In series 2, the evolution of RISA activity in the dialysate over time was described by piecewise linear regression, yielding 3

  11. The Regional Integrated Sciences and Assessments (RISA) Program, Climate Services, and Meeting the National Climate Change Adaptation Challenge

    Science.gov (United States)

    Overpeck, J. T.; Udall, B.; Miles, E.; Dow, K.; Anderson, C.; Cayan, D.; Dettinger, M.; Hartmann, H.; Jones, J.; Mote, P.; Ray, A.; Shafer, M.; White, D.

    2008-12-01

    The NOAA-led RISA Program has grown steadily to nine regions and a focus that includes both natural climate variability and human-driven climate change. The RISAs are, at their core, university-based and heavily invested in partnerships, particularly with stakeholders, NOAA, and other federal agencies. RISA research, assessment and partnerships have led to new operational climate services within NOAA and other agencies, and have become important foundations in the development of local, state and regional climate change adaptation initiatives. The RISA experience indicates that a national climate service is needed, and must include: (1) services prioritized based on stakeholder needs; (2) sustained, ongoing regional interactions with users, (3) a commitment to improve climate literacy; (4) support for assessment as an ongoing, iterative process; (5) full recognition that stakeholder decisions are seldom made using climate information alone; (6) strong interagency partnership; (7) national implementation and regional in focus; (8) capability spanning local, state, tribal, regional, national and international space scales, and weeks to millennia time scales; and (9) institutional design and scientific support flexible enough to assure the effort is nimble enough to respond to rapidly-changing stakeholder needs. The RISA experience also highlights the central role that universities must play in national climate change adaptation programs. Universities have a tradition of trusted regional stakeholder partnerships, as well as the interdisciplinary expertise - including social science, ecosystem science, law, and economics - required to meet stakeholder climate-related needs; project workforce can also shift rapidly in universities. Universities have a proven ability to build and sustain interagency partnerships. Universities excel in most forms of education and training. And universities often have proven entrepreneurship, technology transfer and private sector

  12. The Consortium for Climate Risk in the Urban Northeast: A NOAA RISA Project

    Science.gov (United States)

    Rosenzweig, C.

    2011-12-01

    The Consortium for Climate Risk in the Urban Northeast, or CCRUN, was funded in October 2010 under NOAA's Regional Integrated Sciences and Assessments (RISA) program to serve stakeholder needs in assessing and managing risks from climate variability and change. It is currently also the only RISA team with a principal focus on climate change adaptation in urban settings. While CCRUN's initial focus is on the major cities of the urban Northeast corridor (Philadelphia, New York and Boston), its work will ultimately expand to cover small and medium-sized cities in the relevant portions of Massachusetts, Rhode Island, Connecticut, New York, New Jersey and Pennsylvania as well, so that local needs for targeted climate-risk information can be served in a coordinated way. CCRUN is designed to address the complex challenges that are associated with densely populated, highly interconnected urban areas, including such as urban heat island effects; poor air quality; intense coastal development, and multifunctional settlement along inland waterways; complex overlapping institutional jurisdictions; integrated infrastructure systems; and highly diverse, and in some cases, fragile socio-economic communities. These challenges can best be addressed by the stakeholder-driven interdisciplinary approach taken by the CCRUN RISA team. As an important added benefit, the research accomplishments and lessons learned through stakeholder engagement will provide a foundation for managing climate risks in other urban areas in the United States. CCRUN's initial projects are focused in three broad sectors: Water, Coasts, and Health. Research in each of these sectors is linked through the cross-cutting themes of climate change and community vulnerability, the latter of which is especially important in considerations of environmental justice and equity. CCRUN's stakeholder-driven approach to research can therefore support investigations of the impacts of a changing climate, population growth, and

  13. Risa y aprendizaje: el papel del humor en la labor docente

    Directory of Open Access Journals (Sweden)

    Eduardo Jáuregui Narváez

    2009-01-01

    Full Text Available Numerosas corrientes pedagógicas en las últimas décadas han fomentado el humor, la diversión y la risa en la labor docente, citando numerosos beneficios, establecer una mejor relación con los estudiantes, reducir el estrés y la ansiedad, gestionar el conflicto, proporcionar una recompensa emocional que motive la participación y el estudio, y comunicar la materia más eficazmente, estimulando la atención, la creatividad y la memoria. En este artículo se evalúa la justificación teórica y empírica de este modelo más "lúdico" del aprendizaje, y se matizan algunas de las ideas que suelen proponerse en este sentido.

  14. Genetic diversity of Carica papaya as revealed by AFLP markers.

    Science.gov (United States)

    Kim, M S; Moore, P H; Zee, F; Fitch, M M M; Steiger, D L; Manshardt, R M; Paull, R E; Drew, R A; Sekioka, T; Ming, R

    2002-06-01

    Genetic relationships among Carica papaya cultivars, breeding lines, unimproved germplasm, and related species were established using amplified fragment length polymorphism (AFLP) markers. Seventy-one papaya accessions and related species were analyzed with nine EcoRI-MseI primer combinations. A total of 186 informative AFLP markers was generated and analyzed. Cluster analysis suggested limited genetic variation in papaya, with an average genetic similarity among 63 papaya accessions of 0.880. Genetic diversity among cultivars derived from the same or similar gene pools was smaller, such as Hawaiian Solo hermaphrodite cultivars and Australian dioecious cultivars with genetic similarity at 0.921 and 0.912, respectively. The results indicated that self-pollinated hermaphrodite cultivars were as variable as open-pollinated dioecious cultivars. Genetic diversity between C. papaya and six other Carica species was also evaluated. Carica papaya shared the least genetic similarity with these species, with an average genetic similarity of 0.432; the average genetic similarity among the six other species was 0.729. The results from AFLP markers provided detailed estimates of the genetic variation within and among papaya cultivars, and supported the notion that C. papaya diverged from the rest of Carica species early in the evolution of this genus.

  15. Expresión de emociones de alegría para personajes virtuales mediante la risa y la sonrisa

    OpenAIRE

    Mascaró Oliver, Miquel

    2014-01-01

    La animación facial es uno de los tópicos todavía no resueltos tanto en el campo de la interacción hombre máquina como en el de la informática gráfica. Las expresiones de alegría asociadas a risa y sonrisa son por su significado e importancia, parte fundamental de estos campos. En esta tesis se hace una aproximación a la representación de los diferentes tipos de risa en animación facial a la vez que se presenta un nuevo método capaz de reproducir todos estos tipos. El método se...

  16. [The current structure of rheumatology in German universities. The Rhesus and RISA-II studies].

    Science.gov (United States)

    Keyszer, G; Burmester, G-R

    2008-11-01

    The teaching of rheumatology requires competent rheumatological structures in German university hospitals. In 2002, the nationwide 'RISA' survey on the extent and quality of rheumatological training in Germany brought a variety of deficits to light. In the same year, a new law regulating the licensing process to practise medicine came into force. Since this law aimed at a more practise-based training of medical students, hopes were high that the conditions for the rheumatological education of students would improve over time. Therefore, our survey was repeated four years later, supplemented by a questionnaire covering scientific activities in rheumatology at university hospitals. In addition, another survey, known as the Rhesus study, was started in 2007 to analyse the size and capacity of rheumatological departments and units at German medical faculties. The results show that rheumatology represents one of the smallest subjects of internal medicine in Germany. Several German university hospitals do not include a rheumatological department at all. Since 2002, no significant progress has been made with regard to the extent of training for medical students in rheumatology, and the new licensing law has not yet shown beneficial effects in this respect. The current data represent only a snap-shot. The development of rheumatology requires cautious observation to prevent this important area of medicine from being sacrificed to economic interests or structural changes.

  17. AFLP studies on downy-mildew-resistant and downy-mildew ...

    Indian Academy of Sciences (India)

    between DM-resistant and DM-susceptible opium poppy genotypes and development of DM-resistant opium poppy genotype- specific AFLP ... Keywords. AFLP; disease resistance; DNA markers; downy mildew; Papaver somniferum; Peronospora arborescens. ...... 1996 Identification of molecular markers in soybean.

  18. AFLP analysis of genetic variability in New Guinea impatiens.

    Science.gov (United States)

    Carr, Jason; Xu, Mingliang; Dudley, John W; Korban, Schuyler S

    2003-05-01

    New Guinea impatiens ( Impatiens hawkeri) is an economically important floral crop, however, little work has been conducted to further our understanding of the genetics of this crop. In this study, we used amplified fragment length polymorphism (AFLP) technology to investigate the level of polymorphism present among 41 commercial cultivars of New Guinea impatiens, study their genetic relatedness, and assess the genetic diversity in this material. An efficient DNA extraction protocol was developed, and a total of 48 EcoRI and MseI primer combinations were used for PCR amplification. Amplification products were then subjected to polyacrylamide gel electrophoresis. The AFLP analysis showed that all 41 cultivars generated between 73 and 130 scoreable polymorphic bands per primer combination. Gower's Genetic Dissimilarity estimates for the entire set of cultivars ranged between 0.940 and 0.488. A dendogram was generated from these dissimilarity data that revealed four groupings among these 41 cultivars. The implications of these results on genotypic variation, genetic relationships, and genetic diversity in New Guinea impatiens will be discussed.

  19. Terapia de la risa en un grupo de mujeres adultas/ Laughter therapy in a group of elderly women

    Directory of Open Access Journals (Sweden)

    María M. Villam

    2013-05-01

    Full Text Available Objetivo: explorar los beneficios de la terapia de la risa en un grupo de mujeres adultas pertenecientes a un centro gerontológico del Municipio de Envigado (Colombia. Metodología: estudio con enfoque cualitativo mediante entrevista semiestructurada a 10 adultas entre 59 y 97 años de edad, antes y después de la aplicación de 5 sesiones, una semanal, de terapia de la risa por parte del grupo Mediclaun “payasos hospitalarios”. Resultados: muchos de los cambios percibidos en las adultas coinciden con la literatura en lo que respecta a una actitud más positiva, incremento de la confianza en el otro y la aceptación; expresan el pasado con menos dolor y un mayor agrado frente al acompañamiento familiar. Conclusiones: La terapia de la risa permite al adulto mayor encontrar fortalezas que puedan ayudarle a mejorar su presente, a su vez, lograr cambios en el individuo que se le revierten positivamente y a su relación con el entorno Objective: to explore the benefits of laughter therapy in a group of elderly women belonging to a gerontology center (Envigado, Colombia. Methodology: a qualitative study using a semi-structured interview with 10 adult women aged 59 to 97. The participants were interviewed before and after applying 5 weekly sessions of laughter therapy. Said therapy was administered by the Mediclaun "hospital clowns" group. Results: many of the changes observed in adult women are consistent with the results described in the literature in relation to a more positive attitude, increased confidence in people and acceptance; the participants expressed the past with less pain and had a greater liking towards family support. Conclusions: laughter therapy allows seniors to find the strength to improve their present situation, thus causing positive changes in their own self and in their relationship with their surroundings

  20. La risa natal. Fundamentos antropológicos y religiosos de la comicidad clerical en Navidad

    Directory of Open Access Journals (Sweden)

    del Campo Tejedor, Alberto

    2014-12-01

    Full Text Available The comicalness of many of the popular and clerical festivals in the winter cycle has been mostly interpreted as a pagan and profane survival, objected to Christian faith. This paper discusses this simplistic thesis and adduces evidences that allows to understand the struggles between detractors and sympathizers of the polemic burlesque festivals on Christmas. We study the type of paschal joy that certain theology has justified in consideration of reasons such as the eutrapelia or the exemplary character of the humiliation and the humility in rituals based on investment of roles. Christmas laugh appears then as a fundamental ingredient of a mytho-logic in which turbulence, joviality, even obscenity, constitute liminal forms in collaborating with the eternal cycle of birth, death and resurrection.La comicidad de muchas de las fiestas populares y clericales del ciclo invernal ha sido interpretada mayoritariamente como supervivencia pagana y profana, contraria a la fe cristiana. Este artículo discute esta tesis reduccionista y aporta evidencias que permiten comprender las pugnas entre detractores y simpatizantes de las polémicas fiestas burlescas en torno a la Navidad. Para ello se indaga el tipo de alegría pascual que cierta teología ha justificado en atención a razones como la eutrapelia o el carácter ejemplar de la humillación y la humildad en los rituales de inversión de roles. La risa navideña se muestra como un ingrediente fundamental de una mito-lógica en la que la turbulencia, la jovialidad, incluso la obscenidad, constituyen formas liminales de colaborar en el eterno ciclo de nacimiento, muerte y resurrección.

  1. AFLP marker linked to water-stress-tolerant bulks in barley (Hordeum vulgare L.

    Directory of Open Access Journals (Sweden)

    A. Altinkut

    2003-01-01

    Full Text Available The amplified fragment length polymorphism (AFLP assay is an efficient method for the identification of molecular markers, useful in the improvement of numerous crop species. Bulked Segregant Analysis (BSA was used to identify AFLP markers associated with water-stress tolerance in barley, as this would permit rapid selection of water-stress tolerant genotypes in breeding programs. AFLP markers linked to water-stress tolerance was identified in two DNA pools (tolerant and sensitive, which were established using selected F2 individuals resulting from a cross between water-stress-tolerant and sensitive barley parental genotypes, based on their paraquat (PQ tolerance, leaf size, and relative water content (RWC. All these three traits were previously shown to be associated with water-stress tolerance in segregating F2 progeny of the barley cross used in a previous study. AFLP analysis was then performed on these DNA pools, using 40 primer pairs to detect AFLP fragments that are present/absent, respectively, in the two pools and their parental lines. One separate AFLP fragment, which was present in the tolerant parent and in the tolerant bulk, but absent in the sensitive parent and in the sensitive bulk, was identified. Polymorphism of the AFLP marker was tested among tolerant and sensitive F2 individuals. The presence of this marker that is associated with water-stress tolerance will greatly enhance selection for paraquat and water-stress tolerant genotypes in future breeding programs.

  2. The relative contribution of band number to phylogenetic accuracy in AFLP data sets.

    Science.gov (United States)

    García-Pereira, M J; Caballero, A; Quesada, H

    2011-11-01

    We examined the effect of increasing the number of sampled amplified fragment length polymorphism (AFLP) bands to reconstruct an accurate and well-supported AFLP-based phylogeny. In silico AFLP was performed using simulated DNA sequences evolving along balanced and unbalanced model trees with recent, uniform and ancient radiations and average branch lengths (from the most internal node to the tip) ranging from 0.02 to 0.05 substitutions per site. Trees were estimated by minimum evolution (ME) and maximum parsimony (MP) methods from both DNA sequences and virtual AFLP fingerprints. The comparison of the true tree with the estimated AFLP trees suggests that moderate numbers of AFLP bands are necessary to recover the correct topology with high bootstrap support values (i.e. >70%). Fewer numbers of bands are necessary for shorter tree lengths and for balanced than for unbalanced tree topologies. However, branch length estimation was rather unreliable and did not improve substantially after a certain number of bands were sampled. These results hold for different levels of genome coverage and number of taxa analysed. In silico AFLP using bacterial genomic DNA sequences recovered a well-supported tree topology that mirrored an empirical phylogeny based on a set of 31 orthologous gene sequences when as few as 263 AFLP bands were scored. These results suggest that AFLPs may be an efficient alternative to traditional DNA sequencing for accurate topology reconstruction of shallow trees when not very short ancestral branches exist. © 2011 The Authors. Journal of Evolutionary Biology © 2011 European Society For Evolutionary Biology.

  3. Evaluating the relationship between evolutionary divergence and phylogenetic accuracy in AFLP data sets.

    Science.gov (United States)

    García-Pereira, María Jesús; Caballero, Armando; Quesada, Humberto

    2010-05-01

    Using in silico amplified fragment length polymorphism (AFLP) fingerprints, we explore the relationship between sequence similarity and phylogeny accuracy to test when, in terms of genetic divergence, the quality of AFLP data becomes too low to be informative for a reliable phylogenetic reconstruction. We generated DNA sequences with known phylogenies using balanced and unbalanced trees with recent, uniform and ancient radiations, and average branch lengths (from the most internal node to the tip) ranging from 0.02 to 0.4 substitutions per site. The resulting sequences were used to emulate the AFLP procedure. Trees were estimated by maximum parsimony (MP), neighbor-joining (NJ), and minimum evolution (ME) methods from both DNA sequences and virtual AFLP fingerprints. The estimated trees were compared with the reference trees using a score that measures overall differences in both topology and relative branch length. As expected, the accuracy of AFLP-based phylogenies decreased dramatically in the more divergent data sets. Above a divergence of approximately 0.05, AFLP-based phylogenies were largely inaccurate irrespective of the distinct topology, radiation model, or phylogenetic method used. This value represents an upper bound of expected tree accuracy for data sets with a simple divergence history; AFLP data sets with a similar divergence but with unbalanced topologies and short ancestral branches produced much less accurate trees. The lack of homology of AFLP bands quickly increases with divergence and reaches its maximum value (100%) at a divergence of only 0.4. Low guanine-cytosine (GC) contents increase the number of nonhomologous bands in AFLP data sets and lead to less reliable trees. However, the effect of the lack of band homology on tree accuracy is surprisingly small relative to the negative impact due to the low information content of AFLP characters. Tree-building methods based on genetic distance displayed similar trends and outperformed parsimony

  4. RisaAligner software for aligning fluorescence data between Agilent 2100 Bioanalyzer chips: Application to soil microbial community analysis.

    Science.gov (United States)

    Navarro, Elisabeth; Fabrègue, Olivier; Scorretti, Riccardo; Reboulet, Jérémy; Simonet, Pascal; Dawson, Lorna; Demanèche, Sandrine

    2015-12-01

    Ribosomal Intergenic Spacer Analysis (RISA) is a high-resolution and highly reproducible fingerprinting technique for discriminating between microbial communities. The community profiles can be visualized using the Agilent 2100 Bioanalyzer. Comparison between fingerprints relies upon precise estimation of all amplified DNA fragment lengths; however, size standard computation can vary between gel runs. For complex samples such as soil microbial communities, discrimination by fragment size is not always sufficient. In such cases, the comparison of whole fluorescence data as a function of time (electrophoregrams) is more appropriate. When electrophoregrams [fluorescence = f (time)] are used, and more than one chip is involved, electrophoregram comparisons are challenging due to experimental variations between chips and the lack of correction by the Agilent software in such situations. Here we present RisaAligner software for analyzing and comparing electrophoregrams from Agilent chips using a nonlinear ladder-alignment algorithm. We demonstrate the robustness and substantial improvement of data analysis by analyzing soil microbial profiles obtained with Agilent DNA 1000 and High Sensitivity chips.

  5. A Three-Legged Stool or Race? Governance Models for NOAA RISAs, DOI CSCs, and USDA Climate Hubs

    Science.gov (United States)

    Foster, J. G.

    2014-12-01

    NOAAs Regional Integrated Sciences and Assessments (RISA) Teams, DOIs Climate Science Centers (CSCs), and USDAs Regional Climate Hubs (RCHs) have common missions of integrating climate and related knowledge across scientific disciplines and regions to create "actionable" information that decision-makes can use to manage climate risks and impacts at state and local scales. However, the sponsoring agency programs, university investigators, and local federal officials govern each differently. The three models of program and center governance are 1) exclusively university (RISAs), 2) a hybrid of Federal government and (host) university (CSCs,), and 3) exclusively Federal (Hubs). Each model has it's advantages and disadvantages in terms of legal definition and authority, scientific mission requirements and strategies, flexibility and legitimacy to conduct research and to collaborate regionally with constituencies, leadership and governance approach and "friction points,", staff capacity and ability to engage stakeholders, necessity to deliver products and services, bureaucratic oversight, performance evaluation, and political support at Congressional, state, and local levels. Using available sources of information and data, this paper will compare and contrast the strengths and weakness of these three regional applied climate science center governance models.

  6. A Three-Legged Stool or Race? Governance Models for NOAA RISAs, DOI CSCs, and USDA Climate Hub

    Science.gov (United States)

    Foster, J. G.

    2014-12-01

    NOAAs Regional Integrated Sciences and Assessments (RISA) Teams, DOIs Climate Science Centers (CSCs), and USDAs Regional Climate Hubs (RCHs) have common missions of integrating climate and related knowledge across scientific disciplines and regions to create "actionable" information that decision-makes can use to manage climate risks and impacts at state and local scales. However, the sponsoring agency programs, university investigators, and local federal officials govern each differently. The three models of program and center governance are 1) exclusively university (RISAs), 2) a hybrid of Federal government and (host) university (CSCs,), and 3) exclusively Federal (Hubs). Each model has it's advantages and disadvantages in terms of legal definition and authority, scientific mission requirements and strategies, flexibility and legitimacy to conduct research and to collaborate regionally with constituencies, leadership and governance approach and "friction points,", staff capacity and ability to engage stakeholders, necessity to deliver products and services, bureaucratic oversight, performance evaluation, and political support at Congressional, state, and local levels. Using available sources of information and data, this paper will compare and contrast the strengths and weakness of these three regional applied climate science center governance models.

  7. Development of a simple and powerful method, cDNA AFLP-SSPAG ...

    African Journals Online (AJOL)

    AJB SERVER

    2006-12-18

    SSPAG was descry- bed. Using this method, Differential mRNA expression was found between high and low heterosis groups of maize. Differential cDNAs were easily obtained from silver stained cDNA-AFLP separated on.

  8. Cambios en la depresión y el sentimiento de soledad después de la terapia de la risa en adultos mayores internados

    Directory of Open Access Journals (Sweden)

    Ángela Quintero

    2015-03-01

    Conclusión. Se resalta la importancia que tiene la terapia de la risa en la disminución del grado de depresión en adultos mayores. Los resultados concuerdan con la afirmación de que el constructo de soledad es independiente del de depresión.

  9. Cyclic di-GMP regulation of the bvg-repressed genes and the orphan response regulator RisA in Bordetella pertussis

    Science.gov (United States)

    Expression of Bordetella pertussis virulence factors is activated by the BvgAS two-component system. Under modulating growth conditions BvgAS indirectly represses another set of genes through the action of BvgR, a bvg-activated protein. BvgR blocks activation of the response regulator RisA which is ...

  10. Genomic variations of Mycoplasma capricolum subsp capripneumoniae detected by amplified fragment length polymorphism (AFLP) analysis

    DEFF Research Database (Denmark)

    Kokotovic, Branko; Bolske, G.; Ahrens, Peter

    2000-01-01

    The genetic diversity of Mycoplasma capricolum subsp. capripneumoniae strains based on determination of amplified fragment length polymorphisms (AFLP) is described. AFLP fingerprints of 38 strains derived from different countries in Africa and the Middle East consisted of over 100 bands in the size...... found by 16S rDNA analysis. The present data support previous observations regarding genetic homogeneity of M. capricolum subsp. capripneumoniae, and confirm the two evolutionary lines of descent found by analysis of 16S rRNA genes....

  11. Use of AFLP markers to estimate molecular diversity of Phakopsora pachyrhizi

    Directory of Open Access Journals (Sweden)

    Carla Maria Lourdes Rocha

    2015-11-01

    Conclusions: The study proposed combining a simple collection of urediniospore with a subsequent analysis by AFLP was useful to examine the molecular polymorphism of samples of P. pachyrhizi collected and might have a significant contribution to the knowledge of its genetic diversity. Also, AFLP analysis is an important and potent molecular tool for the study of genetic diversity and could be useful to carry out wider genetic diversity studies.

  12. Biochemical and genetic variation of some Syrian wheat varieties using NIR, RAPD and AFLPs techniques

    International Nuclear Information System (INIS)

    Saleh, B.

    2012-01-01

    This study was performed to assess chemical components and genetic variability of five Syrian wheat varieties using NIR, RAPD and AFLP techniques. NIR technique showed that Cham6 was the best variety in term of wheat grain quality due to their lowest protein (%), hardness, water uptake and baking volume and the highest starch (%) compared to the other tested varieties. PCR amplifications with 21 RAPD primers and 13 AFLP PCs primer combinations gave 104 and 466 discernible loci of which 24 (18.823%) and 199 (45.527%) were polymorphic for the both techniques respectively. Our data indicated that the three techniques gave similar results regarding the degree of relatedness among the tested varieties. In the present investigation, AFLP fingerprinting was more efficient than the RAPD assay. Where the letter exhibited lower Marker Index (MI) average (0.219) compared to AFLP one (3.203). The pattern generated by RAPD, AFLPs markers or by NIR separated the five wheat varieties into two groups. The first group consists of two subclusters. The first subcluster involved Cham8 and Bohous6, while the second one includes Cham6 that is very closed to precedent varieties. The second group consists of Bohous9 and Cham7 that were also closely related. Based on this study, the use of NIR, RAPD and AFLP techniques could be a powerful tool to detect the effectiveness relationships of these technologies. (author)

  13. Identifying commercially relevant Echinacea species by AFLP molecular markers.

    Science.gov (United States)

    Russi, Luigi; Moretti, Chiaraluce; Raggi, Lorenzo; Albertini, Emidio; Falistocco, Egizia

    2009-11-01

    The rising interest in medicinal plants has brought several species of the genus Echinacea to the attention of many scientists. Echinacea angustifolia, E. pallida, and E. purpurea are the most important for their immunological properties, well known and widely used by the native Americans. The three species are easily distinguishable on the basis of their morphological characteristics, but it would be difficult, if not impossible, to distinguish them in commercial preparations of ground, dry plant parts of E. purpurea (the most valuable species for chemotherapeutic properties) mixed with the other two species. Species-specific molecular markers could be useful to address this issue. In the present work, using fresh material collected from cultivated Echinacea spp., AFLP analysis was used to discriminate the three species and to detect species-specific DNA fragments. By using 14 primer combinations it was possible to detect a total of 994 fragments, of which 565 were polymorphic. Overall, 89 fragments were unique to E. purpurea, 32 to E. angustifolia, and 26 to E. pallida. E+CAC/M+AAT or E+CAC/M+AGC alone provided 13, 9, and 4 or 7, 5, and 5 specific fragments for E. purpurea, E. angustifolia, and E. pallida, respectively. A validation trial to confirm the results was carried out on bulked samples of 23 accessions covering most of the genetic diversity of the three species. The results are discussed in terms of practical applications in the field of popular medicine, detecting frauds, and implications for the genus Echinacea.

  14. Improved coverage of cDNA-AFLP by sequential digestion of immobilized cDNA

    Directory of Open Access Journals (Sweden)

    Karlovsky Petr

    2008-10-01

    Full Text Available Abstract Background cDNA-AFLP is a transcriptomics technique which does not require prior sequence information and can therefore be used as a gene discovery tool. The method is based on selective amplification of cDNA fragments generated by restriction endonucleases, electrophoretic separation of the products and comparison of the band patterns between treated samples and controls. Unequal distribution of restriction sites used to generate cDNA fragments negatively affects the performance of cDNA-AFLP. Some transcripts are represented by more than one fragment while other escape detection, causing redundancy and reducing the coverage of the analysis, respectively. Results With the goal of improving the coverage of cDNA-AFLP without increasing its redundancy, we designed a modified cDNA-AFLP protocol. Immobilized cDNA is sequentially digested with several restriction endonucleases and the released DNA fragments are collected in mutually exclusive pools. To investigate the performance of the protocol, software tool MECS (Multiple Enzyme cDNA-AFLP Simulation was written in Perl. cDNA-AFLP protocols described in the literatur and the new sequential digestion protocol were simulated on sets of cDNA sequences from mouse, human and Arabidopsis thaliana. The redundancy and coverage, the total number of PCR reactions, and the average fragment length were calculated for each protocol and cDNA set. Conclusion Simulation revealed that sequential digestion of immobilized cDNA followed by the partitioning of released fragments into mutually exclusive pools outperformed other cDNA-AFLP protocols in terms of coverage, redundancy, fragment length, and the total number of PCRs. Primers generating 30 to 70 amplicons per PCR provided the highest fraction of electrophoretically distinguishable fragments suitable for normalization. For A. thaliana, human and mice transcriptome, the use of two marking enzymes and three sequentially applied releasing enzymes for each

  15. Assessment of genetic diversity in Chinese eared pheasant using fluorescent-AFLP markers

    DEFF Research Database (Denmark)

    Li, Xiujuan; Zhu, Yaohong; Liu, Panqi

    2010-01-01

    using Jaccard’s similarity coefficients (SC) and the corresponding dendrogram. It was found that there was a moderate genetic distance between the four species (SC = 0.674–0.832). Brown eared pheasant was genetically closely related to blue eared pheasant (SC = 0.832), while white eared pheasant...... on the list of the world’s threatened species. In this paper, 74 individuals from the four eared pheasant species were assessed for population genetic diversity by means of fluorescent-AFLP markers. A total of 429 AFLP peaks were amplified by 11 pairs of fluorescent EcoRI/TaqI primer combinations. Out of all...... markers, 329 AFLPs were polymorphic. Each primer combination produced in reactions from 19 to 72 fragments and the polymorphic peaks percentage ranged from 53.33% to 86.11% with an average of 74.36% polymorphic bands. Genetic distance between species and genetic diversity within species were evaluated...

  16. AFLP studies on downy-mildew-resistant and downy-mildew-susceptible genotypes of opium poppy.

    Science.gov (United States)

    Dubey, Mukesh K; Shasany, Ajit K; Dhawan, Om P; Shukla, Ashutosh K; Khanuja, Suman P S

    2010-04-01

    Downy mildew (DM) caused by Peronospora arborescens, is a serious disease in opium poppy (Papaver somniferum), which has a world-wide spread. The establishment of DM-resistant cultivars appears to be a sustainable way to control the In this paper, we present the results of a study aimed at the identification of amplified fragment length polymorphism (AFLP) markers for DM-resistance in opium poppy. Three opium poppy genotypes (inbred over about 10 years): Pps-1 (DM-resistant), Jawahar-16 (DM-susceptible) and H-9 (DM-susceptible) were crossed in a diallel manner and the F(1) progeny along with the parents were subjected to AFLP analysis of chloroplast (cp) and nuclear DNA with seven and nine EcoRI / MseI primer combinations, respectively. cpDNA AFLP analysis identified 24 Pps-1 (DM-resistant)-specific unique fragments that were found to be maternally inherited in both the crosses, Pps-1 x Jawahar-16 and Pps-1 x H-9. In the case of nuclear DNA AFLP analysis, it was found that 17 fragments inherited from Pps-1 were common to the reciprocal crosses of both (i) Pps-1 and Jawahar-16 as well as (ii) Pps-1 and H-9. This is the first molecular investigation on the identification of polymorphism between DM-resistant and DM-susceptible opium poppy genotypes and development of DM-resistant opium poppy genotypespecific AFLP markers. These AFLP markers could be used in future genetic studies for analysis of linkage to the downy mildew resistance trait.

  17. Distribution of Penicillium commune isolates in cheese dairies mapped using secondary metabolite profiles, morphotypes, RAPD and AFLP fingerprinting

    DEFF Research Database (Denmark)

    Lund, Flemming; Nielsen, A.B.; Skouboe, P.

    2003-01-01

    ) and amplified fragment length polymorphism, (AFLP). For a sub-set of 272 P. commune isolates RAPD analysis generated 33 RAPD groups whereas AFLP profiling revealed 55 AFLP groups. This study conclusively showed that the discriminatory power of AFLP was high compared to RAPD and that AFLP fingerprinting matched...... morphotyping, P. commune isolates with identical profiles using all four typing techniques were interpreted as closely related isolates with a common origin and the distribution of these isolates in the processing environment indicated possible contamination points in the cheese dairies. The coating process...... and unpacking of cheeses with growth of P. commune seemed to cause the contamination problems. Several identical P. commune isolates remained present in the processing environment for more than 7 years in both dairies....

  18. Application of fluorescence-based semi-automated AFLP analysis in barley and wheat

    DEFF Research Database (Denmark)

    Schwarz, G.; Herz, M.; Huang, X.Q.

    2000-01-01

    of semi-automated codominant analysis for hemizygous AFLP markers in an F-2 population was too low, proposing the use of dominant allele-typing defaults. Nevertheless, the efficiency of genetic mapping, especially of complex plant genomes, will be accelerated by combining the presented genotyping......Genetic mapping and the selection of closely linked molecular markers for important agronomic traits require efficient, large-scale genotyping methods. A semi-automated multifluorophore technique was applied for genotyping AFLP marker loci in barley and wheat. In comparison to conventional P-33...

  19. AFLP analysis of genetic relationships among papaya and its wild relatives (Caricaceae) from Ecuador.

    Science.gov (United States)

    Van Droogenbroeck, B.; Breyne, P.; Goetghebeur, P.; Romeijn-Peeters, E.; Kyndt, T.; Gheysen, G.

    2002-08-01

    The AFLP technique was used to assess the genetic relationships among the cultivated papaya ( Carica papaya L.) and related species native to Ecuador. Genetic distances based on AFLP data were estimated for 95 accessions belonging to three genera including C. papaya, at least eight Vasconcella species and two Jacaratia species. Cluster analysis using different methods and principal co-ordinate analysis (PCO), based on the AFLP data from 496 polymorphic bands generated with five primer combinations, was performed. The resulted grouping of accessions of each species corresponds largely with their taxonomic classifications and were found to be consistent with other studies based on RAPD, isozyme and cpDNA data. The AFLP analysis supports the recent rehabilitation of the Vasconcella group as a genus; until recently Vasconcella was considered as a section within the genus Carica. Both cluster and PCO analysis clearly separated the species of the three genera and illustrated the large genetic distance between C. papaya accessions and the Vasconcella group. The specific clustering of the highly diverse group of Vasconcella x heilbornii accessions also suggests that these genotypes may be the result of bi-directional introgression events between Vasconcella stipulata and Vasconcella cundinamarcensis.

  20. Phylogeny and infrageneric delimitation in Spiraea (Rosaceae) inferred from AFLP markers and a comparison with morphology

    Czech Academy of Sciences Publication Activity Database

    Záveská Drábková, Lenka; Pospíšková, M.; Businský, R.

    2017-01-01

    Roč. 185, č. 4 (2017), s. 525-541 ISSN 0024-4074 R&D Projects: GA ČR(CZ) GA16-14649S Institutional support: RVO:61389030 Keywords : classification * spiraeoideae * networks * aflp * Bayesian analysis * maximum parsimony * neighbour network * taxonomy Subject RIV: EF - Botanics OBOR OECD: Plant sciences, botany Impact factor: 2.277, year: 2016

  1. Bootsie: estimation of coefficient of variation of AFLP data by bootstrap analysis

    Science.gov (United States)

    Bootsie is an English-native replacement for ASG Coelho’s “DBOOT” utility for estimating coefficient of variation of a population of AFLP marker data using bootstrapping. Bootsie improves on DBOOT by supporting batch processing, time-to-completion estimation, built-in graphs, and a suite of export t...

  2. An AFLP marker linked to turnip mosaic virus resistance gene in pak ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-06-03

    Jun 3, 2009 ... difficult to control by chemicals, and the natural plant resistance is the ... controlling TuMV-C4 resistance in Chinese cabbage. Zhang et al. ..... Plant Dis. 69: 28-31. Han HP, Sun RF, Zhang SJ, Li F, Zhang SF, Niu XK (2004). AFLP marker linked to turnip mosaic virus susceptible gene in Chinese cabbage ...

  3. On some surprising statistical properties of a DNA fingerprinting technique called AFLP

    NARCIS (Netherlands)

    Gort, G.

    2010-01-01

    AFLP is a widely used DNA fingerprinting technique, resulting in band absence - presence profiles, like a bar code. Bands represent DNA fragments, sampled from the genome of an individual plant or other organism. The DNA fragments travel through a lane of an electrophoretic gel or microcapillary

  4. Characterization of North American Armillaria species: Genetic relationships determined by ribosomal DNA sequences and AFLP markers

    Science.gov (United States)

    M. -S. Kim; N. B. Klopfenstein; J. W. Hanna; G. I. McDonald

    2006-01-01

    Phylogenetic and genetic relationships among 10 North American Armillaria species were analysed using sequence data from ribosomal DNA (rDNA), including intergenic spacer (IGS-1), internal transcribed spacers with associated 5.8S (ITS + 5.8S), and nuclear large subunit rDNA (nLSU), and amplified fragment length polymorphism (AFLP) markers. Based on rDNA sequence data,...

  5. AFLP variability, toxin production, and pathogenicity of Alternaria species from Argentinean tomato fruits and puree.

    Science.gov (United States)

    Somma, Stefania; Pose, Graciela; Pardo, Alejandro; Mulè, Giuseppina; Pinto, Virginia Fernandez; Moretti, Antonio; Logrieco, Antonio Francesco

    2011-02-28

    Large amounts of tomato fruits and derived products are produced in Argentina and may be contaminated by Alternaria toxins. Limited information is available on the genetic variability, toxigenicity, and pathogenicity of Alternaria strains occurring on tomato. We analyzed 65 Alternaria strains isolated in Argentina from tomato fruits affected by black mould and from tomato puree, using amplified fragment length polymorphisms (AFLPs) technique. AFLP analysis resolved the set of strains in 3 main clusters (DICE similarity values of 58 and 60%) corresponding to A. alternata/tenuissima (44 strains), A. arborescens (15 strains) and to an unknown group (6 strains). Most of the representative strains, belonging to each AFLP cluster, when cultured on rice, produced tenuazonic acid (up to 46,760 mg/kg), alternariol monomethyl ether (AME, up to 1860 mg/kg), and alternariol (up to 70 mg/kg). The toxin profile related to the strains was not related to any AFLP cluster, except for AME which was produced at lower level by A. arborescens. Most of strains were pathogenic on two types of commonly cultivated tomato fruits. These findings provide new information on the variability within the Alternaria species complex associated with tomato disease. Copyright © 2011 Elsevier B.V. All rights reserved.

  6. Species relationships in Lactuca S.L. (Lactuceae, Asteraceae) inferred from AFLP fingerprints

    NARCIS (Netherlands)

    Koopman, W.J.M.; Zevenbergen, M.J.; Berg, van den R.G.

    2001-01-01

    An AFLP data set comprising 95 accessions from 20 species of Lactuca s.l. (sensu lato) and related genera was generated using the primer combinations E35/M48 and E35/M49. In phenetic analyses of a data subset, clustering with UPGMA based on Jaccard's similarity coefficient resulted in the highest

  7. A detailed linkage map of lettuce based on SSAP, AFLP and NBS markers

    NARCIS (Netherlands)

    Syed, N.; Sorensen, A.P.; Antonise, R.; Wiel, van de C.C.M.; Linden, van der C.G.; Westende, van 't W.P.C.; Hooftman, D.A.P.; Nijs, den H.C.M.; Flavell, A.

    2006-01-01

    Molecular markers based upon a novel lettuce LTR retrotransposon and the nucleotide binding site-leucine-rich repeat (NBS-LRR) family of disease resistance-associated genes have been combined with AFLP markers to generate a 458 locus genetic linkage map for lettuce. A total of 187

  8. Development of a simple and powerful method, cDNA AFLP-SSPAG ...

    African Journals Online (AJOL)

    Differential cDNAs were easily obtained from silver stained cDNA-AFLP separated on polyacylamide gels. The cDNA was then reamplified, cloned and fragments were sequenced. Sequenced clones were used as probes in northern dot blot analyses and library screening. Full-length cDNA was cloned from a library ...

  9. Genetic diversity of Chilean and Brazilian Alstroemeria species assessed by AFLP analysis

    NARCIS (Netherlands)

    Han, T.H.; Jeu, de M.J.; Eck, van H.J.; Jacobsen, E.

    2000-01-01

    One to three accessions of 22 Alstroemeria species, an interspecific hybrid (A. aurea ́ A. inodora), and single accessions of Bomarea salsilla and Leontochir ovallei were evaluated using the AFLP-marker technique to estimate the genetic diversity within the genus Alstroemeria. Three primer

  10. Genotyping and genetic diversity of Arcobacter butzleri by amplified fragment length polymorphism (AFLP) analysis

    DEFF Research Database (Denmark)

    On, Stephen L.W.; Atabay, H.I.; Amisu, K.O.

    2004-01-01

    Aims: To investigate the potential of amplified fragment length polymorphism (AFLP) profiling for genotyping Arcobacter butzleri and to obtain further data on the genetic diversity of this organism. Methods and Results: Seventy-three isolates of Danish, British, Turkish, Swedish, Nigerian and Nor...

  11. AFLPs reveal genomic regions not detected by RFLPs: a case study in tomato

    NARCIS (Netherlands)

    Bonnema, G.; Berg, van den P.; Lindhout, P.

    2002-01-01

    A set of three tomato chromosome 7 introgression lines (ILs) containing overlapping segments of Lycopersicon pennellii DNA was screened with a set of 10 EcoRI–MseI and 10 PstI–MseI AFLP primer combinations. A large number of markers were identified that mapped to one of the four regions of

  12. An AFLP marker linked to turnip mosaic virus resistance gene in pak ...

    African Journals Online (AJOL)

    An AFLP marker linked to turnip mosaic virus resistance gene in pak-choi. W Xinhua, C Huoying, Z Yuying, H Ruixian. Abstract. Pak-choi is one of the most important vegetable crops in China. Turnip mosaic virus (TuMV) is one of its main pathogen. Screening the molecular marker linked to the TuMV resistance gene is an ...

  13. Identification and characterization of some aromatic rice mutants using amplified fragment length polymorphism (AFLP) technique

    International Nuclear Information System (INIS)

    Fahmy, E.M.; Sobieh, S. E. S.; Ayaad, M. H.; El-Gohary, A. A.; Rownak, A.

    2012-12-01

    Accurate identifying of the genotypes is considered one of the most important mechanisms used in the recording or the protection of plant varieties. The investigation was conducted at the experimental form belonging to the egyptian Atomic Energy Authority, Inshas. The aim was to evaluate grain quality characteristics and molecular genetic variation using Amplified Fragment Length Polymorphism (AFLP) technique among six rice genotypes, Egyptian Jasmine aromatic rice cultivar and five aromatic rice mutants in (M3 mutagenic generation). Two mutation (Egy22 and Egy24) were selected from irradiated Sakha 102 population with 200 and 400Gy of gamma rays in the M2 generation, respectively, and three mutations ( Egy32, Egy33, and Egy34) were selected from irradiated Sakha 103 population with 200, 300, 400Gy of gamma rays in the M2 generation, respectively. The obtained results showed that the strong aroma was obtained for mutant Egy22 as compared with Egyptian Jasmine rice cultivar (moderate aroma). Seven primer combinations were used through six rice genotypes on the molecular level using AFLP marker. The size of AFLP Fragments Were Ranged from 51- 494bp. The total number of amplified bands was 997 band among them 919 polymorphic bans representing 92.2%. The highest similarity index (89%) was observed between Egyptian Jasmine and Egy32 followed by (82%) observed between Egyptian Jasmine and Egy34. On the other hand, the lowest similarity index was (48%) between Egyptian Jasmine and Egy24. In six rice genotypes, Egy24 produced the highest number of the AFLP makers giving 49 unique markers (23 positive and 26 negative), then Egy22 showed 23 unique markers (27 positive and 6 negative) while Egy33 was characterized by 17 unique markers (12 positive and 5 negative). At last Egyptian Jasmine was discriminated by the lowest number of markets, 10 (6 positive and 4 negative). The study further confirmed that AFLP technique was able to differentiate rice genotypes by a higher number

  14. Comparison of RAPD, RFLP, AFLP and SSR markers for diversity studies in tropical maize inbred lines

    Directory of Open Access Journals (Sweden)

    Antonio A. F. Garcia

    2004-01-01

    Full Text Available In order to compare their relative efficiencies as markers and to find the most suitable marker for maize diversity studies we evaluated 18 inbred tropical maize lines using a number of different loci as markers. The loci used were: 774 amplified fragment length polymorphisms (AFLPs; 262 random amplified polymorphic DNAs (RAPDs; 185 restriction fragment length polymorphisms (RFLPs; and 68 simple sequence repeats (SSR. For estimating genetic distance the AFLP and RFLP markers gave the most correlated results, with a correlation coefficient of r = 0.87. Bootstrap analysis were used to evaluate the number of loci for the markers and the coefficients of variation (CV revealed a skewed distribution. The dominant markers (AFLP and RAPD had small CV values indicating a skewed distribution while the codominant markers gave high CV values. The use of maximum values of genetic distance CVs within each sample size was efficient in determining the number of loci needed to obtain a maximum CV of 10%. The number of RFLP and AFLP loci used was enough to give CV values of below 5%, while the SSRs and RAPD loci gave higher CV values. Except for the RAPD markers, all the markers correlated genetic distance with single cross performance and heterosis which showed that they could be useful in predicting single cross performance and heterosis in intrapopulation crosses for broad-based populations. Our results indicate that AFLP seemed to be the best-suited molecular assay for fingerprinting and assessing genetic relationships among tropical maize inbred lines with high accuracy.

  15. Lack of genetic diversity of a critically endangered important medicinal plant Chlorophytum borivilianum in Central India revealed by AFLP markers.

    Science.gov (United States)

    Tripathi, Niraj; Saini, Navinder; Nair, Priya; Tiwari, Sharad

    2012-04-01

    Chlorophytum borivilianum is a traditional medicinal plant distributed throughout the tropics and subtropics. In the present investigation, AFLP analysis was used to assess the genetic similarity among 34 accessions. Nine primer sets of AFLP amplified 612 fragments, of which 246 fragments were found to be polymorphic. The average number of polymorphic bands per AFLP primer pair was 27.33. The amplified fragments ranged from 50 base pairs to 600 base pairs. Significant correlation was observed between total number of amplified fragments and polymorphic bands (p > 0.05) per primers. Cluster analysis based on AFLP data revealed limited genetic variation within the thirty four accessions collected from various parts of Central Indian forests.

  16. Methylated site display (MSD)-AFLP, a sensitive and affordable method for analysis of CpG methylation profiles.

    Science.gov (United States)

    Aiba, Toshiki; Saito, Toshiyuki; Hayashi, Akiko; Sato, Shinji; Yunokawa, Harunobu; Maruyama, Toru; Fujibuchi, Wataru; Kurita, Hisaka; Tohyama, Chiharu; Ohsako, Seiichiroh

    2017-03-09

    It has been pointed out that environmental factors or chemicals can cause diseases that are developmental in origin. To detect abnormal epigenetic alterations in DNA methylation, convenient and cost-effective methods are required for such research, in which multiple samples are processed simultaneously. We here present methylated site display (MSD), a unique technique for the preparation of DNA libraries. By combining it with amplified fragment length polymorphism (AFLP) analysis, we developed a new method, MSD-AFLP. Methylated site display libraries consist of only DNAs derived from DNA fragments that are CpG methylated at the 5' end in the original genomic DNA sample. To test the effectiveness of this method, CpG methylation levels in liver, kidney, and hippocampal tissues of mice were compared to examine if MSD-AFLP can detect subtle differences in the levels of tissue-specific differentially methylated CpGs. As a result, many CpG sites suspected to be tissue-specific differentially methylated were detected. Nucleotide sequences adjacent to these methyl-CpG sites were identified and we determined the methylation level by methylation-sensitive restriction endonuclease (MSRE)-PCR analysis to confirm the accuracy of AFLP analysis. The differences of the methylation level among tissues were almost identical among these methods. By MSD-AFLP analysis, we detected many CpGs showing less than 5% statistically significant tissue-specific difference and less than 10% degree of variability. Additionally, MSD-AFLP analysis could be used to identify CpG methylation sites in other organisms including humans. MSD-AFLP analysis can potentially be used to measure slight changes in CpG methylation level. Regarding the remarkable precision, sensitivity, and throughput of MSD-AFLP analysis studies, this method will be advantageous in a variety of epigenetics-based research.

  17. Characterization of Streptococcus suis through serotyping, SE-AFLP and virulence profile

    Directory of Open Access Journals (Sweden)

    Franco F. Calderaro

    Full Text Available Abstract: Streptococcus suis is one of most important pathogens in the swine industry worldwide. Despite its importance, studies of S. suis characterization in South America are still rare. This study evaluates S. suis isolates from distinct Brazilian states, from 1999 to 2004, and its molecular and serological characterization. A total of 174 isolates were studied. S. suis identification was confirmed by PCR and isolates were further serotyped and genotyped by SE-AFLP and amplification of virulence markers. Serotype 1, 2, 3, 4, 7, 18, 22 and 32 were identified among the studied isolates, and only 4% were characterized as non-typeable. The mrp+/epf+/sly+ genotype was the most frequent. The SE-AFLP analysis resulted in 29 patterns distributed in three main clusters with over 65% of genetic similarity. Isolates presented a slight tendency to cluster according to serotype and origin; however, no further correlation with virulence genotypes was observed.

  18. Identification of taxonomic and epidemiological relationships among Campylobacter species by numerical analysis of AFLP profiles

    DEFF Research Database (Denmark)

    Ona, Stephen L.W.; Harringtona, Clare S.

    2000-01-01

    at higher S-levels. All outbreak or 'genetically identical' strains of C. jejuni subsp. jejuni, Campylobacter coli, C. hyointestinalis and C. sputorum clustered at S-levels > 92% and were distinguished from unrelated strains. Numerical analysis of AFLP profiles is useful for concurrent identification......Amplified fragment length polymorphism (AFLP)-based profiling was performed on 138 strains representing all named Campylobacter species and subspecies. Profiles of 15/16 species comprised 6 to greater than 100 fragments and were subjected to numerical analysis. The mean similarity of 48 duplicate......, outbreak and/or 'identical' strain profiles exceeded 94%. Species were clearly distinguished at the 17.90% similarity (S-) level in the dendrogram. Subspecies of Campylobacter jejuni and Campylobacter. hyointestinalis, and biovars of Campylobacter lari and Campylobacter sputorum were distinguished...

  19. AFLP analysis of rice transformed with maize DNA by particle beam

    International Nuclear Information System (INIS)

    Ji Shengdong; Chen Peng; Wang Jiachuan; Yuan Zhao; Yue Chunhui; Wang Zhifeng

    2009-01-01

    Many stable heritable rice lines were obtained via five years agricultural selection, which were derived from rice (oryza stative Japonica) Yujing-6 transgened with large fraction DNA of Zhengdan-14 (zea mays L.) by particle beam method. 18 pairs optimum selective primers were got by screening from 64 pairs AFLP selective primers via experiment on two mutant lines, which could amplify many DNA fingerprints and also could amplify polymorphic bands and target bands, both in this two mutant lines. Then the two mutant lines and two controls were analyzed with AFLP, the results showed that many polymorphic bands (such as novel bands, target bands, missing bands) were found in mutant lines. The discrepancy in DNA level indicated that rice, transgened with large fraction DNA of Zhengdan-14 by particle beam, might be inserted maize DNA and inherited steadily in some degree. It also indicated that it was possible to cultivate novel rice variety transformed with wide DNA by particle beam. (authors)

  20. [Genetic monitoring of populations of Matthiola fragrans (Bunge) using RAPD and AFLP analysis].

    Science.gov (United States)

    Khadeeva, N V; Goriunova, S V; Kochumova, A A; Iakovleva, E Iu; Mel'nikova, N V; Zholobova, O O; Korotkov, O I; Kudriavtsev, A M

    2011-01-01

    The possibility of using RAPD and AFLP methods for genetic monitoring of populations of Matthiola fragrans (Bunge), a species included in the Red Book of the USSR, was shown for the first time. An analysis of inter- and intrapopulation and interspecies genome polymorphism was performed. Differences in the genetic structure of Matthiola populations from various geographical collection points were revealed. A simple method of performing RAPD analysis and the great number of unique markers found in each population compared with the AFLP analysis, as well as the good division of populations under statistical treatment, allow us to draw the conclusion that using the RAPD method in genetic monitoring of rare and insufficiently studied species is well founded.

  1. Genetic diversity of wild and cultivated Rubus species in Colombia using AFLP and SSR markers

    Directory of Open Access Journals (Sweden)

    Sandra Bibiana Aguilar

    2007-01-01

    Full Text Available The Andean blackberry belongs to the genus Rubus, the largest of the Rosaceae family and one of the mostdiverse of the plant kingdom. In Colombia Rubus glaucus Benth, known as the Andean raspberry or blackberry, is one of thenine edible of the genus out of forty-four reported species. In this study wild and cultivated genotypes, collected in the CentralAndes of Colombia were analyzed by AFLP and SSR markers. Sexual reproduction seems to play an important role inmaintaining the genetic variability in R. glaucus, and the viability of using the SSR of Rubus alceifolius to characterizeColombian Rubus species was clearly demonstrated. All species evaluated produced very specific banding patterns,differentiating them from the others. Both AFLP and SSR produced bands exclusive to each of the following species: R.robustus, R. urticifolius, R. glaucus, and R. rosifolius. The SSR markers differentiated diploid and tetraploid genotypes of R.glaucus.

  2. Preliminary analysis of population genetic diversity of cultivated Laminaria japonica sporophyte via AFLP technique

    Science.gov (United States)

    Yi, Heng; Sui, Zhenghong; Bao, Zhenmin

    2010-03-01

    The amplified fragment length polymorphic DNA (AFLP) technique was adopted to estimate the population genetic polymorphism among 30 sporophytes of Laminaria japonica collected from a cultivating farm in Rongcheng, China. Three methods were used for genomic DNA extraction from Laminaria japonica sporophyte and only the products obtained using the improved genomic DNA extraction kit method proved qualified for AFLP analysis. The parameters of the method were optimized. Samples of forty milligrams and the cell lysis time of 120 min were suggested to replace the parameters recommended by the manufacturer. Thirty individuals of Laminaria japonica from the same cultivating site were investigated using one pair of selective primers. A total of 21 loci were obtained and 17 of them were polymorphic. The mean percent age of polymorphic loci of this population was 80.95%. The Nei’s gene diversity (H) within this population was 0.3028 and the average Shannon’s Information index (I) was 0.4498. A genetic distance matrix among different individuals was constructed as well. Through this study, an applicable AFLP genetic analysis working system for Laminaria japonica sporophyte was established. The results of this research also revealed a high level of genetic diversity within the studied population.

  3. DNA-fingerprinting (AFLP and RFLP) for genotypic identification in species of the Pleurotus eryngii complex.

    Science.gov (United States)

    Urbanelli, S; Della Rosa, V; Punelli, F; Porretta, D; Reverberi, M; Fabbri, A A; Fanelli, C

    2007-03-01

    Wild populations of edible species are important source of genetic variability for cultivated lines that can undergo a drastic loss of diversity resulting from man's selection. The development of tools aimed at the clear-cut and safe identification and assessment of genetic variability of the wild and cultivated strains is thus a fundamental goal of molecular genetic research. In this study, we used two polymerase chain reaction (PCR)-based fingerprinting methods-amplified fragment length polymorphism (AFLP) and restriction fragment length polymorphism (RFLP) of laccase and manganese peroxidase genes-to assess genetic differences among strains and independently evolving lineages belonging to the Pleurotus eryngii complex. Both laccase RFLP and AFLP have been proved to distinguish unambiguously the three taxa studied: Pleurotus ferulae, P. eryngii, and P. eryngii var. nebrodensis. AFLP also showed enough sensitivity to detect polymorphisms among the strains, proving to be an efficient DNA fingerprinting tool in studies of strain assignment. The divergent RFLP laccase and manganese peroxidase patterns are also discussed in relation to the role played by these genes in the interaction between these fungi and their host plants.

  4. Molecular fingerprinting of Fusarium oxysporum f. sp. passiflorae isolates using AFLP markers

    Directory of Open Access Journals (Sweden)

    Aline dos Santos Silva

    2013-04-01

    Full Text Available Fusarium oxysporum f. sp. passiflorae W.L. Gordon (FOP is one of the most important fungal pathogens of passion fruits. Understanding molecular variation of isolates from different areas is of utmost importance. Molecular fingerprinting on 14 isolates of FOP were conducted using AFLP molecular markers (Amplified Fragment Length Polymorphism, and their genetic variability were estimated. Twenty-five AFLP primer combinations were selected for amplification of FOP isolates and one for Fusarium oxysporum f. sp. cubense W.C. Snyder & H.N. Hansen (FOC, resulting in 99% polymorphic fragments, with an average of 40 fragments per primer combination. Specific fingerprints could be generated for most of the isolates evaluated; we observed a high power of discrimination of the AFLP primer combinations, with the presence/absence of up to 26 specific fragments per isolate. Thus, specific fingerprinting was obtained for 10 of the 15 isolates analyzed. The values of the polymorphic information content, the index and the resolving power of the markers showed wide variation and reflected the high informative contents of the primers used in the characterization of the FOP isolates. The FOP isolates were divided into four groups, irrespective of their geographic origins, with the allocation of 5, 7, 1 and 1 FOP isolates into Groups II, III, IV and V, respectively. A wide genetic diversity was observed in FOP isolates, which should be taken into consideration when implementing strategies for the improvement of passion fruit in the search for cultivars with multiple resistance to different isolates.

  5. Genetic Divergent of Tomato Lines Based on AFLP Molecular Markers and Relationship with Heterosis

    Directory of Open Access Journals (Sweden)

    M Nabipoor

    2012-10-01

    Full Text Available Tomato as a highly nutritious vegetable crop is widely grown in the world. Hybrid seed is preferably used for tomato production. Identification of superior hybrid combination is one of the most important steps in the hybrid breeding programs. Breeding of high yielding hybrids is expensive and involves testing large numbers of hybrid combinations in multi-environment trials. Successful prediction of heterosis from the genetic similarity of their parents based on molecular markers has been reported in several crops and can be very helpful in hybrid breeding. The present study was carried out to evaluate genetic divergent among tomato lines and to assess the relationship between genetic distance and heterosis among them. Thirty genotypes were examined for DNA polymorphism, using amplified fragment length polymorphisms (AFLPs. A total of 165 polymorphic variants were generated and genetic distances ranged from 0.04 to 0.23. Our result indicated that AFLP markers were successful in identification of polymorphism and genetic distances among tomato lines, but correlation of genetic distance based on AFLPs with mid-parent heterosis of yield, fruit weight, fruit number and fruit durability time was low and not useful for predicting heterosis in tomato genotypes.

  6. AFLP genome scanning reveals divergent selection in natural populations of Liriodendron chinense (Magnoliaceae along a latitudinal transect

    Directory of Open Access Journals (Sweden)

    Aihong eYang

    2016-05-01

    Full Text Available Understanding adaptive genetic variation and its relation to environmental factors are important for understanding how plants adapt to climate change and for managing genetic resources. Genome scans for the loci exhibiting either notably high or low levels of population differentiation (outlier loci provide one means of identifying genomic regions possibly associated with convergent or divergent selection. In this study, we combined AFLP genome scan and environmental association analysis to test for signals of natural selection in natural populations of Liriodendron chinense (Chinese Tulip Tree; Magnoliaceae along a latitudinal transect. We genotyped 276 individuals from 11 populations of L. chinense using 987 AFLP markers. Two complementary methods (Dfdist and BayeScan and association analysis between AFLP loci and climate factors were applied to detect outlier loci. Our analyses recovered both neutral and potentially adaptive genetic differentiation among populations of L. chinense. We found moderate genetic diversity within populations and high genetic differentiation among populations with reduced genetic diversity towards the periphery of the species ranges. Nine AFLP marker loci showed evidence of being outliers for population differentiation for both detection methods. Of these, six were strongly associated with at least one climate factor. Temperature, precipitation and radiation were found to be three important factors influencing local adaptation of L. chinense. The outlier AFLP loci are likely not the target of natural selection, but the neighboring genes of these loci might be involved in local adaptation. Hence, these candidates should be validated by further studies.

  7. Divergência genética entre genótipos de alface por meio de marcadores AFLP Genetics divergence among lettuce genotypes by AFLP markers

    Directory of Open Access Journals (Sweden)

    Cristina Soares de Sousa

    2007-01-01

    Full Text Available Considerando a restrita diversidade de espécies disponíveis para nutrir a carência de vitaminas no Brasil, Kerr e colaboradores, desde 1981, vêm desenvolvendo pesquisas para melhoramento genético de hortaliças ricas em vitamina A. Dentre elas, obtiveram uma cultivar de alface, denominada Uberlândia 10.000 com 10.200 UI de vitamina A em 100 gramas de folha fresca. Este trabalho objetivou comparar o grau de divergência genética entre a cultivar Uberlândia 10.000 e seus parentais para avaliar a eficiência da seleção utilizada, por meio da técnica AFLP. Foram utilizados os seguintes genótipos de alface: Maioba, Salad Bowl-Mimosa, Moreninha-de-Uberlândia, Vitória de Santo Antão, Uberlândia 10.000 lisa 8.ª e 9.ª geração e Uberlândia 10.000 crespa 8.ª e 9.ª geração. A técnica AFLP foi eficiente para identificar genótipos muito próximos e para estudos de progênies em alface. O primer PR15 permitiu a separação da forma lisa e crespa com 1,8% de divergência genética e a oitava da nona geração com apenas 0,71%. Com o estudo da filogenia da cultivar pode-se observar que o programa de melhoramento foi desenvolvido com sucesso, pois a cultivar obtida Uberlândia 10.000 possui alto teor de vitamina A e 92% de similaridade com o parental Vitória de Santo Antão. O primer PR11 conseguiu identificar polimorfismo entre cultivares de alta e baixa resistência à septoriose, sugerindo a possibilidade destas bandas estarem relacionadas à resistência.Considering the restricted diversity of species available to counteract vitamin deficiencies in Brazil, Kerr and coworkers have been engaged since 1981, in developing genetic improved garden vegetables rich in vitamin A. One of these vegetables is the lettuce cultivar Uberlândia 10,000, which contains 10,200 UI of vitamin A per 100 grams of fresh leaves. This study compares the genetic diversity between Uberlândia 10,000 and its parental, evaluating selection efficiency through

  8. AFLP analysis of genetic diversity and phylogenetic relationships of Brassica oleracea in Ireland.

    Science.gov (United States)

    El-Esawi, Mohamed A; Germaine, Kieran; Bourke, Paula; Malone, Renee

    2016-01-01

    Brassica oleracea L. is one of the most economically important vegetable crop species of the genus Brassica L. This species is threatened in Ireland, without any prior reported genetic studies. The use of this species is being very limited due to its imprecise phylogeny and uncompleted genetic characterisation. The main objective of this study was to assess the genetic diversity and phylogenetic relationships of a set of 25 Irish B. oleracea accessions using the powerful amplified fragment length polymorphism (AFLP) technique. A total of 471 fragments were scored across all the 11 AFLP primer sets used, out of which 423 (89.8%) were polymorphic and could differentiate the accessions analysed. The dendrogram showed that cauliflowers were more closely related to cabbages than kales were, and accessions of some cabbage types were distributed among different clusters within cabbage subgroups. Approximately 33.7% of the total genetic variation was found among accessions, and 66.3% of the variation resided within accessions. The total genetic diversity (HT) and the intra-accessional genetic diversity (HS) were 0.251 and 0.156, respectively. This high level of variation demonstrates that the Irish B. oleracea accessions studied should be managed and conserved for future utilisation and exploitation in food and agriculture. In conclusion, this study addressed important phylogenetic questions within this species, and provided a new insight into the inclusion of four accessions of cabbages and kales in future breeding programs for improving varieties. AFLP markers were efficient for assessing genetic diversity and phylogenetic relationships in Irish B. oleracea species. Copyright © 2016 Académie des sciences. Published by Elsevier SAS. All rights reserved.

  9. Assessment of genetic stability in micropropagules of Jatropha curcas genotypes by RAPD and AFLP analysis

    KAUST Repository

    Sharma, Sweta K.

    2011-07-01

    Jatropha curcas (Euphorbiaceae), a drought resistant non edible oil yielding plant, has acquired significant importance as an alternative renewable energy source. Low and inconsistent yields found in field plantations prompted for identification of high yielding clones and their large scale multiplication by vegetative propagation to obtain true to type plants. In the current investigation plantlets of J. curcas generated by axillary bud proliferation (micropropagation) using nodal segments obtained from selected high yielding genotypes were assessed for their genetic stability using Randomly Amplified Polymorphic DNA (RAPD) and Amplified Fragment Length Polymorphism (AFLP) analyses. For RAPD analysis, 21 out of 52 arbitrary decamer primers screened gave clear reproducible bands. In the micropropagated plantlets obtained from the 2nd sub-culture, 4 out of a total of 177 bands scored were polymorphic, but in the 8th and 16th sub-cultures (culture cycle) no polymorphisms were detected. AFLP analysis revealed 0.63%, 0% and 0% polymorphism in the 2nd, 8th and 16th generations, respectively. When different genotypes, viz. IC 56557 16, IC 56557 34 and IC 56557 13, were assessed by AFLP, 0%, 0.31% and 0.47% polymorphisms were found, respectively, indicating a difference in genetic stability among the different genotypes. To the best of our knowledge this is the first report on assessment of genetic stability of micropropagated plantlets in J. curcas and suggests that axillary shoot proliferation can safely be used as an efficient micropropagation method for mass propagation of J. curcas. © 2011 Elsevier B.V.

  10. Toxigenic profile and AFLP variability of Alternaria alternata and Alternaria infectoria occurring on wheat

    Directory of Open Access Journals (Sweden)

    María Silvina Oviedo

    2013-01-01

    Full Text Available The objectives of this study were to evaluate the ability to produce alternariol (AOH, alternariol monomethyl ether (AME and tenuazonic acid (TA by A. alternata and A. infectoria strains recovered from wheat kernels obtained from one of the main production area in Argentina; to confirm using AFLPs molecular markers the identify of the isolates up to species level, and to evaluate the intra and inter-specific genetic diversity of these two Alternaria species. Among all the Alternaria strains tested (254, 84% of them were able to produce mycotoxins. The most frequent profile of toxin production found was the co-production of AOH and AME in both species tested. TA was only produced by strains of A. alternata. Amplified fragment polymorphism (AFLPs analysis was applied to a set of 89 isolates of Alternaria spp (40 were A. infectoria and 49 were A. alternata in order to confirm the morphological identification. The results showed that AFLPs are powerful diagnostic tool for differentiating between A. alternata and A. infectoria. Indeed, in the current study the outgroup strains, A. tenuissima was consistently classified. Characteristic polymorphic bands separated these two species regardless of the primer combination used. Related to intraspecific variability, A. alternata and A. infectoria isolates evaluated seemed to form and homogeneous group with a high degree of similarity among the isolates within each species. However, there was more scoreable polymorphism within A. alternata than within A. infectoria isolates. There was a concordance between morphological identification and separation up to species level using molecular markers. Clear polymorphism both within and between species showed that AFLP can be used to asses genetic variation in A. alternata and A. infectoria. The most important finding of the present study was the report on AOH and AME production by A. infectoria strains isolated from wheat kernels in Argentina on a semisynthetic

  11. Genetic variation of space flight carried rice and mutant analysis by AFLP molecular marker

    International Nuclear Information System (INIS)

    Pu Zhigang; Zhang Zhiyong; Xiang Yuewu; Zhang Zhixiong; Cai Pingzhong; Wen Chunmiao; Zheng Jiakui

    2006-01-01

    Rice seeds were carried by 'Shenzhou No.3' space shuttle, a mutant with golden chaff, stem and leaf was selected and named Golden 1 after the seeds returned to the earth. Except the golden color, other traits of Golden 1 are no obviously different with its original material H9808. Genetic analysis identified that color variation was control by a pair of recessive gene. The DNA fragments of the mutant were compared with its parent by AFLP molecular markers. Five specific bands were found through a serial selection. (authors)

  12. Toxigenic profile and AFLP variability of Alternaria alternata and Alternaria infectoria occurring on wheat.

    Science.gov (United States)

    Oviedo, María Silvina; Sturm, María Elena; Reynoso, María Marta; Chulze, Sofia Noemi; Ramirez, María Laura

    2013-01-01

    The objectives of this study were to evaluate the ability to produce alternariol (AOH), alternariol monomethyl ether (AME) and tenuazonic acid (TA) by A. alternata and A. infectoria strains recovered from wheat kernels obtained from one of the main production area in Argentina; to confirm using AFLPs molecular markers the identify of the isolates up to species level, and to evaluate the intra and inter-specific genetic diversity of these two Alternaria species. Among all the Alternaria strains tested (254), 84% of them were able to produce mycotoxins. The most frequent profile of toxin production found was the co-production of AOH and AME in both species tested. TA was only produced by strains of A. alternata. Amplified fragment polymorphism (AFLPs) analysis was applied to a set of 89 isolates of Alternaria spp (40 were A. infectoria and 49 were A. alternata) in order to confirm the morphological identification. The results showed that AFLPs are powerful diagnostic tool for differentiating between A. alternata and A. infectoria. Indeed, in the current study the outgroup strains, A. tenuissima was consistently classified. Characteristic polymorphic bands separated these two species regardless of the primer combination used. Related to intraspecific variability, A. alternata and A. infectoria isolates evaluated seemed to form and homogeneous group with a high degree of similarity among the isolates within each species. However, there was more scoreable polymorphism within A. alternata than within A. infectoria isolates. There was a concordance between morphological identification and separation up to species level using molecular markers. Clear polymorphism both within and between species showed that AFLP can be used to asses genetic variation in A. alternata and A. infectoria. The most important finding of the present study was the report on AOH and AME production by A. infectoria strains isolated from wheat kernels in Argentina on a semisynthetic media for the

  13. Using AFLP markers and the Geneland program for the inference of population genetic structure

    DEFF Research Database (Denmark)

    Guillot, Gilles; Santos, Filipe

    2010-01-01

    the computer program Geneland designed to infer population structure has been adapted to deal with dominant markers; and (ii) we use Geneland for numerical comparison of dominant and codominant markers to perform clustering. AFLP markers lead to less accurate results than bi-allelic codominant markers...... such as single nucleotide polymorphisms (SNP) markers but this difference becomes negligible for data sets of common size (number of individuals n≥100, number of markers L≥200). The latest Geneland version (3.2.1) handling dominant markers is freely available as an R package with a fully clickable graphical...

  14. A high density genetic map of maritime pine based on AFLPs

    OpenAIRE

    Chagné, David; Lalanne, Céline; Madur, Delphine; Kumar, Satish; Frigério, Jean-Marc; Krier, Catherine; Decroocq, Stéphane; Savouré, Arnould; Magida Bou-Dagher-Kharrat,; Bertocchi, Evangelista; Brach, Jean; Plomion, Christophe

    2002-01-01

    International audience; We constructed a high-density linkage map of maritime pine (Pinus pinaster Ait.) based on AFLP (Amplified Fragment Length Polymorphism) markers using a three-generation outbred pedigree. In a first step, male and female maps were established independently with test-cross markers segregating 1:1 (presence:absence of the amplified fragment in the full-sib progeny). In a second step, both maps were merged using intercross markers segregating 3:1 in the progeny. A combinat...

  15. Beyond an AFLP genome scan towards the identification of immune genes involved in plague resistance in Rattus rattus from Madagascar.

    Science.gov (United States)

    Tollenaere, C; Jacquet, S; Ivanova, S; Loiseau, A; Duplantier, J-M; Streiff, R; Brouat, C

    2013-01-01

    Genome scans using amplified fragment length polymorphism (AFLP) markers became popular in nonmodel species within the last 10 years, but few studies have tried to characterize the anonymous outliers identified. This study follows on from an AFLP genome scan in the black rat (Rattus rattus), the reservoir of plague (Yersinia pestis infection) in Madagascar. We successfully sequenced 17 of the 22 markers previously shown to be potentially affected by plague-mediated selection and associated with a plague resistance phenotype. Searching these sequences in the genome of the closely related species Rattus norvegicus assigned them to 14 genomic regions, revealing a random distribution of outliers in the genome (no clustering). We compared these results with those of an in silico AFLP study of the R. norvegicus genome, which showed that outlier sequences could not have been inferred by this method in R. rattus (only four of the 15 sequences were predicted). However, in silico analysis allowed the prediction of AFLP markers distribution and the estimation of homoplasy rates, confirming its potential utility for designing AFLP studies in nonmodel species. The 14 genomic regions surrounding AFLP outliers (less than 300 kb from the marker) contained 75 genes encoding proteins of known function, including nine involved in immune function and pathogen defence. We identified the two interleukin 1 genes (Il1a and Il1b) that share homology with an antigen of Y. pestis, as the best candidates for genes subject to plague-mediated natural selection. At least six other genes known to be involved in proinflammatory pathways may also be affected by plague-mediated selection. © 2012 Blackwell Publishing Ltd.

  16. Comparative analysis of population genetic structure in Athyrium distentifolium (Pteridophyta) using AFLPs and SSRs from anonymous and transcribed gene regions.

    Science.gov (United States)

    Woodhead, M; Russell, J; Squirrell, J; Hollingsworth, P M; Mackenzie, K; Gibby, M; Powell, W

    2005-05-01

    To examine the performance and information content of different marker systems, comparative assessment of population genetic diversity was undertaken in nine populations of Athyrium distentifolium using nine genomic and 10 expressed sequence tag (EST) microsatellite (SSR) loci, and 265 amplified fragment length polymorphism (AFLP) loci from two primer combinations. In range-wide comparisons (European vs. North American populations), the EST-SSR loci showed more reliable amplification and produced more easily scorable bands than genomic simple sequence repeats (SSRs). Genomic SSRs showed significantly higher levels of allelic diversity than EST-SSRs, but there was a significant correlation in the rank order of population diversities revealed by both marker types. When AFLPs, genomic SSRs, and EST-SSRs are considered, comparisons of different population diversity metrics/markers revealed a mixture of significant and nonsignificant rank-order correlations. However, no hard incongruence was detected (in no pairwise comparison of populations did different marker systems or metrics detect opposingly significant different amounts of variation). Comparable population pairwise estimates of F(ST) were obtained for all marker types, but whilst absolute values for genomic and EST-SSRs were very similar (F(ST) = 0.355 and 0.342, respectively), differentiation was consistently higher for AFLPs in pairwise and global comparisons (global AFLP F(ST) = 0.496). The two AFLP primer combinations outperformed 18 SSR loci in assignment tests and discriminatory power in phenetic cluster analyses. The results from marker comparisons on A. distentifolium are discussed in the context of the few other studies on natural plant populations comparing microsatellite and AFLP variability.

  17. Bacterial diversity in soil samples from two uranium waste piles as determined by rep-APD, RISA and 16S rDNA retrieval.

    Science.gov (United States)

    Selenska-Pobell, S; Kampf, G; Hemming, K; Radeva, G; Satchanska, G

    2001-06-01

    The bacterial diversity in two uranium waste piles was studied. Total DNA was recovered from a large number of soil samples collected from different sites and depths in the piles using two procedures for direct lysis. Significant differences in the bacterial composition of the samples were revealed by the use of rep-APD, RISA and 16S ARDREA. The 16S rDNA analyses showed that the uranium wastes were dominated by Acidithiobacillusferrooxidans and by several Pseudomonas species classified in the gamma-subdivision of the Proteobacteria. The three kinds of A. ferrooxidans 16S and IGS rDNA specific fragments that were found corresponded to the three phylogenetic groups recognised in this species. This microdiversity probably reflects the genetic adaptation of the uranium waste strains to different concentrations of heavy metals.

  18. Heterogeneous Cell Density and Genetic Structure of Bacterial Pools Associated with Various Soil Microenvironments as Determined by Enumeration and DNA Fingerprinting Approach (RISA).

    Science.gov (United States)

    Ranjard; Poly; Combrisson; Richaume; Gourbière; Thioulouse; Nazaret

    2000-05-01

    The cell density and the genetic structure of bacterial subcommunities (further named pools) present in the various microenvironments of a silt loam soil were investigated. The microenvironments were isolated first using a procedure of soil washes that separated bacteria located outside aggregates (outer part) from those located inside aggregates (inner part). A nondestructive physical fractionation was then applied to the inner part in order to separate bacteria located inside stable aggregates of different size (size fractions, i.e., two macroaggregate fractions, two microaggregate fractions, and the dispersible day fraction). Bacterial densities measured by acridine orange direct counts (AODC) and viable heterotrophic (VH) cell enumerations showed the heterogeneous quantitative distribution of cells in soil. Bacteria were preferentially located in the inner part with 87.6% and 95.4% of the whole AODC and VH bacteria, respectively, and in the microaggregate and dispersible clay fractions of this part with more than 70% and 80% of the whole AODC and VH bacteria, respectively. The rRNA intergenic spacer analysis (RISA) was used to study the genetic structure of the bacterial pools. Different fingerprints and consequently different genetic structures were observed between the unfractionated soil and the microenvironments, and also among the various microenvironments, giving evidence that some populations were specific to a given location in addition to the common populations of all the microenvironments. Cluster and multivariate analysis of RISA profiles showed the weak contribution of the pools located in the macroaggregate fractions to the whole soil community structure, as well as the clear distinction between the pool associated to the macroaggregate fractions and the pools associated to the microaggregate ones. Furthermore, these statistical analyses allowed us to ascertain the influence of the clay and organic matter content of microenvironments on the genetic

  19. Genetic Diversity of Hibiscus tiliaceus (Malvaceae) in China Assessed using AFLP Markers

    Science.gov (United States)

    TANG, TIAN; ZHONG, YANG; JIAN, SHUGUANG; SHI, SUHUA

    2003-01-01

    Amplified fragment length polymorphism (AFLP) markers were used to investigate the genetic variations within and among nine natural populations of Hibiscus tiliaceus in China. DNA from 145 individuals was amplified with eight primer pairs. No polymorphisms were found among the 20 samples of a marginal population of recent origin probably due to a founder effect. Across the other 125 individuals, 501 of 566 bands (88·5 %) were polymorphic, and 125 unique AFLP phenotypes were observed. Estimates of genetic diversity agreed with life history traits of H. tiliaceus and geographical distribution. AMOVA analysis revealed that most genetic diversity resided within populations (84·8 %), which corresponded to results reported for outcrossing plants. The indirect estimate of gene flow based on ϕST was moderate (Nm = 1·395). Long-distance dispersal of floating seeds and local environments may play an important role in shaping the genetic diversity of the population and the genetic structure of this species. PMID:12930729

  20. [AFLP Analysis of Genetic Diversity in the Genus Mallus Mill. (Apple)].

    Science.gov (United States)

    Savelyeva, E N; Kudryavtsev, A M

    2015-10-01

    The first molecular genetic analysis of the apple species and varieties from Russian collections with the AFLP marker system was performed in order to study the genetic diversity of the genus Malus, as well as to clarify the phylogeny and solve some systematic issues of the genus. Nienty-one apple accessions, including species from five sections of the genus Malus and hybrid species, were examined. The level of polymorphism constituted 90.2%. It was demonstrated that the classical taxonomy of the genus Malus, which identifies five sections based on differences in their morphological characters, is valid and may be used to classify apple species. The species assignment of the Antonovka landraces was established. All of them belonged to the species M. domestica. It was demonstrated that the Yakutskaya apple variety was a domesticated species of the section Gymnomeles, presumably, M. baccata. AFLP analysis confirmed the hybrid nature of many species. The relationships between apple varieties of the Golden group with American wild species were demonstrated. The data suggest that the species M. sieversii was the ancestor of not only the domestic apple but also of other species of the Malus sections.

  1. AFLP analysis reveals a clonal population of Phytophthora pinifolia in Chile.

    Science.gov (United States)

    Durán, Alvaro; Gryzenhout, Marieka; Drenth, André; Slippers, Bernard; Ahumada, Rodrigo; Wingfield, Brenda D; Wingfield, Michael J

    2010-09-01

    Phytophthora pinifolia is the causal agent of the recently discovered needle disease of Pinus radiata in Chile, referred to as "Daño Foliar del Pino" (DFP). The genetic structure of the pathogen population is unknown, which hinders our understanding of its appearance and spread in Chile since 2004. In this study, a population of 88 cultures of P. pinifolia isolated from P. radiata at several localities in Chile was evaluated for genotypic diversity using amplified fragment length polymorphisms (AFLPs). Results of the AFLP analyses showed that the P. pinifolia population in Chile consists of two near identical genotypes but with no genetic differentiation based on geography, year of isolation or the part of the tree from which the isolates were obtained. Mating experiments did not lead to the production of gametangia suggesting that the organism is sterile. The fact that a single clonal genotype dominates the population of P. pinifolia in Chile supports the hypothesis that P. pinifolia was recently introduced into this country and that its impact is due to a new and susceptible host encounter. Copyright © 2010 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

  2. Characterization of Macrophomina phaseolina isolates by their response to different osmotic potentials and AFLP

    Directory of Open Access Journals (Sweden)

    Bárbara J. Gutiérrez Cedeño

    2014-01-01

    Full Text Available Charcoal rot of Phaseolus vulgaris is caused by the fungus Macrophomina phaseolina, the disease is associated with high temperature and water stress. The objective of this study was to characterize isolates of M. phaseolina by their response to different osmotic potentials and AFLP. The growth of 11 isolates was determined on potato dextrose agar at 48 and 72 h in a gradient of osmotic potential induced using NaCl as well as their effects on germination of sclerotia. Three water groups were statistically different indicating differential response to osmotic potential and all sclerotia grown under these conditions, germinated between 24 and 48h. There were groups of isolates that were tolerant to water stress induced. The AFLP genotyping allowed the formation of five genetic groups, showing a wide genetic variability. Of the nine starters CTA-AT showed a high degree of confidence in the identification of genotypes of M. phaseolina and CAA-AC had the lowest discriminatory power. These results show that M. phaseolina isolates responded differently to osmotic potential and are genetically different between them. Although there was a clear correspondence of genetic groups to water groups; these responses are important features in the search for alternative management in black bean pathosystem. Keywords: molecular marker, M. phaseolina, water deficit

  3. Sesame mutant induced space flight treatment and analysis of polymorphism by AFLP molecular marker

    International Nuclear Information System (INIS)

    Lu Haixia; Zhang Yanxin; Wang Linhai; Wei Wenliang; Li Donghua; Zhang Xiaoyan; Zhang Xiurong

    2011-01-01

    Seeds of two sesame varieties (Yuzhi 8 and H98) were carried by 'Shijian 8' satellite for space treatment. Variants is SP 2 and SP 1 were observed and the genetic diversity of mutation generation was analyzed using 30 pair of AFLP markers. The results showed that: (1) variants of leaf, plant height, plant characters, floral organs, capsule, fertility, pre-flowering date were observed in SP 2 and SP 3 of two varieties, variations frequency and variations type of two sesame varieties were significantly different, but only the small capsule variations and tall plant variations could be inherited from SP 2 to SP 3 generation; (2) AFLP analysis of primers randomly selected to analyze variant plants in SP 2 and SP 3 generation, showed that multiple sites in sesame genome were induced by space environment and mutation rate was high, while mutation rate was different in molecular level between varieties; (3) variation sites were diverse between different variations types, and mutation sites were also diverse between different plants of same mutation type, this result indicated that variation of sesame genome DNA could not been expressed totally; (4) The same mutant of botany characteristics and the same locus mutation of molecular level were both detected. (authors)

  4. Disseminated Cryptococcus deuterogattii (AFLP6/VGII) infection in an Arabian horse from Dubai, United Arab Emirates.

    Science.gov (United States)

    Kinne, Jörg; Joseph, Marina; Wernery, Ulrich; Nogradi, Nora; Hagen, Ferry

    During the past decades there has been an increase in cryptococcal infections caused by the basidiomycetous yeast species Cryptococcus gattii sensu lato, among humans and animals that live in endemic regions in Australia, Europe and the Americas. Unlike human cryptococcosis, little epidemiological data are available about C. gattii sensu lato infections in horses. A fatal case of a disseminated C. gattii sensu lato infection in an 11-year-old Arabian gelding imported from South Africa into the United Arab Emitares is reported. Tissue samples were studied by conventional mycology procedures and the obtained cryptococcal isolate was molecularly characterized by mating-type determination, amplified fragment length polymorphism (AFLP) fingerprinting, and multi-locus sequence typing (MLST). Phylogenetic analysis was performed to investigate the geographic origin of the cryptococcal isolate. The isolate was identified as Cryptococcus deuterogattii (AFLP6/VGII), mating-type α. Phylogenetic analysis showed that it was closely related to another C. deuterogattii isolate from the Middle East. A second case of a C. deuterogattii infection in the Middle East is described. It is likely that the horse acquired the infection in the Middle East, as the isolate is closely related to that of a recent human case from that region. Copyright © 2017 Asociación Española de Micología. Publicado por Elsevier España, S.L.U. All rights reserved.

  5. Genetic diversity in bambara groundnut (Vigna subterranea (L.) Verdc) landraces revealed by AFLP markers.

    Science.gov (United States)

    Massawe, F J; Dickinson, M; Roberts, J A; Azam-Ali, S N

    2002-12-01

    Bambara groundnut (Vigna subterranea (L.) Verdc), an African indigenous legume, is popular in most parts of Africa. The present study was undertaken to establish genetic relationships among 16 cultivated bambara groundnut landraces using fluorescence-based amplified fragment length polymorphism (AFLP) markers. Seven selective primer combinations generated 504 amplification products, ranging from 50 to 400 bp. Several landrace-specific products were identified that could be effectively used to produce landrace-specific markers for identification purposes. On average, each primer combination generated 72 amplified products that were detectable by an ABI Prism 310 DNA sequencer. The polymorphisms obtained ranged from 68.0 to 98.0%, with an average of 84.0%. The primer pairs M-ACA + P-GCC and M-ACA + P-GGA produced more polymorphic fragments than any other primer pairs and were better at differentiating landraces. The dendrogram generated by the UPGMA (unweighted pair-group method with arithmetic averaging) grouped 16 landraces into 3 clusters, mainly according to their place of collection or geographic origin. DipC1995 and Malawi5 were the most genetically related landraces. AFLP analysis provided sufficient polymorphism to determine the amount of genetic diversity and to establish genetic relationships in bambara groundnut landraces. The results will help in the formulation of marker-assisted breeding in bambara groundnut.

  6. Genetic diversity of a germplasm collection of Cucurbita pepo using SRAP and AFLP markers.

    Science.gov (United States)

    Ferriol, M; Picó, B; Nuez, F

    2003-07-01

    Cucurbita pepo is a highly polymorphic species. The cultivars can be grouped into eight morphotypes in two subspecies, ssp. pepo and ssp. ovifera. A collection of 69 accessions representative of the morphotypes and some unclassified types was used for analysing the morphological and molecular diversity of this species. This collection includes commercial cultivars and Spanish landraces, which represent the great diversification of types that have arisen in Europe after this species arrived from America. For the molecular variability studies, two PCR-based systems were employed, AFLP and SRAP, which preferentially amplify ORFs. Principal coordinates analysis and cluster analysis using the UPGMA method clearly separate the accessions into the two subspecies through the use of both markers. However, the gene diversity and the genetic identity values among morphotypes and subspecies varied between the two marker systems. The information given by SRAP markers was more concordant to the morphological variability and to the evolutionary history of the morphotypes than that of AFLP markers. In ssp. ovifera, the accessions of the different morphotypes were basically grouped according to the fruit colour. This may indicate different times of development and also the extent of breeding in the accessions used. This study has allowed identification of new types that can be employed for the development of new cultivars. The landraces of the spp. ovifera, used as ornamental in Europe, have proved to be of great interest for preserving the diversity of C. pepo.

  7. AFLP analysis of genetic relationships in the genus Fosterella L.B. Smith (Pitcairnioideae, Bromeliaceae).

    Science.gov (United States)

    Rex, Martina; Patzolt, Kerstin; Schulte, Katharina; Zizka, Georg; Vásquez, Roberto; Ibisch, Pierre L; Weising, Kurt

    2007-01-01

    The neotropical genus Fosterella L.B. Smith (Pitcairnioideae, Bromeliaceae) comprises about 30 species, with a centre of diversity in semiarid to humid habitats of the Andean slopes and valleys of Bolivia. Morphologic differentiation of species is difficult because of a paucity of diagnostic characters, and little is known about the infrageneric phylogeny. Here, we present the results of an amplified fragment length polymorphism (AFLP) analysis of 77 Fosterella specimens, covering 18 recognized species and 9 as-yet undescribed morphospecies. Eight primer combinations produced 310 bands, which were scored as presence/absence characters. Neighbour-joining tree reconstruction revealed 12 clusters (A-L) with various levels of support. Well-supported species groups were also recovered by a principal coordinates analysis. With few exceptions, morphologically defined species boundaries were confirmed by the molecular data. Phylogenetic relationships between species groups remained ambiguous, however, because of short internal branch lengths. The AFLP data were complemented by a survey of the leaf anatomy of 19 Fosterella species. Species concepts and assemblages are discussed in the context of molecular, morphologic, anatomic, ecologic, and biogeographic data. The data suggest that accidental long-distance dispersal and founder events have been important for Fosterella speciation.

  8. [Morphologic and AFLP analysis of relationships between tulip species Tulipa biebersteiniana (Liliaceae)].

    Science.gov (United States)

    Kutlunina, N A; Polezhaeva, M A; Permiakova, M V

    2013-04-01

    In populations of four species of tulips, (Tulipa biebersteiniana, T. patens, T. scytica and T. riparia) from the Volgograd, Kurgansk, Orenburg, and Chelyabinsk regions and the Republic of Bashkortostan, genetic diversity was studied by means of morphological and AFLP analysis. A morphological analysis of seven quantitative and two qualitative criteria was carried out. Three selective EcoRI/MseI primer pairs allowed one to genotype 81 individuals from 13 tulip populations with 87 loci. The low level of variability by AFLP loci were revealed in all species, including T. biebersteiniana (P = 20.41%, UH(e) = 0.075), T. patens (26.97%, 0.082), T. scytica (27.53%, 0.086), and T. riparia (27.72%, 0.096). According to the AMOVA results, the variability proportion that characterizes the differences between the four Tulip species was lower (F(CT) = 0.235) than between populations within species (F(ST) = 0.439). Tulipa patens is well differentiated by means of Nei's distances, coordination, and analysis in the STRUCTURE program. An analysis in the STRUCTURE revealed four genetic groups of tulips that are not completely in accordance with the analyzed species. This acknowledges the presence of complicated genetic process in the tulip population.

  9. Selection criteria for scoring amplified fragment length polymorphisms (AFLPs) positively affect the reliability of population genetic parameter estimates.

    Science.gov (United States)

    Herrmann, Doris; Poncet, Bénédicte N; Manel, Stéphanie; Rioux, Delphine; Gielly, Ludovic; Taberlet, Pierre; Gugerli, Felix

    2010-04-01

    A reliable data set is a fundamental prerequisite for consistent results and conclusions in population genetic studies. However, marker scoring of genetic fingerprints such as amplified fragment length polymorphisms (AFLPs) is a highly subjective procedure, inducing inconsistencies owing to personal or laboratory-specific criteria. We applied two alternative marker selection algorithms, the newly developed script scanAFLP and the recently published AFLPScore, to a large AFLP genome scan to test how population genetic parameters and error rates were affected. These results were confronted with replicated random selections of marker subsets. We show that the newly developed marker selection criteria reduced the mismatch error rate and had a notable influence on estimates of genetic diversity and differentiation. Both effects are likely to influence biological inference. For example, genetic diversity (HS) was 29% lower while genetic differentiation (FST) was 8% higher when applying scanAFLP compared with AFLPScore. Likewise, random selections of markers resulted in substantial deviations of population genetic parameters compared with the data sets including specific selection criteria. These randomly selected marker sets showed surprisingly low variance among replicates. We conclude that stringent marker selection and phenotype calling reduces noise in the data set while retaining patterns of population genetic structure.

  10. Genetic structure of Eurasian and North American Leymus (Triticeae) wildryes assessed by chloroplast DNA sequences and AFLP profiles

    Science.gov (United States)

    C. Mae Culumber; Steve R. Larson; Kevin B. Jensen; Thomas A. Jones

    2011-01-01

    Leymus is a genomically defined allopolyploid of genus Triticeae with two distinct subgenomes. Chloroplast DNA sequences of Eurasian and North American species are distinct and polyphyletic. However, phylogenies derived from chloroplast and nuclear DNA sequences are confounded by polyploidy and lack of polymorphism among many taxa. The AFLP technique can resolve...

  11. Identification of a male-specific AFLP marker in a functionally dioecious fig, Ficus fulva Reinw. ex Bl. (Moraceae)

    NARCIS (Netherlands)

    Parrish, T.L.; Koelewijn, H.P.; van Dijk, P.J.

    2004-01-01

    A male-specific amplified fragment length polymorphism (AFLP) marker was identified in the functionally dioecious fig species, Ficus fulva. A total of 89 polymorphic fragments from three primer combinations were produced, of which one (246 bp) was present in all males (n=23) and absent in all

  12. Phylogeny and infrageneric delimitation in the genus Spiraea (Rosaceae) inferred from AFLP markers and compared with morphology

    Czech Academy of Sciences Publication Activity Database

    Záveská Drábková, Lenka; Pospíšková, M.; Businský, R.

    2017-01-01

    Roč. 185, č. 4 (2017), s. 525-541 ISSN 0024-4074 R&D Projects: GA ČR(CZ) GA16-14649S Institutional support: RVO:67985939 Keywords : morphological analysis * Spiraea * AFLP Subject RIV: EF - Botanics OBOR OECD: Plant sciences, botany Impact factor: 2.277, year: 2016

  13. First genetic linkage map of Taraxacum koksaghyz Rodin based on AFLP, SSR, COS and EST-SSR markers.

    Science.gov (United States)

    Arias, Marina; Hernandez, Monica; Remondegui, Naroa; Huvenaars, Koen; van Dijk, Peter; Ritter, Enrique

    2016-08-04

    Taraxacum koksaghyz Rodin (TKS) has been studied in many occasions as a possible alternative source for natural rubber production of good quality and for inulin production. Some tire companies are already testing TKS tire prototypes. There are also many investigations on the production of bio-fuels from inulin and inulin applications for health improvement and in the food industry. A limited amount of genomic resources exist for TKS and particularly no genetic linkage map is available in this species. We have constructed the first TKS genetic linkage map based on AFLP, COS, SSR and EST-SSR markers. The integrated linkage map with eight linkage groups (LG), representing the eight chromosomes of Russian dandelion, has 185 individual AFLP markers from parent 1, 188 individual AFLP markers from parent 2, 75 common AFLP markers and 6 COS, 1 SSR and 63 EST-SSR loci. Blasting the EST-SSR sequences against known sequences from lettuce allowed a partial alignment of our TKS map with a lettuce map. Blast searches against plant gene databases revealed some homologies with useful genes for downstream applications in the future.

  14. Genetic diversity and relationship in American and African oil palm as revealed by RFLP and AFLP molecular markers

    Directory of Open Access Journals (Sweden)

    Barcelos Edson

    2002-01-01

    Full Text Available The objective of this work was to evaluate the genetic diversity, its organization and the genetic relationships within oil palm (Elaeis oleifera (Kunth Cortés, from America, and E. guineensis (Jacq., from Africa germplasm using Restriction Fragment Length Polymorphism (RFLP and Amplified Fragment Length Polymorphism (AFLP. In complement to a previous RFLP study on 241 E. oleifera accessions, 38 E. guineensis accessions were analyzed using the same 37 cDNA probes. These accessions covered a large part of the geographical distribution areas of these species in America and Africa. In addition, AFLP analysis was performed on a sub-set of 40 accessions of E. oleifera and 22 of E. guineensis using three pairs of enzyme/primer combinations. Data were subjected to Factorial Analysis of Correspondence (FAC and cluster analysis, with parameters of genetic diversity being also studied. Results appeared congruent between RFLP and AFLP. In the E. oleifera, AFLP confirmed the strong structure of genetic diversity revealed by RFLP, according to geographical origin of the studied material, with the identification of the same four distinct genetic groups: Brazil, French Guyana/Surinam, Peru, north of Colombia/Central America. Both markers revealed that genetic divergence between the two species is of the same magnitude as that among provenances of E. oleifera. This finding is in discrepancy with the supposed early tertiary separation of the two species.

  15. Insight into the genomic diversity and relationship of Astragalus glycyphyllos symbionts by RAPD, ERIC-PCR, and AFLP fingerprinting.

    Science.gov (United States)

    Gnat, Sebastian; Małek, Wanda; Oleńska, Ewa; Trościańczyk, Aleksandra; Wdowiak-Wróbel, Sylwia; Kalita, Michał; Wójcik, Magdalena

    2015-11-01

    We assessed the genomic diversity and genomic relationship of 28 Astragalus glycyphyllos symbionts by three methodologies based on PCR reaction, i.e., RAPD, ERIC-PCR, and AFLP. The AFLP method with one PstI restriction enzyme and selective PstI-GC primer pair had a comparable discriminatory power as ERIC-PCR one and these fingerprinting techniques distinguished among the studied 28 A. glycyphyllos symbionts 18 and 17 genomotypes, respectively. RAPD method was less discriminatory in the genomotyping of rhizobia analyzed and it efficiently resolved nine genomotypes. The cluster analysis of RAPD, ERIC-PCR, and AFLP profiles resulted in a generally similar grouping of the test strains on generated dendrograms supporting a great potential of these DNA fingerprinting techniques for study of genomic polymorphism and evolutionary relationship of A. glycyphyllos nodulators. The RAPD, ERIC-PCR, and AFLP pattern similarity coefficients between A. glycyphyllos symbionts studied was in the ranges 8-100, 18-100, and 23-100%, respectively.

  16. Reduction of species in the wild potato Solanum section Petota series Longipedicellata : AFLP, RAPD and chloroplast SSR data

    NARCIS (Netherlands)

    Berg, van den R.G.; Bryan, G.J.; Rio, del A.; Spooner, D.M.

    2002-01-01

    Species boundaries were assessed with three molecular markers [AFLPs, RAPDs and chloroplast simple sequence repeats (cpSSRs)] for all six species of wild potatoes (Solanum section Petota) assigned to ser. Longipedicellata: Solanum fendleri, S. hjertingii, S. matehualae, S. papita, S. polytrichon and

  17. AFLP markers for the assessment of genetic diversity in european and North American potato varieties cultivated in Iran

    Directory of Open Access Journals (Sweden)

    Saeed Tarkesh Esfahani

    2009-01-01

    Full Text Available Information about the genetic diversity of potato germplasm in Iran is important for variety identification andto enhance the classification of germplasm collections and exploit them in breeding programs and for the development andintroduction of new varieties. AFLP fingerprinting was applied to a group of cultivated potato varieties to find if there is anygeographical differentiation in potato diversity from Europe and North America. The high level of polymorphism within potatovarieties and the high number of variety-specific bands suggest that AFLPs are powerful markers for diversity analysis inpotato varieties. No region-specific AFLP markers were found (present in varieties from the same origin and absent inothers. The UPGMA dendrogram revealed four distinct clusters corresponding almost to the geographical origin of thevarieties. However, the bootstrap support for branches was rather weak. No clusters clearly distinguished varieties fromEurope and North America. Varieties from the same geographical origins however tended to group together within eachcluster. The mean similarity and the UPGMA dendrogram both suggest that North American varieties have nearly identicalgenetic diversity to European varieties. The results of AMOVA revealed large within-region variations which accounted for94.5% of the total molecular variance. The between-region variation, although accounting for only 5.5% of the total variation,was statistically significant. AFLP technology was successfully used to evaluate diversity between different geographicalgroups of potatoes and is recommended for potato genetic studies.

  18. First genetic linkage map of Taraxacum koksaghyz Rodin based on AFLP, SSR, COS and EST-SSR markers

    Science.gov (United States)

    Arias, Marina; Hernandez, Monica; Remondegui, Naroa; Huvenaars, Koen; van Dijk, Peter; Ritter, Enrique

    2016-01-01

    Taraxacum koksaghyz Rodin (TKS) has been studied in many occasions as a possible alternative source for natural rubber production of good quality and for inulin production. Some tire companies are already testing TKS tire prototypes. There are also many investigations on the production of bio-fuels from inulin and inulin applications for health improvement and in the food industry. A limited amount of genomic resources exist for TKS and particularly no genetic linkage map is available in this species. We have constructed the first TKS genetic linkage map based on AFLP, COS, SSR and EST-SSR markers. The integrated linkage map with eight linkage groups (LG), representing the eight chromosomes of Russian dandelion, has 185 individual AFLP markers from parent 1, 188 individual AFLP markers from parent 2, 75 common AFLP markers and 6 COS, 1 SSR and 63 EST-SSR loci. Blasting the EST-SSR sequences against known sequences from lettuce allowed a partial alignment of our TKS map with a lettuce map. Blast searches against plant gene databases revealed some homologies with useful genes for downstream applications in the future. PMID:27488242

  19. Faraona dievišķās varas manifestācija Ozīrisa un Hora svētkos 1872.-30.g.p.m.ē

    OpenAIRE

    Andrejauska, Ieva

    2012-01-01

    Bakalaura darba „Faraona dievišķās varas manifestācija Ozīrisa un Hora svētkos 1872. - 30. g.p.m.ē.” mērķis ir apskatīt konkrēto svētku ceremonijas ar faraona klātbūtni un izpētīt, kā caur rituāliem tiek leģitimēta dievišķā vara. Senās Ēģiptes valdniekam piemita dievišķa vara, ko noteiktā laikā bija nepieciešams atjaunot, stiprināt, leģitimēt. Tas bija iespējams Ozīrisa un Hora svētku ceremonijās, kuru laikā faraons veica ar Ozīrisa mitoloģiju saistītus rituālus. Pētījuma gaitā noskaidrots, ...

  20. Identification of AFLP molecular linked to row- type gene in barley

    International Nuclear Information System (INIS)

    Sayed- Tabatabaei, B.E.

    2005-01-01

    Formation of the two-and six-rowed types in barley is predominantly controlled by alleles at a single locus (vrzl) which is located in long armn of chromosome 2H. This gene is a key character on the study of barley domestication and yield. Near-isogenic lines of barley were produced from crosses between Kanto Nakate Gold (tow-rowed) and Azumamugi (six-rowed). The selected lines were used for screening of AFLP polymorphic bands which are linked to vrs1 locus. After screening of a total of 1792 primer combination, five polymorphic bands were identified. A construction of high resolution map around the vrs1 locus was made using recombinant inbred lines. These markers can be used for a map-based cloning of the genes at the vrsl locus

  1. Molecular characterization of cultivated species of the genus Pachyrhizus Rich. ex DC. by AFLP markers

    DEFF Research Database (Denmark)

    Santayana, Monica; Rossel, Genoveva; Núñez, Jorge

    2014-01-01

    ) molecular markers in order to estimate genetic diversity and interspecific relationships. To complement molecular marker information, individuals from each accession were analyzed in order to confirmploidy levels. Eight AFLP primer combinations detected 136 (68.7 %) polymorphic bands. Shannon’s diversity...... indices (Hs) for each species were 1.04 (P. ahipa), 1.07 (P. tuberosus), and 2.42 (P. erosus), while the total diversity index was 2.45. Phylogenetic analysis, principal coordinate analysis and analysis of molecular variance (FST=0.796) all showed significant species differentiation. All accessions were...... diploid (2n=2x=22), which is characteristic of the tribe Phaseoleae. Finally, a misclassified accession of P. tuberosus was identified. Molecular characterization of accessions is necessary for efficient management of germplasm collections....

  2. AFLP analysis of genetic diversity in determinate and indeterminate snap bean accessions

    Directory of Open Access Journals (Sweden)

    Felipe Aranha de Andrade

    2016-01-01

    Full Text Available The present study aimed to estimate and characterize the genetic divergence between determinate and indeterminate snap bean accessions from the Universidade Estadual de Londrina (UEL germplasm bank based on amplified fragment length polymorphism (AFLP markers. A total of 40 and 32 accessions with determinate and indeterminate growth habits, respectively, were characterized for this purpose. Seven combinations of primers corresponding to EcoR1 and Mse1 were tested for the AFLP analysis, and the combinations E-AAG/M-CTC, E-ACT/M-CTT and E-ACC/M-CTT were selected. The resulting products were denatured and subjected to capillary electrophoresis. The Jaccard distance was used to estimate the genetic distances between accessions, and the Unweighted Pair Cluster Method with Arithmetic Mean (UPGMA, principal coordinates analysis (PCoA and Bayesian statistics were used for the clustering analysis. The three combinations of primer/enzyme revealed 485 informative loci in total, and the combination E-ACC/M-CTT detected the greatest number of informative loci (49%. The analysis of dissimilarity frequency distribution showed that the distribution was uniform, ranging from 0.1285 to 0.7310 with a mean of 0.4801, and the accessions with indeterminate growth habits exhibited greater variability than the accessions with determinate growth habits. The clustering UPGMA, PCoA and Bayesian analyses showed the formation of two large clusters, wherein there is a possible association between snap bean growth habit and gene pool. The determinate accessions may be more closely associated with the Andean gene pool, while the indeterminate ones may be associated with the Mesoamerican gene pool. The Bayesian analysis showed accessions intermediate to both groups, suggesting introgression between the Andean and Mesoamerican gene pools.

  3. DIVERSIDAD GENÉTICA DE MARACUYÁ EN GUATEMALA REVELADA POR MARCADORES AFLP

    Directory of Open Access Journals (Sweden)

    Karla Melina Ponciano-Samayoa

    2012-01-01

    Full Text Available Diversidad genética de maracuyá en Guatemala revelada por marcadores AFLP. Los objetivos de este estudio fueron caracterizar con AFLP nueve genotipos colectados en Guatemala y determinar la diversidad genética existente. En el Instituto de Ciencia y Tecnología Agrícolas (ICTA, en el período julio 2010/mayo 2011, se realizó este análisis preliminar amplifi cando diez combinaciones selectivas con las que se detectaron 106 polimorfi smos. Las combinaciones selectivas E+ACG/M+CAG, E+ACA/M+CTA, E+ACT/M+CTG y E+AAC/M+CTT dieron el mayor grado de información. En promedio se visualizaron diez loci por amplifi cación selectiva. El análisis de similaridad reveló que los genotipos no están duplicados. Los análisis de correspondencia y conglomerados identifi caron dos grupos bien defi nidos. El primero incluyó a los materiales de P. edulis f. edulis Sims y el segundo a los materiales de P. edulis f. fl avicarpa Degener. La diversidad genética de Nei para la colección fue 0,3160. La diferenciación genética (Gst fue 0,2542. El 25,42% de la diversidad se expresó entre grupos mientras que el 74,58% dentro de estos. Los resultados dan evidencia de la cercanía evolutiva de los tipos amarilla y morada de P. edulis Sims. El fl ujo genético fue alto (Nm=1,4670 como se esperaba en una especie alógama en la que se favorece el intercambio inter e intraespecífi co.

  4. Microbial population responses to pH and salt shock during phenols degradation under high salt conditions revealed by RISA and AFDRA.

    Science.gov (United States)

    Yan, Bin; Wang, Ping; Liao, Wenchao; Ye, Qian; Xu, Meilan; Zhou, Jiti

    2013-01-01

    The responses of microbial community to pH and salt shock during phenols degradation under high salt conditions were revealed by two DNA fingerprint methods, i.e. ribosomal intergenic spacer analysis (RISA) and amplified functional DNA restriction analysis (AFDRA), together with 16S rDNA clone library analysis. It was shown that the phenols removal rate was improved with increasing NaCl concentration from 0 to 50 mg/L, and could remain at a high level even in the presence of 100 mg/L NaCl. The degradation efficiency remained stable under neutral conditions (pH 7.0-9.0), but decreased sharply under acidic (below pH 5.0) or more alkaline conditions (above pH 10.0). The community structure was dramatically changed during salt fluctuations, with Halomonas sp. and Marinobacter sp. as the predominant salt-tolerant species. Meanwhile, Marinobacter sp. and Alcaligenes faecalis sp. were the major species which might play the key role for stabilizing the treatment systems under different pH conditions. Moreover, the changes of phenol hydroxylase genes were analyzed by AFDRA, which showed that these functional genes were substantially different under any shock conditions.

  5. Una risa en el desierto: el arte de la resurrección y sermones y prédicas del Cristo de Elqui

    Directory of Open Access Journals (Sweden)

    Jorge Ladino Gaitán Bayona

    2015-01-01

    Full Text Available En este artículo de reflexión se analiza la propuesta carnavalesca de la novela El arte de la resurrección (2010, de Hernán Rivera Letelier, y los poemarios Sermones y prédicas del Cristo de Elqui (1977 y Nuevos sermones y prédicas del Cristo de Elqui (1979, de Nicanor Parra. En estas obras interviene como protagonista un excéntrico predicador de existencia real en la historia de Chile: Domingo Zárate Vega, mejor conocido como el Cristo de Elqui. Se retoman planteamientos teóricos de Mijail Bajtín para explorar la risa y la locura como recursos estéticos que generan una visión crítica sobre la miseria de los mineros en las salitreras del desierto chileno, la dictadura militar de Augusto Pinochet y La matanza de la Escuela Santa María de Iquique (21 de diciembre de 1907.

  6. Genetic diversity among proso millet (Panicum miliaceum biotypes assessed by AFLP technique Diversidade genética entre biótipos de proso millet (Panicum miliaceum revelada pela técnica de AFLP

    Directory of Open Access Journals (Sweden)

    D. Karam

    2004-06-01

    Full Text Available The Amplified Fragment Length Polymorphism (AFLP technique was used to access genetic diversity between three domestic and nine wild proso millet biotypes from the United States and Canada. Eight primer combinations detected 39 polymorphic DNA fragments, with the genetic distance estimates among biotypes ranging from 0.02 to 0.04. Colorado-Weld County black seeded and Wyoming-Platte County were the most distinct biotypes according to the dissimilarity level. A UPGMA cluster analysis revealed two distinct groups of proso millet without any geographic association. Six weed biotypes exhibiting some characters of cultivated plants were grouped together with domesticated biotypes of proso millet while the three typical wild phenotypes were clearly clustered into another group according to AFLP markers.A técnica de AFLP (Amplified Fragment Length Polymorphism foi empregada para acessar a diversidade genética entre três biótipos domesticados e nove biótipos selvagens de proso millet dos Estados Unidos e do Canadá. Oito combinações de primers detectaram 39 fragmentos polimórficos de DNA, e a estimativa da distância genética entre os biótipos variou de 0,02 a 0,04. Colorado-Weld County de sementes pretas e Wyoming-Platte County foram os biótipos mais distintos de acordo com o índice de dissimilaridade. A análise de cluster por UPGMA revelou dois grupos distintos de proso millet mas sem nenhuma relação geográfica. Seis biótipos selvagens que exibiam algumas características de plantas cultivadas foram agrupados juntamente com os biótipos domesticados de proso millet, enquanto os três fenótipos tipicamente selvagens formaram outro grupo distinto por marcadores AFLP.

  7. Some AFLP amplicons are highly conserved DNA sequences mapping to the same linkage groups in two F2 populations of carrot

    Directory of Open Access Journals (Sweden)

    Santos Carlos A.F.

    2002-01-01

    Full Text Available Amplified fragment length polymorphism (AFLP is a fast and reliable tool to generate a large number of DNA markers. In two unrelated F2 populations of carrot (Daucus carota L., Brasilia x HCM and B493 x QAL (wild carrot, it was hypothesized that DNA 1 digested with the same restriction endonuclease enzymes and amplified with the same primer combination and 2 sharing the same position in polyacrylamide gels should be conserved sequences. To test this hypothesis AFLP fragments from polyacrylamide gels were eluted, reamplified, separated in agarose gels, purified, cloned and sequenced. Among thirty-one paired fragments from each F2 population, twenty-six had identity greater than 91% and five presented identity of 24% to 44%. Among the twenty-six conserved AFLPs only one mapped to different linkage groups in the two populations while four of the five less-conserved bands mapped to different linkage groups. Of eight SCAR (sequence characterized amplified regions primers tested, one conserved AFLP resulted in co-dominant markers in both populations. Screening among 14 carrot inbreds or cultivars with three AFLP-SCAR primers revealed clear and polymorphic PCR products, with similar molecular sizes on agarose gels. The development of co-dominant markers based on conserved AFLP fragments will be useful to detect seed mixtures among hybrids, to improve and to merge linkage maps and to study diversity and phylogenetic relationships.

  8. Genetic structure in cultivated and wild carrots (¤Daucus carota¤ L.) revealed by AFLP analysis

    DEFF Research Database (Denmark)

    Shim, S.I.; Bagger Jørgensen, Rikke

    2000-01-01

    showed that the old varieties released between 1974 and 1976 were more heterogeneous than the newly developed F-1 hybrid varieties. The analysis of molecular variation (AMOVA) showed that the major part of the genetic variation in the plant material was found within populations/varieties. The presence......Genetic variation within and among five Danish populations of wild carrot and five cultivated varieties was investigated using amplified fragment length polymorphism (AFLP). Ten AFLP primer combinations produced 116 polymorphic bands. Based on the marker data an UPGMA-cluster analysis and principal...... component analysis (PCA) separated the Daucus collections into three groups, consisting of the wild populations, the old varieties, and the recently bred varieties. The genetic distance between the wild populations reflected the physical distance between collection sites. Analysis of genetic diversity...

  9. Genetic differentiation in Pyrenophora teres f. teres populations from Syria and Tunisia as assessed by AFLP markers.

    Science.gov (United States)

    Bouajila, A; Zoghlami, N; Murad, S; Baum, M; Ghorbel, A; Nazari, K

    2013-06-01

    To investigate the level of genetic differentiation and diversity among Pyrenophora teres isolate populations originating from different agro-ecological areas of Syria and Tunisia and to determine the potential of AFLP profiling in genotyping Pyrenophora teres f. teres. In this study, AFLP markers have been employed to identify patterns of population structure in 20 Pyrenophora teres f. teres populations from Syria and Tunisia. Ninety-four isolates were studied by the use of a protocol that involved stringent PCR amplification of fragments derived from digestion of genomic DNA with restriction enzymes EcoRI and MesI. Based on 401 amplified polymorphic DNA markers (AFLP), variance analyses indicated that most of the variation was partitioned within rather than between populations. Genotypic diversity (GD) was high for populations from Rihane, local landraces and different agro-ecological zones (GD = 0·75-0·86). There was high genetic differentiation among pathogen populations from different host populations in Syria (Gst  = 0·31, ht = 0·190) and Tunisia (Gst  = 0·39, ht = 0·263), which may be partly explained by the low gene flow around the areas sampled. A phenetic tree revealed three groups with high bootstrap values (55, 68, 76) and reflected the grouping of isolates based on host, or agro-ecological areas. AFLP profiling is an effective method for typing the genetically diverse pathogen Pyrenophora teres f. teres. The study represents a comparative analysis of the genetic diversity in P. teres isolates from two countries spanning two continents and also shows that several distinct P. teres genotypes may be found in a given environment. The implications of these findings for Pyrenophora teres f. teres evolutionary potential and net blotch-resistance breeding in Syria and Tunisia were also discussed. © 2012 The Society for Applied Microbiology.

  10. Genetic diversity and structure of Brazilian ginger germplasm (Zingiber officinale) revealed by AFLP markers.

    Science.gov (United States)

    Blanco, Eleonora Zambrano; Bajay, Miklos Maximiliano; Siqueira, Marcos Vinícius Bohrer Monteiro; Zucchi, Maria Imaculada; Pinheiro, José Baldin

    2016-12-01

    Ginger is a vegetable with medicinal and culinary properties widely cultivated in the Southern and Southeastern Brazil. The knowledge of ginger species' genetic variability is essential to direct correctly future studies of conservation and genetic improvement, but in Brazil, little is known about this species' genetic variability. In this study, we analyzed the genetic diversity and structure of 55 Brazilian accessions and 6 Colombian accessions of ginger, using AFLP (Amplified Fragment Length Polymorphism) molecular markers. The molecular characterization was based on 13 primers combinations, which generated an average of 113.5 polymorphic loci. The genetic diversity estimates of Nei (Hj), Shannon-Weiner index (I) and an effective number of alleles (n e ) were greater in the Colombian accessions in relation to the Brazilian accessions. The analysis of molecular variance showed that most of the genetic variation occurred between the two countries while in the Brazilian populations there is no genetic structure and probably each region harbors 100 % of genetic variation found in the samples. The bayesian model-based clustering and the dendrogram using the dissimilarity's coefficient of Jaccard were congruent with each other and showed that the Brazilian accessions are highly similar between themselves, regardless of the geographic region of origin. We suggested that the exploration of the interspecific variability and the introduction of new varieties of Z.officinale are viable alternatives for generating diversity in breeding programs in Brazil. The introduction of new genetic materials will certainly contribute to a higher genetic basis of such crop.

  11. AFLPs reveal different population genetic structure under contrasting environments in the marine snail Nucella lapillus L.

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    Belén Carro

    Full Text Available Dispersal has received growing attention in marine ecology, particularly since evidence obtained with up-to-date techniques challenged the traditional view. The dogwhelk Nucella lapillus L., a sedentary gastropod with direct development, is a good example: dispersal was traditionally assumed to be limited until studies with microsatellites disputed this idea. To shed some light on this controversy, the genetic structure of dogwhelk populations in northwest Spain was investigated with highly polymorphic AFLP markers giving special attention to the influence of hydrodynamic stress. In agreement with the expectations for a poor disperser, our results show a significant genetic structure at regional (<200 km and areal scales (<15 km. However, the spatial genetic structure varied with wave-exposure in the present case study: IBD was evident under sheltered conditions but absent from the exposed area where genetic differentiation was stronger. Our results provide evidence that differences in wave-exposure can exert a detectable influence on the genetic structure of coastal organisms, even in species without a planktonic larva.

  12. Genetic variability and population structure of Disanthus cercidifolius subsp. longipes (Hamamelidaceae based on AFLP analysis.

    Directory of Open Access Journals (Sweden)

    Yi Yu

    Full Text Available Disanthus cercidifolius subsp. longipes is an endangered species in China. Genetic diversity and structure analysis of this species was investigated using amplified fragments length polymorphism (AFLP fingerprinting. Nei's gene diversity ranged from 0.1290 to 0.1394. The AMOVA indicated that 75.06% of variation was distributed within populations, while the between-group component 5.04% was smaller than the between populations-within-group component 19.90%. Significant genetic differentiation was detected between populations. Genetic and geographical distances were not correlated. PCA and genetic structure analysis showed that populations from East China were together with those of the Nanling Range. These patterns of genetic diversity and levels of genetic variation may be the result of D. c. subsp. longipes restricted to several isolated habitats and "excess flowers production, but little fruit set". It is necessary to protect all existing populations of D. c. subsp. longipes in order to preserve as much genetic variation as possible.

  13. Sex-linked AFLP markers indicate a pseudoautosomal region in hemp ( Cannabis sativa L.).

    Science.gov (United States)

    Peil, A; Flachowsky, H; Schumann, E; Weber, W E

    2003-06-01

    In dioecious plants of hemp ( Cannabis sativa L.), males are regarded as heterogametic XY and females as homogametic XX, although it is difficult to discriminate the X cytologically from the Y. The Y chromosome is somewhat larger than the X. Our aim was to analyse AFLP markers on X and Y, and to use them to gain some insight into the structure of the sex chromosomes. Markers located on the sex chromosomes can be grouped into different classes, depending on the presence or absence of a fragment on the X and/or the Y. They are detected by separately analysing male and female progenies of a single cross. Five markers were found to be located on both chromosomes. A few recombinants were observed for marker pairs of this class in the male progenies. Two completely linked markers located on the Y chromosome in the male parent show a recombination rate of r = 0.25 with sex. Recombination must have occurred between the sex chromosomes in the male parent. The recombination analysis led to the conclusion that there is a pseudoautosomal region (PAR) on the sex chromosomes, allowing recombination between the X and the Y chromosome. The other regions of the sex chromosomes show only a few recombination events, for the Y as well as for the X. These results are discussed in comparison to other dioecious plants.

  14. Comparative assessment of DNA fingerprinting techniques (RAPD, ISSR and AFLP) for genetic analysis of cashew (Anacardium occidentale L.) accessions of India.

    Science.gov (United States)

    Archak, S; Gaikwad, A B; Gautam, D; Rao, E V V B; Swamy, K R M; Karihaloo, J L

    2003-06-01

    Nineteen cashew accessions were analysed with 50 random primers, 12 ISSR primers and 6 AFLP primer pairs to compare the efficiency and utility of these techniques for detecting variation in cashew germplasm. Each marker system could discriminate between all of the accessions, albeit with varied efficiency of polymorphism detection. AFLP exhibited maximum discrimination efficiency with a genotype index of 1. The utility of each molecular marker technique, expressed as marker index, was estimated as a function of average band informativeness and effective multiplex ratio. Marker index was calculated to be more than 10 times higher in AFLP than in RAPD and ISSR. Similarity matrices were determined based on the data generated by molecular and morphometric analyses, and compared for congruency. AFLP displayed no correspondence with RAPD and ISSR. Correlation between ISSR and RAPD similarity matrices was low but significant (r = 0.63; p < 0.005). The similarity matrix based on morphometric markers exhibited no correlation with any of the molecular markers. AFLP, with its superior marker utility, was concluded to be the marker of choice for cashew genetic analysis.

  15. Genetic diversity of populations and clones of Rhopilema esculentum in China based on AFLP analysis

    Science.gov (United States)

    Qiao, Hongjin; Liu, Xiangquan; Zhang, Xijia; Jiang, Haibin; Wang, Jiying; Zhang, Limin

    2013-03-01

    Amplified fragment length polymorphisms (AFLP) markers were developed to assess the genetic variation of populations and clones of Rhopilema esculentum Kishinouye (Scyphozoa, Rhizostomatidae). One hundred and seventy-nine loci from 56 individuals of two hatchery populations and two wild populations were genotyped with five primer combinations. The polymorphic ratio, Shannon's diversity index and average heterozygosity were 70.3%, 0.346 and 0.228 for the white hatchery population, 74.3%, 0.313, and 0.201 for the red hatchery population, 79.3%, 0.349, and 0.224 for the Jiangsu wild population, and 74.9%, 0.328 and 0.210 for the Penglai wild population, respectively. Thus, all populations had a relatively high level of genetic diversity. A specific band was identified that could separate the white from the red hatchery population. There was 84.85% genetic differentiation within populations. Individual cluster analysis using unweighted pair-group method with arithmetic mean (UPGMA) suggested that hatchery populations and wild populations could be divided. For the hatchery populations, the white and red populations clustered separately; however, for the wild populations, Penglai and Jiangsu populations clustered together. The genetic diversity at the clone level was also determined. Our data suggest that there are relatively high genetic diversities within populations but low genetic differentiation between populations, which may be related to the long-term use of germplasm resources from Jiangsu Province for artificial seeding and releasing. These findings will benefit the artificial seeding and conservation of the germplasm resources.

  16. Use of RAPD and AFLP markers to identify inter- and intraspecific hybrids of Mentha.

    Science.gov (United States)

    Shasany, A K; Darokar, M P; Dhawan, S; Gupta, A K; Gupta, S; Shukla, A K; Patra, N K; Khanuja, S P S

    2005-01-01

    Three controlled crosses were carried out involving Mentha arvensis and Mentha spicata [M. spicata CIMAP/C30 x M. spicata CIMAP/C33 (cv. Neera); M. arvensis CIMAP/C18 x CIMAP/C17 (cv. Kalka); and M. arvensis CIMAP/C17 x M. spicata CIMAP/C33]. The parents were subjected to random amplified polymorphic DNA (RAPD) analysis with 80 primers, and polymorphic primers were tested for detecting coinherited RAPD profiles among the progeny of these crosses. Of 50 seedlings tested from each intraspecific cross, all demonstrated dominant profiles with the selected RAPD primers except the detected hybrid from respective crosses. Coinherited markers could be detected with the primers OPJ 01, MAP 06, OPT 08, and OPO 20 for M. arvensis; OPJ 05, OPJ 14, OPO 19, and OPT 09 for M. spicata; and OPJ 07, OPJ 10, OPJ 11, OPJ 14, and OPO 02 for the cross M. arvensis x M. spicata. In our amplified fragment length polymorphism (AFLP) analysis, 40 coinherited marker fragments were identified for the cross involving M. arvensis, 32 for the cross involving M. spicata, and 41 for the interspecific cross between M. arvensis and M. spicata. In all crosses, similarity values between the parents were less than those between the parents and the hybrids. Although RAPD markers are generally considered dominant, it is possible to identify a few codominant markers that behave like restriction fragment length polymorphism (RFLP) markers. This molecular marker system may be helpful in rapidly screening out hybrids in crops where cross-pollination is a problem.

  17. AFLP analysis of Genetic Diversity Among Different Jatropha curcas L. Genotypes from Africa and Ecuador

    Directory of Open Access Journals (Sweden)

    Konan, NO.

    2018-01-01

    Full Text Available Six populations amounting to a total number of seventy genotypes of Jatropha curcas L. originating from Africa (Senegal, Mali, Burkina Faso and Madagascar and Ecuador were investigated for genetic diversity using two AFLP primer combinations. The results revealed a high genetic diversity in the populations studied. The population with greatest genetic diversity was Madagascar (He = 0.2638 and I = 0.4066 and the least diverse was Senegal-Tamba (He = 0.1962 and I = 0.3079. AMOVA (analysis of molecular variance detected the highest proportion of variation within populations (81% of the total molecular variation. This may be attributed to the high level of allogamy observed in this species. The Nei's standard unbiased genetic distance (D between the populations ranged from 0.010 (Senegal-Tamba and Burkina Faso to 0.131 (Mali and Ecuador; the average was 0.063. Analysis of the genetic relationships among the 6 populations using both neighbor-joining cluster analysis and principal component analysis (PCoA showed five clusters with globally, groupings of i most of Burkina Faso and Senegal-Tamba genotypes, ii most of Mali and Senegal-Diobass genotypes , iii most of Madagascar and Ecuador genotypes, and iv some mixings of genotypes with different origins. Considering the distance existing between the different origins there are prospects to develop F1 hybrids. The greatest heterosis might be expected from crossing involving genotypes of cluster I and cluster V which group the more distant genotypes. Such crossing schemes might produce greater success in the production of genetic variability and might maximize the exploitation of heterosis and segregation.

  18. Preliminary assessment of AFLP fingerprinting of Rubus glaucus Benth. elite genotypes

    Directory of Open Access Journals (Sweden)

    Duarte Delgado Diana

    2011-04-01

    Full Text Available

    The Andean blackberry (Rubus glaucus Benth. is a promissory fruit crop for Colombia with potential to become an international commodity due to its high nutritional and nutraceutical value. Farmer genotypes from the national R. glaucus collection were selected from eight outstanding accessions according to their nutritional and agronomic value, for distribution among local producers. The goal of this work is to evaluate the genomic fingerprint by AFLP analysis of these elite genotypes using three primer combinations. From 179 total amplified loci produced by the three combinations, 20% resulted polymorphic. The EAGG/MCTT combination was the most informative with a 32% polymorphism and greater discrimination power. The genotypes tested showed a high average similarity (96% and the accessions San Antonio and ILS-1863 formed independent groups with good statistical support in the clustering analysis. The remaining accessions did not form discrete groups with good support (<50%, probably due to genetic homogeneity among them and/or low resolving power of markers. This study is one of the first attempts to generate a genomic fingerprint of these farmer elite genotypes for protection, seed certification and future support to breeding programs.

     

  19. Using AFLP-RGA markers to assess genetic diversity among pigeon pea (Cajanus cajan genotypes in relation to major diseases

    Directory of Open Access Journals (Sweden)

    Prakash G Pati

    2014-06-01

    Full Text Available Resistance gene analog (RGA-anchored amplified fragment length polymorphism (AFLP-RGA marker system was used in order to evaluate genetic relationships among 22 pigeon pea genotypes with varied responses to Fusarium wilt and sterility mosaic disease. Five AFLP-RGA primer combinations (E-CAG/wlrk-S, M-GTG/wlrk-S, M-GTG/wlrk-AS, E-CAT/S1-INV and E-CAG/wlrk-AS produced 173 scorable fragments, of which 157 (90.7% were polymorphic, with an average of 31.4 fragments per primer combination. The polymorphism rates obtained with the five primers were 83.3%, 92.0%, 92.3%, 93.0% and 93.1%, respectively. Mean polymorphic information content (PIC values ranged from 0.24 (with E-CAT/S1-INV to 0.30 (with E-CAG/wlrk-AS, whereas resolving power (RP values varied from 11.06 (with M-GTG/wlrk-S to 25.51 (with E-CAG/wlrk-AS and marker index (MI values ranged from 5.98 (with M-GTG/wlrk-S to 12.30 (with E-CAG/wlrk-AS. We identified a positive correlation between MI and RP (r²=0.98, p<0.05, stronger that that observed for the comparison between PIC and RP (r²=0.88, p<0.05. That implies that either MI or RP is the best parameter for selecting more informative AFLP-RGA primer combinations. The Jaccard coefficient ranged from 0.07 to 0.72, suggesting a broad genetic base in the genotypes studied. A neighbor-joining tree, based on the unweighted pair group method with arithmetic mean, distinguished cultivated species from wild species. The grouping of resistant genotypes in different clusters would help in the selection of suitable donors for resistance breeding in pigeon pea.

  20. Identificación y mapeo de AFLPs ligados al gen de resistencia al PVX en Solanum commersonii

    Directory of Open Access Journals (Sweden)

    Mónica Blanco

    2005-01-01

    Full Text Available Solanum commersonii es una especie silvestre de papa considerada como una fuente de genes de resistencia al PVX. Para identificar marcadores moleculares relacionados con los genes de resistencia a este virus, se realizó un análisis en el que se combinó la técnica de BSA con el uso de AFLPs. Del cruce de 2 padres heterocigotos y resistentes al PVX, provenientes de una F1, se obtuvo una F2. La población fue inoculada con el PVXMS y 30 días después mediante un ELISA, la progenie fue dividida en individuos infectados y no infectados con el PVXMS; a estos 2 grupos se les realizó un BSA. El ADN de los individuos resistentes fue mezclado aparte del ADN de los individuos susceptibles y con la ayuda de AFLPs se logró identificar 22 combinaciones de imprimadores que produjeron bandas específicas relacionadas con el carácter de resistencia al PVX. Las combinaciones de imprimadores seleccionadas fueron utilizadas para evaluar cada uno de los individuos de la F2 en forma independiente. Producto de este análisis se obtuvo 63 bandas polimórficas relacionadas al carácter de resistencia, cuya información fue introducida en el programa MAPRF6. Como resultado se obtuvo 4 grupos de ligamiento. Se encontró un RGA, obtenido en otro estudio que co-segrega (0 cM con el locus del gen de resistencia extrema (Rx y los AFLPs 42 y 39 que están rodeando el mismo locus a 22,6 cM o más. La información obtenida será básica para implementar programas de selección asistida por marcadores moleculares en el mejoramiento genético.

  1. Huyendo del miedo, desterrando el enojo, escapando de la tristeza y cayendo en brazos de la risa: los chistes en México en tiempos de la influenza 2009

    Directory of Open Access Journals (Sweden)

    Anna María Fernandez Poncela

    2012-03-01

    Full Text Available Se trata de revisar el humor, los chistes y la risa en tiempos de la influenza en México en el año 2009. La relación entre narrativas sociales populares (chistes y reacciones emocionales de la sociedad en un momento de incertidumbre y temor social. El por qué y para qué de los chistes, su función social y psicológica. El objetivo es que el chiste nos acompañe a develar la realidad social, política, emocional y cultural. Para ello se aborda un poco el humor, lo cómico, la risa y los chistes. Presentamos algunas definiciones de estos fenómenos y mostramos su funcionalidad psicológica y social, entre otras cosas, como parte de los sentimientos humanos y la cultura en general. También reflexionamos algo en torno al mundo de las emociones y su evolución o desarrollo, y en determinadas situaciones sociales, en concreto en el contexto de los días de la contingencia sanitaria por el virus A H1N1 en México, entre abril y mayo del año 2009.

  2. Huyendo del miedo, desterrando el enojo, escapando de la tristeza y   cayendo en brazos de la risa: los chistes en México en tiempos de la influenza 2009

    Directory of Open Access Journals (Sweden)

    Anna María Fernández Poncela

    2012-07-01

    Full Text Available Se trata de revisar el humor, los chistes y la risa en tiempos de la influenza en México en el año 2009. La relación entre narrativas sociales populares (chistes y reacciones emocionales de la sociedad en un momento de incertidumbre y temor social. El por qué y para qué de los chistes, su función social y psicológica. El objetivo es que el chiste nos acompañe a develar la realidad social, política, emocional y cultural. Para ello se aborda un poco el humor, lo cómico, la risa y los chistes. Presentamos algunas definiciones de estos fenómenos y mostramos su funcionalidad psicológica y social, entre otras co‐ sas, como parte de los sentimientos humanos y la cultura en general. También reflexionamos algo en torno al mundo de las emociones y su evolución o desarrollo, y en determinadas situaciones sociales, en concreto en el contexto de los días de la contingencia sanitaria por el virus A H1N1 en México, en‐ tre abril y mayo del año 2009. 

  3. The uses of AFLP for detecting DNA polymorphism, genotype identification and genetic diversity between yeasts isolated from Mexican agave-distilled beverages and from grape musts.

    Science.gov (United States)

    Flores Berrios, E P; Alba González, J F; Arrizon Gaviño, J P; Romano, P; Capece, A; Gschaedler Mathis, A

    2005-01-01

    The objectives were to determine the variability and to compare the genetic diversity obtained using amplified fragment length polymorphism (AFLP) markers in analyses of wine, tequila, mezcal, sotol and raicilla yeasts. A molecular characterization of yeasts isolated from Mexican agave musts, has been performed by AFLP marker analysis, using reference wine strains from Italian and South African regions. A direct co-relation between genetic profile, origin and fermentation process of strains was found especially in strains isolated from agave must. In addition, unique molecular markers were obtained for all the strains using six combination primers, confirming the discriminatory power of AFLP markers. This is the first report of molecular characterization between yeasts isolated from different Mexican traditional agave-distilled beverages, which shows high genetic differences with respect to wine strains.

  4. Species phylogeny and diversification process of Northeast Asian Pungitius revealed by AFLP and mtDNA markers

    DEFF Research Database (Denmark)

    Takahashi, Hiroshi; Møller, Peter Rask; Shedko, Sergei V.

    2016-01-01

    clade with conspecific allopatric populations. The phylogeny showed that two lineages arose early; one gave rise to two species (circumpolar species P. pungitius and Paratethys species P. platygaster) and the other to five species endemic to Northeast Asia (P. sinensis, P. tymensis, P. polyakovi, P....... kaibarae, and P. bussei). The brackish-water, freshwater, and Omono types previously discovered in Japan were reidentified as P. pungitius, P. sinensis, and P. kaibarae, respectively. A marked incongruence was noted between the phylogenies of AFLP and mtDNA markers, suggesting the occasional occurrence...

  5. Differentiation of species of the family Acetobacteraceae by AFLP DNA fingerprinting: Gluconacetobacter kombuchae is a later heterotypic synonym of Gluconacetobacter hansenii.

    Science.gov (United States)

    Cleenwerck, Ilse; De Wachter, Marjan; González, Angel; De Vuyst, Luc; De Vos, Paul

    2009-07-01

    Amplified fragment length polymorphism (AFLP) DNA fingerprinting was investigated as a tool for fast and accurate identification of acetic acid bacteria (AAB) to the species level. One hundred and thirty five reference strains and 15 additional strains, representing 50 recognized species of the family Acetobacteraceae, were subjected to AFLP analysis using the restriction enzyme combination ApaI/TaqI and the primer combination A03/T03. The reference strains had been previously subjected to either DNA-DNA hybridization or 16S-23S rRNA spacer region gene sequence analysis and were regarded as being accurately classified at the species level. The present study revealed that six of these strains should be reclassified, namely Gluconacetobacter europaeus LMG 1518 and Gluconacetobacter xylinus LMG 1510 as Gluconacetobacter xylinus and Gluconacetobacter europaeus, respectively; Gluconacetobacter kombuchae LMG 23726(T) as Gluconacetobacter hansenii; and Acetobacter orleanensis strains LMG 1545, LMG 1592 and LMG 1608 as Acetobacter cerevisiae. Cluster analysis of the AFLP DNA fingerprints of the reference strains revealed one cluster for each species, showing a linkage level below 50 % with other clusters, except for Acetobacter pasteurianus, Acetobacter indonesiensis and Acetobacter cerevisiae. These three species were separated into two, two, and three clusters, respectively. At present, confusion exists regarding the taxonomic status of Gluconacetobacter oboediens and Gluconacetobacter intermedius; the AFLP data from this study supported their classification as separate taxa. The 15 additional strains could all be identified at the species level. AFLP analysis further revealed that some species harboured genetically diverse strains, whereas other species consisted of strains showing similar banding patterns, indicating a more limited genetic diversity. It can be concluded that AFLP DNA fingerprinting is suitable for accurate identification and classification of a broad

  6. Differentiation of Arcobacter species by numerical analysis of AFLP profiles and description of a novel Arcobacter from pig abortions and turkey faeces

    DEFF Research Database (Denmark)

    On, Stephen L.W.; Harrington, C.S.; Atabay, H.I.

    2003-01-01

    , and a previously unclassified porcine abortion strain were studied. AFLP profiling was performed using a BglII-Csp6I-based protocol previously used to characterize Campylobacter species. Duplicate profiles of 20 isolates were 93.25% similar, indicating high reproducibility. Numerical analysis of all 72 strains...... of A. cryaerophilus were differentiated at the 39.5% similarity level. For strain typing, 62 distinct types were defined, with evidence of clonal lineages within A. butzleri, A. cryaerophilus and A. skirrowii. Conclusions: AFLP profiling is an effective means of determining taxonomic and strain...

  7. Caracterización molecular de introducciones colombianas de caña flecha utilizando la técnica AFLP Molecular characterization of colombian wild cane accesions with AFLP

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    Hernando Rivera Jiménez

    2008-12-01

    Full Text Available La fibra de la caña flecha Gynerium sagittatum (Aubl. se utiliza como materia prima para fabricar el "sombrero vueltiao", sombrero típico de la costa caribeña colombiana. Se realizó la caracterización molecular con AFLP para estimar variabilidad genética teniendo en cuenta criterios geográficos y morfológicos de 25 introducciones colombianas del banco de germoplasma de la Universidad de Córdoba. El análisis de correspondencia múltiple discriminó las introducciones en cuatro grupos, donde se identificaron características de importancia artesanal (comercial y atributos agronómicos. Se observó escasa correlación entre distancia geográfica y diferenciación genética, lo cual indicó flujos antrópicos por la reproducción asexual del material.Wild cane (Gynerium sagittatum Aubl. fiber is used as raw material for to make "hat vueltiao". A molecular characterization using AFLP was carriet out to estimate genetic variability of 25 accessions planted at the University of Cordoba, associated with geographical and morphological traits. Multiple discrimination correspondence analyses of introductions separated four groups, based on craft handling and agronomic attributes desirable. There was little correlation between geographic distance and genetic differentiation, indicating an anthropic flows by asexual reproduction.

  8. THE EFFECT OF INDIVIDUAL SELECTION FOR GENETIC DIVERSITY OF Acacia mangium SEEDLING SEED ORCHARD USING AFLP MARKERS

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    A. Y.P.B.C. Widyatmoko

    2006-07-01

    Full Text Available Establishment of seed orchard is aimed at producing good quality seeds which is an important activity for breeding program. Seed orchard is also a base population, thus its genetic diversity is depending on its design and composition (provenance, family and individual tree. Selection of an individual tree in seed orchard is needed for the enhancement of  retaining good-character trees. However, selection of individual tree can change the genetic diversity of seed orchard, and the degrees to which the genetic diversity will change depend on the used selection methods. In order to investigate the effects of selection methods, 4 simulations of selection methods based on height, diameter and stem performance of individual trees were used. The differences among the 4 methods were the ranking of individual trees those selected, and families and provenances those have been represented. Seedling seed orchard of Acacia mangium in Wonogiri, Central Java was used as materials. Analysis of genetic diversity was carried out using AFLP markers. Nine primer combinations were used to produce 1025 AFLP banding patterns. Among those banding patterns, only 109 were polymorphic markers. No significant effect of individual tree selection was revealed in this study. Even though the selection was done intensively, only 7.1% of genetic diversity was reduced. In other words, the selection activity did not reduce the genetic diversity of seed orchard significantly. The result is important for developing future tree improvement of A. mangium, including development of hybrid between A. mangium and A. auriculiformis.

  9. Genetic relatedness between cassava (Manihot esculenta Crantz and M. flabellifolia and M. Peruviana based on both RAPD and AFLP markers

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    Colombo Carlos

    2000-01-01

    Full Text Available The taxonomy of the genus Manihot is still uncertain and the genetic origin of cassava (M. esculenta Crantz continues to be controversial. We studied the degree of genetic relatedness between cassava and two naturally occurring species (M. flabellifolia and M. peruviana which are probably involved in the evolution of cassava, using RAPD and AFLP molecular markers. Thirty-three clonal accessions of cassava of known genetic diversity and 15 accessions of the wild species M. flabellifolia and M. peruviana were analyzed using 92 polymorphic RAPD bands and 73 polymorphic AFLP bands. The genetic markers were unable to differentiate the two wild species, which confirms their botanical similarity. Half of the total number of amplified bands were monomorphic in all of the genotypes evaluated. The mean genetic similarity (Jaccard between cassava and the species M. flabellifolia/M. peruviana was 0.59. A grouping analysis (neighbor-joining method with RAPD markers of cultivated cassava, M. flabellifolia/M. peruviana and the other wild species located the genotypes of cassava and M. flabellifolia/M. peruviana at one extremity and the three Mexican species (M. aesculifolia, M. michaelis and M. chlorostica at the other. An intermediate position between these groups was occupied by two wild species (M. glaziovii and M. reptans native to central and northeastern Brazil. These results are consistent with the hypothesis that the species M. flabellifolia and M. peruviana gave rise to the cultivated species.

  10. Non PCR-amplified Transcripts and AFLP fragments as reduced representations of the quail genome for 454 Titanium sequencing

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    Leterrier Christine

    2010-07-01

    Full Text Available Abstract Background SNP (Single Nucleotide Polymorphism discovery is now routinely performed using high-throughput sequencing of reduced representation libraries. Our objective was to adapt 454 GS FLX based sequencing methodologies in order to obtain the largest possible dataset from two reduced representations libraries, produced by AFLP (Amplified Fragment Length Polymorphism for genomic DNA, and EST (Expressed Sequence Tag for the transcribed fraction of the genome. Findings The expressed fraction was obtained by preparing cDNA libraries without PCR amplification from quail embryo and brain. To optimize the information content for SNP analyses, libraries were prepared from individuals selected in three quail lines and each individual in the AFLP library was tagged. Sequencing runs produced 399,189 sequence reads from cDNA and 373,484 from genomic fragments, covering close to 250 Mb of sequence in total. Conclusions Both methods used to obtain reduced representations for high-throughput sequencing were successful after several improvements. The protocols may be used for several sequencing applications, such as de novo sequencing, tagged PCR fragments or long fragment sequencing of cDNA.

  11. Genetic variation in wild populations of the tuber crop Amorphophallus konjac (Araceae) in central China as revealed by AFLP markers.

    Science.gov (United States)

    Pan, C; Gichira, A W; Chen, J M

    2015-12-29

    Amorphophallus konjac is an economically important crop. In order to provide baseline information for sustainable development and conservation of the wild plant resources of A. konjac, we studied the genetic diversity and population structure of this species using amplified fragment length polymorphism (AFLP) molecular markers. We sampled 139 individuals from 10 wild populations of A. konjac in central China. Using five AFLP primer combinations, we scored a total of 270 DNA fragments, most of which were polymorphic (98.2%). Percentage of polymorphic loci, Nei's genetic diversity index, and Shannon's information index showed high levels of genetic variation within A. konjac populations. Analysis of molecular variance indicated that most of the variance (68%) resided within populations. The coefficient of genetic differentiation between populations was 0.348 and the estimated gene flow was 0.469, indicating that there was limited gene flow among the populations. Unweighted pair group method with arithmetic mean cluster analysis and principal coordinates analysis indicated that geographically close populations were more likely to cluster together. The Mantel test revealed a significant correlation between geographic and genetic distances (R2 = 0.2521, P konjac and the complex geography of central China are likely to have contributed to the current pattern of genetic variation of this species. In the present study, we provide several suggestions on the future protection of the wild plant genetic resources of A. konjac.

  12. AFLP and DNA sequence variation in an Andean domesticate, pepino (Solanum muricatum, Solanaceae): implications for evolution and domestication.

    Science.gov (United States)

    Blanca, José M; Prohens, Jaime; Anderson, Gregory J; Zuriaga, Elena; Cañizares, Joaquín; Nuez, Fernando

    2007-07-01

    The pepino (Solanum muricatum) is a vegetatively propagated, domesticated native of the Andes, where it grows with wild relatives. We used AFLPs and a 1-kb sequence of the 3-methylcrotonyl-CoA carboxylase gene to study variation of 27 accessions of S. muricatum and 35 collections of 10 species of wild relatives (Solanum section Basarthrum). A total of 298 AFLP fragments and 29 DNA sequence haplotypes were detected. Cluster and principal coordinate analyses and other genetic parameters estimated from both types of markers, show that S. muricatum is closely related to the species from one of the series (Caripensia) of section Basarthrum and that >90% of the variation of the cultigen is also represented in that series. Pepino is highly diverse, either because it is not monophyletic or it has been subjected to regular introgression with wild species, or both. Although a continuous distribution of the genetic variation occurred within the cultivated species, three genetic clusters were recognized. Cluster 1 is mostly centered in Ecuador, cluster 2 in Ecuador and Peru, and cluster 3 in Colombia and Ecuador. Cluster 3 also includes all modern cultivars studied. These results and other evidence suggest that northern Ecuador/southern Colombia is the main center of pepino diversity and the center of origin. The high genetic variation of this cultigen indicates that domestication does not always produce a genetic bottleneck.

  13. Morphological changes of Paulownia seedlings infected phytoplasmas reveal the genes associated with witches' broom through AFLP and MSAP.

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    Xibing Cao

    Full Text Available Paulownia witches' broom (PaWB caused by phytoplasma might result in devastating damage to the growth and wood production of Paulownia. To study the effect of phytoplasma on DNA sequence and to discover the genes related to PaWB occurrence, DNA polymorphisms and DNA methylation levels and patterns in PaWB seedlings, the ones treated with various concentration of methyl methane sulfonate (MMS and healthy seedlings were investigated with amplified fragment length polymorphism (AFLP and methylation-sensitive amplification polymorphism (MSAP. Our results indicated that PaWB seedlings recovered a normal morphology, similar to healthy seedlings, after treatment with more than 20 mg · L-1 MMS; Phytoplasma infection did not change the Paulownia genomic DNA sequence at AFLP level, but changed the global DNA methylation levels and patterns; Genes related to PaWB were discovered through MSAP and validated using quantitative real-time PCR (qRT-PCR. These results implied that changes of DNA methylation levels and patterns were closely related to the morphological changes of seedlings infected with phytoplasmas.

  14. AFLP analysis reveals a lack of phylogenetic structure within Solanum section Petota

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    Vleeshouwers Vivianne GAA

    2008-05-01

    Full Text Available Abstract Background The secondary genepool of our modern cultivated potato (Solanum tuberosum L. consists of a large number of tuber-bearing wild Solanum species under Solanum section Petota. One of the major taxonomic problems in section Petota is that the series classification (as put forward by Hawkes is problematic and the boundaries of some series are unclear. In addition, the classification has received only partial cladistic support in all molecular studies carried out to date. The aim of the present study is to describe the structure present in section Petota. When possible, at least 5 accessions from each available species and 5 individual plants per accession (totally approx. 5000 plants were genotyped using over 200 AFLP markers. This resulted in the largest dataset ever constructed for Solanum section Petota. The data obtained are used to evaluate the 21 series hypothesis put forward by Hawkes and the 4 clade hypothesis of Spooner and co-workers. Results We constructed a NJ tree for 4929 genotypes. For the other analyses, due to practical reasons, a condensed dataset was created consisting of one representative genotype from each available accession. We show a NJ jackknife and a MP jackknife tree. A large part of both trees consists of a polytomy. Some structure is still visible in both trees, supported by jackknife values above 69. We use these branches with >69 jackknife support in the NJ jackknife tree as a basis for informal species groups. The informal species groups recognized are: Mexican diploids, Acaulia, Iopetala, Longipedicellata, polyploid Conicibaccata, diploid Conicibaccata, Circaeifolia, diploid Piurana and tetraploid Piurana. Conclusion Most of the series that Hawkes and his predecessors designated can not be accepted as natural groups, based on our study. Neither do we find proof for the 4 clades proposed by Spooner and co-workers. A few species groups have high support and their inner structure displays also

  15. Marcadores fAFLP na caracterização de três genótipos de umezeiro selecionados como porta-enxertos para pessegueiro fAFLP markers to characterize three mume genotypes selected as rootstocks for peach tree

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    Ester Wickert

    2007-12-01

    Full Text Available O objetivo deste trabalho foi caracterizar a diversidade genética existente em três genótipos de umezeiro (Clone 05, cv. Rigitano e Clone 15 e identificar marcadores moleculares fAFLP (fluorescent Amplified Fragment Lenght Polymorphism passíveis de serem utilizados na discriminação dos três genótipos de umezeiro selecionados como porta-enxertos para pessegueiro. Foram utilizadas 24 diferentes combinações de primers seletivos fAFLP que geraram 648 marcas, das quais 272 foram diferenciadoras dos três genótipos entre si. As marcas diferenciadoras permitiram o agrupamento dos clones de umezeiro de acordo com sua similaridade através do Método da Distância e algorítmo Neighbour Joining. As mesmas marcas foram utilizadas para calcular a distância genética entre os clones. Com o uso de marcadores fAFLP foi possível discriminar os três genótipos de umezeiro entre si, destacando-se as combinações Fam ACT/CAT, Joe AGG/CTT e Ned AGC/CAA, que permitiram a diferenciação individual de cada um dos clones. A maior distância genética foi encontrada entre a cv. Rigitano e o Clone 15. Os marcadores fAFLP revelaram maior proximidade genética entre o Clone 05 e a cv. Rigitano.The objective of this work was the identification of fAFLP markers to be used in molecular characterization of three mume genotypes selected as rootstocks for peach tree. Twenty-four different fAFLP primer combinations were used and allowed the recognition of 648 markers, comprising 272 markers which were able to discriminate the three clones one from the other. These markers were used to calculate the groupment of the clones according to their similarities with the distance method and neighbour joining algorithm. The same markers were also used to calculate the genetic distance among the clones. The fAFLP markers were efficient to identify the clones, mainly by the combinations of selective primers Fam ACT/CAT, Joe AGG/CTT and Ned AGC/CAA. fAFLP markers allowed the

  16. Clinical characteristics and persistence of bovine mastitis caused by different species of coagulase-negative staphylococci identified with API or AFLP

    DEFF Research Database (Denmark)

    Taponen, S.; Simojoki, H.; Haveri, M.

    2006-01-01

    . Staphylococcus simulans (43.6%) followed by S. chromogenes (23.3%) were the most common CNS species isolated from the milk samples. Ninety-nine isolates were genotyped using AFLP-analysis. Only 75.0% of S. chromogenes and S. simulans isolates identified with API test were clustered with the type strains...

  17. Differentially expressed genes in Populus simonii x P. nigra in respnse to NaCl stress using cDNA-AFLP

    Science.gov (United States)

    Salinity is an important environmental factor limiting growth and productivity of plants, and affects almost every aspect of the plant physiology and biochemistry. The objective of this study was to apply cDNA-AFLP and to identify differentially expressed genes in response to NaCl stress vs. no-stre...

  18. Genetic relationship and diversity in a sesame (Sesamum indicum L. germplasm collection using amplified fragment length polymorphism (AFLP

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    Karlovsky Petr

    2006-02-01

    Full Text Available Abstract Background Sesame is an important oil crop in tropical and subtropical areas. Despite its nutritional value and historic and cultural importance, the research on sesame has been scarce, particularly as far as its genetic diversity is concerned. The aims of the present study were to clarify genetic relationships among 32 sesame accessions from the Venezuelan Germplasm Collection, which represents genotypes from five diversity centres (India, Africa, China-Korea-Japan, Central Asia and Western Asia, and to determine the association between geographical origin and genetic diversity using amplified fragment length polymorphism (AFLP. Results Large genetic variability was found within the germplasm collection. A total of 457 AFLP markers were recorded, 93 % of them being polymorphic. The Jaccard similarity coefficient ranged from 0.38 to 0.85 between pairs of accessions. The UPGMA dendrogram grouped 25 of 32 accessions in two robust clusters, but it has not revealed any association between genotype and geographical origin. Indian, African and Chinese-Korean-Japanese accessions were distributed throughout the dendrogram. A similar pattern was obtained using principal coordinates analysis. Genetic diversity studies considering five groups of accessions according to the geographic origin detected that only 20 % of the total diversity was due to diversity among groups using Nei's coefficient of population differentiation. Similarly, only 5% of the total diversity was attributed to differences among groups by the analysis of molecular variance (AMOVA. This small but significant difference was explained by the fact that the Central Asia group had a lower genetic variation than the other diversity centres studied. Conclusion We found that our sesame collection was genetically very variable and did not show an association between geographical origin and AFLP patterns. This result suggests that there was considerable gene flow among diversity centres

  19. Genetic relationship and diversity in a sesame (Sesamum indicum L.) germplasm collection using amplified fragment length polymorphism (AFLP)

    Science.gov (United States)

    Laurentin, Hernán E; Karlovsky, Petr

    2006-01-01

    Background Sesame is an important oil crop in tropical and subtropical areas. Despite its nutritional value and historic and cultural importance, the research on sesame has been scarce, particularly as far as its genetic diversity is concerned. The aims of the present study were to clarify genetic relationships among 32 sesame accessions from the Venezuelan Germplasm Collection, which represents genotypes from five diversity centres (India, Africa, China-Korea-Japan, Central Asia and Western Asia), and to determine the association between geographical origin and genetic diversity using amplified fragment length polymorphism (AFLP). Results Large genetic variability was found within the germplasm collection. A total of 457 AFLP markers were recorded, 93 % of them being polymorphic. The Jaccard similarity coefficient ranged from 0.38 to 0.85 between pairs of accessions. The UPGMA dendrogram grouped 25 of 32 accessions in two robust clusters, but it has not revealed any association between genotype and geographical origin. Indian, African and Chinese-Korean-Japanese accessions were distributed throughout the dendrogram. A similar pattern was obtained using principal coordinates analysis. Genetic diversity studies considering five groups of accessions according to the geographic origin detected that only 20 % of the total diversity was due to diversity among groups using Nei's coefficient of population differentiation. Similarly, only 5% of the total diversity was attributed to differences among groups by the analysis of molecular variance (AMOVA). This small but significant difference was explained by the fact that the Central Asia group had a lower genetic variation than the other diversity centres studied. Conclusion We found that our sesame collection was genetically very variable and did not show an association between geographical origin and AFLP patterns. This result suggests that there was considerable gene flow among diversity centres. Future germplasm

  20. Levels of Intra-specific AFLP Diversity in Tuber-Bearing Potato Species with Different Breeding Systems and Ploidy Levels

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    Glenn J. Bryan

    2017-09-01

    Full Text Available DNA-based marker analysis of plant genebank material has become a useful tool in the evaluation of levels of genetic diversity and for the informed use and maintenance of germplasm. In this study, we quantify levels of amplified fragment length polymorphism (AFLP in representative accessions of wild and cultivated potato species of differing geographic origin, ploidy, and breeding system. We generated 449 polymorphic AFLP fragments in 619 plants, representing multiple plants (16–23 from 17 accessions of 14 potato taxa as well as single plants sampled from available accessions (from 3 to 56 of the same 14 taxa. Intra-accession diversities were compared to those of a synthetic ‘taxon-wide’ population comprising a single individual from a variable number of available accessions of each sampled taxon. Results confirm the expected considerably lower levels of polymorphism within accessions of self-compatible as compared to self-incompatible taxa. We observed broadly similar levels of ‘taxon-wide’ polymorphism among self-compatible and self-incompatible species, with self-compatible taxa showing only slightly lower rates of polymorphism. The most diverse accessions were the two cultivated potato accessions examined, the least diverse being the Mexican allohexaploids Solanum demissum and S. iopetalum. Generally allopolyploid self-compatible accessions exhibited lower levels of diversity. Some purported self-incompatible accessions showed relatively low levels of marker diversity, similar to the more diverse self-compatible material surveyed. Our data indicate that for self-compatible species a single plant is highly representative of a genebank accession. The situation for self-incompatible taxa is less clear, and sampling strategies used will depend on the type of investigation. These results have important implications for those seeking novel trait variation (e.g., disease resistance in gene banks as well as for the selection of individuals

  1. AFLP polymorphisms allow high resolution genetic analysis of American Tegumentary Leishmaniasis agents circulating in Panama and other members of the Leishmania genus.

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    Carlos M Restrepo

    Full Text Available American Tegumentary Leishmaniasis is caused by parasites of the genus Leishmania, and causes significant health problems throughout the Americas. In Panama, Leishmania parasites are endemic, causing thousands of new cases every year, mostly of the cutaneous form. In the last years, the burden of the disease has increased, coincident with increasing disturbances in its natural sylvatic environments. The study of genetic variation in parasites is important for a better understanding of the biology, population genetics, and ultimately the evolution and epidemiology of these organisms. Very few attempts have been made to characterize genetic polymorphisms of parasites isolated from Panamanian patients of cutaneous leishmaniasis. Here we present data on the genetic variability of local isolates of Leishmania, as well as specimens from several other species, by means of Amplified Fragment Length Polymorphisms (AFLP, a technique seldom used to study genetic makeup of parasites. We demonstrate that this technique allows detection of very high levels of genetic variability in local isolates of Leishmania panamensis in a highly reproducible manner. The analysis of AFLP fingerprints generated by unique selective primer combinations in L. panamensis suggests a predominant clonal mode of reproduction. Using fluorescently labeled primers, many taxon-specific fragments were identified which may show potential as species diagnostic fragments. The AFLP permitted a high resolution genetic analysis of the Leishmania genus, clearly separating certain groups among L. panamensis specimens and highly related species such as L. panamensis and L. guyanensis. The phylogenetic networks reconstructed from our AFLP data are congruent with established taxonomy for the genus Leishmania, even when using single selective primer combinations. Results of this study demonstrate that AFLP polymorphisms can be informative for genetic characterization in Leishmania parasites, at

  2. Identification of DNA sequence variation in Campylobacter jejuni strains associated with the Guillain-Barré syndrome by high-throughput AFLP analysis

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    Endtz Hubert P

    2006-04-01

    Full Text Available Abstract Background Campylobacter jejuni is the predominant cause of antecedent infection in post-infectious neuropathies such as the Guillain-Barré (GBS and Miller Fisher syndromes (MFS. GBS and MFS are probably induced by molecular mimicry between human gangliosides and bacterial lipo-oligosaccharides (LOS. This study describes a new C. jejuni-specific high-throughput AFLP (htAFLP approach for detection and identification of DNA polymorphism, in general, and of putative GBS/MFS-markers, in particular. Results We compared 6 different isolates of the "genome strain" NCTC 11168 obtained from different laboratories. HtAFLP analysis generated approximately 3000 markers per stain, 19 of which were polymorphic. The DNA polymorphisms could not be confirmed by PCR-RFLP analysis, suggesting a baseline level of 0.6% AFLP artefacts. Comparison of NCTC 11168 with 4 GBS-associated strains revealed 23 potentially GBS-specific markers, 17 of which were identified by DNA sequencing. A collection of 27 GBS/MFS-associated and 17 enteritis control strains was analyzed with PCR-RFLP tests based on 11 of these markers. We identified 3 markers, located in the LOS biosynthesis genes cj1136, cj1138 and cj1139c, that were significantly associated with GBS (P = 0.024, P = 0.047 and P Conclusion This study shows that bacterial GBS markers are limited in number and located in the LOS biosynthesis genes, which corroborates the current consensus that LOS mimicry may be the prime etiologic determinant of GBS. Furthermore, our results demonstrate that htAFLP, with its high reproducibility and resolution, is an effective technique for the detection and subsequent identification of putative bacterial disease markers.

  3. Population structure and genetic diversity in insular populations of Nasutitermes takasagoensis (Isoptera: Termitidae) analyzed by AFLP markers.

    Science.gov (United States)

    García, Julio; Maekawa, Kiyoto; Miura, Toru; Matsumoto, Tadao

    2002-10-01

    Dispersal ability and degree of inbreeding in a population can indirectly be assessed using genetic markers. In general, it was suggested that winged termites are not able to fly distances greater than several hundred meters. Here, amplified fragment length polymorphism (AFLP) was used to analyze genetic diversity, population substructure, and gene flow among insular populations of the termite Nasutitermes takasagoensis (Isoptera: Termitidae) in the Yaeyama Islands, Okinawa, Japan. Samples were collected from 77 nests on seven islands of the Yaeyama Group. Using three primer combinations a total of 155 bands were generated with 78 (50%) polymorphic bands. Genetic distance and G(st) values among insular populations were calculated. Relatively high genetic diversity and low values of G (st), suggest there is moderate subpopulation structure. Based on these results, we discussed two possibilities; first, winged termites are able to fly over distances of several kilometers, and second, these results were obtained because insular populations share a recent common origin.

  4. Metabolic profiles and cDNA-AFLP analysis of Salvia miltiorrhiza and Salvia castanea Diel f. tomentosa Stib.

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    Dongfeng Yang

    Full Text Available Plants of the genus Salvia produce various types of phenolic compounds and tanshinones which are effective for treatment of coronary heart disease. Salvia miltiorrhiza and S. castanea Diels f. tomentosa Stib are two important members of the genus. In this study, metabolic profiles and cDNA-AFLP analysis of four samples were employed to identify novel genes potentially involved in phenolic compounds and tanshinones biosynthesis, including the red roots from the two species and two tanshinone-free roots from S. miltiorrhiza. The results showed that the red roots of S. castanea Diels f. tomentosa Stib produced high contents of rosmarinic acid (21.77 mg/g and tanshinone IIA (12.60 mg/g, but low content of salvianolic acid B (1.45 mg/g. The red roots of S. miltiorrhiza produced high content of salvianolic acid B (18.69 mg/g, while tanshinones accumulation in this sample was much less than that in S. castanea Diels f. tomentosa Stib. Tanshinones were not detected in the two tanshinone-free samples, which produced high contents of phenolic compounds. A cDNA-AFLP analysis with 128 primer pairs revealed that 2300 transcript derived fragments (TDFs were differentially expressed among the four samples. About 323 TDFs were sequenced, of which 78 TDFs were annotated with known functions through BLASTX searching the Genbank database and 14 annotated TDFs were assigned into secondary metabolic pathways through searching the KEGGPATHWAY database. The quantitative real-time PCR analysis indicated that the expression of 9 TDFs was positively correlated with accumulation of phenolic compounds and tanshinones. These TDFs additionally showed coordinated transcriptional response with 6 previously-identified genes involved in biosynthesis of tanshinones and phenolic compounds in S. miltiorrhiza hairy roots treated with yeast extract. The sequence data in the present work not only provided us candidate genes involved in phenolic compounds and tanshinones biosynthesis

  5. Dealing with AFLP genotyping errors to reveal genetic structure in Plukenetia volubilis (Euphorbiaceae in the Peruvian Amazon.

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    Jakub Vašek

    Full Text Available An analysis of the population structure and genetic diversity for any organism often depends on one or more molecular marker techniques. Nonetheless, these techniques are not absolutely reliable because of various sources of errors arising during the genotyping process. Thus, a complex analysis of genotyping error was carried out with the AFLP method in 169 samples of the oil seed plant Plukenetia volubilis L. from small isolated subpopulations in the Peruvian Amazon. Samples were collected in nine localities from the region of San Martin. Analysis was done in eight datasets with a genotyping error from 0 to 5%. Using eleven primer combinations, 102 to 275 markers were obtained according to the dataset. It was found that it is only possible to obtain the most reliable and robust results through a multiple-level filtering process. Genotyping error and software set up influence both the estimation of population structure and genetic diversity, where in our case population number (K varied between 2-9 depending on the dataset and statistical method used. Surprisingly, discrepancies in K number were caused more by statistical approaches than by genotyping errors themselves. However, for estimation of genetic diversity, the degree of genotyping error was critical because descriptive parameters (He, FST, PLP 5% varied substantially (by at least 25%. Due to low gene flow, P. volubilis mostly consists of small isolated subpopulations (ΦPT = 0.252-0.323 with some degree of admixture given by socio-economic connectivity among the sites; a direct link between the genetic and geographic distances was not confirmed. The study illustrates the successful application of AFLP to infer genetic structure in non-model plants.

  6. Dealing with AFLP genotyping errors to reveal genetic structure in Plukenetia volubilis (Euphorbiaceae) in the Peruvian Amazon.

    Science.gov (United States)

    Vašek, Jakub; Hlásná Čepková, Petra; Viehmannová, Iva; Ocelák, Martin; Cachique Huansi, Danter; Vejl, Pavel

    2017-01-01

    An analysis of the population structure and genetic diversity for any organism often depends on one or more molecular marker techniques. Nonetheless, these techniques are not absolutely reliable because of various sources of errors arising during the genotyping process. Thus, a complex analysis of genotyping error was carried out with the AFLP method in 169 samples of the oil seed plant Plukenetia volubilis L. from small isolated subpopulations in the Peruvian Amazon. Samples were collected in nine localities from the region of San Martin. Analysis was done in eight datasets with a genotyping error from 0 to 5%. Using eleven primer combinations, 102 to 275 markers were obtained according to the dataset. It was found that it is only possible to obtain the most reliable and robust results through a multiple-level filtering process. Genotyping error and software set up influence both the estimation of population structure and genetic diversity, where in our case population number (K) varied between 2-9 depending on the dataset and statistical method used. Surprisingly, discrepancies in K number were caused more by statistical approaches than by genotyping errors themselves. However, for estimation of genetic diversity, the degree of genotyping error was critical because descriptive parameters (He, FST, PLP 5%) varied substantially (by at least 25%). Due to low gene flow, P. volubilis mostly consists of small isolated subpopulations (ΦPT = 0.252-0.323) with some degree of admixture given by socio-economic connectivity among the sites; a direct link between the genetic and geographic distances was not confirmed. The study illustrates the successful application of AFLP to infer genetic structure in non-model plants.

  7. Analysis of genetic diversity in banana cultivars (Musa cvs.) from the South of Oman using AFLP markers and classification by phylogenetic, hierarchical clustering and principal component analyses*

    Science.gov (United States)

    Opara, Umezuruike Linus; Jacobson, Dan; Al-Saady, Nadiya Abubakar

    2010-01-01

    Banana is an important crop grown in Oman and there is a dearth of information on its genetic diversity to assist in crop breeding and improvement programs. This study employed amplified fragment length polymorphism (AFLP) to investigate the genetic variation in local banana cultivars from the southern region of Oman. Using 12 primer combinations, a total of 1094 bands were scored, of which 1012 were polymorphic. Eighty-two unique markers were identified, which revealed the distinct separation of the seven cultivars. The results obtained show that AFLP can be used to differentiate the banana cultivars. Further classification by phylogenetic, hierarchical clustering and principal component analyses showed significant differences between the clusters found with molecular markers and those clusters created by previous studies using morphological analysis. Based on the analytical results, a consensus dendrogram of the banana cultivars is presented. PMID:20443211

  8. Environmental sampling of Ceratonia siliqua (carob) trees in Spain reveals the presence of the rare Cryptococcus gattii genotype AFLP7/VGIV.

    Science.gov (United States)

    Linares, Carlos; Colom, María Francisca; Torreblanca, Marina; Esteban, Violeta; Romera, Álvaro; Hagen, Ferry

    2015-01-01

    Cryptococcus gattii is a pathogenic basidiomycetous yeast that is emerging in temperate climate zones worldwide. C. gattii has repetitively been isolated from numerous tree species. Ongoing environmental sampling and molecular characterization is essential to understand the presence of this primary pathogenic microorganism in the Mediterranean environment. To report the first isolation of the rare C. gattii genotype AFLP7/VGIV from the environment in Europe. Samples were collected from woody debris of carob trees (Ceratonia siliqua) and olive trees (Olea europaea) in El Perelló, Tarragona, Spain. Cryptococcus species were further characterized by using URA5-RFLP, MALDI-TOF, AFLP and MLST. The antifungal susceptibility profile to amphotericin B, 5-fluorocytosine, fluconazole, itraconazole, posaconazole and voriconazole was determined using Sensititre Yeast One and E-test. Cultures from one carob tree revealed the presence of ten Cryptococcus-like colonies. One colony was identified as C. gattii, and subsequent molecular characterization showed that it was an α mating-type that belonged to the rare genotype AFLP7/VGIV. Antifungal susceptibility testing showed values within the range of sensitivity described for other isolates of the same genotype and within the epidemiological cutoff values for this species. The isolation of the rare C. gattii genotype AFLP7/VGIV in Spain is the first report in the European environment, implying the possible presence in other regions of the Mediterranean area, and underlines that clinicians must be aware for C. gattii infections in healthy individuals. Copyright © 2014 Revista Iberoamericana de Micología. Published by Elsevier Espana. All rights reserved.

  9. ISSR and AFLP analysis of the temporal and spatial population structure of the post-fire annual, Nicotiana attenuata, in SW Utah

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    Preston Catherine A

    2004-09-01

    Full Text Available Abstract Background The native annual tobacco, Nicotiana attenuata, is found primarily in large ephemeral populations (typically for less than 3 growing seasons after fires in sagebrush and pinyon-juniper ecosystems and in small persistent populations (for many growing seasons in isolated washes typically along roadsides throughout the Great Basin Desert of the SW USA. This distribution pattern is due to its unusual germination behavior. Ephemeral populations are produced by the germination of dormant seeds from long-lived seed banks which are stimulated to germinate by a combination of unidentified positive cues found in wood smoke and the removal of inhibitors leached from the unburned litter of the dominant vegetation. Persistent populations may result where these inhibitors do not exist, as in washes or along disturbed roadsides. To determine if this germination behavior has influenced population structure, we conducted an AFLP (244 individuals, ISSR (175 individuals and ISSR+ AFLP (175 individuals analysis on plants originating from seed collected from populations growing in 11 wash and burns over 11 years from the SW USA. Results Genetic variance as measured by both ISSR and AFLP markers was low among sites and comparatively higher within populations. Cluster analysis of the Utah samples with samples collected from Arizona, California, and Oregon as out-groups also did not reveal patterns. AMOVA analysis of the combined AFLP and ISSR data sets yielded significantly low genetic differentiation among sites (Φct, moderate among populations within sites (Φsc and higher genetic differentiation within populations (Φst. Conclusions We conclude that the seed dormancy of this post-fire annual and its resulting age structure in conjunction with natural selection processes are responsible for significantly low among sites and comparatively high within-population genetic variation observed in this species.

  10. Análisis de segregantes agrupados (BSA para la detección de AFLPs ligados al gen de resistencia a PVX en Solanum commersonii

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    Mónica Blanco

    2005-01-01

    Full Text Available Para identificar polimorfismos asociados al gen de resistencia al PVX en la papa silvestre Solanum commersonii, se realizó un análisis de segregantes agrupados (BSA asistido con AFLPs. Estos polimorfismos están basados en la localización de un locus relacionado con la resistencia al virus X de la papa (PVX. Inicialmente, mediante un análisis de ELISA, los individuos de una progenie F2 previamente inoculados con el PVX, fueron ubicados en 2 grupos, uno con los individuos resistentes y otro con los susceptibles. Posteriormente, para el BSA el ADN de todos los individuos resistentes fue mezclado, lo mismo el ADN de todos los individuos susceptibles. Ambos grupos de ADN fueron analizados independientemente, utilizando 64 diferentes combinaciones de AFLPs. El análisis de los geles resultó en la identificación de 22 combinaciones diferentes de AFLPs que generaron bandas relacionadas exclusivamente con el carácter de resistencia al PVX.

  11. Genotypic Characterization of Yersinia enterocolitica Biotype 4/O:3 Isolates from Pigs and Slaughterhouses Using SE-AFLP, ERIC-PCR, and PFGE

    Directory of Open Access Journals (Sweden)

    Renata Paixão

    2013-01-01

    Full Text Available Yersinia enterocolitica is a foodborne pathogen that causes illness in humans and animals. The biotype 4/O:3 has been commonly associated with yersiniosis and is characterized by the presence of chromosomal and extra-chromosomal virulence genes. Molecular typing methods have been successfully used to characterize Y. enterocolitica genetic heterogeneity and to study the epidemiology of the bacteria from different origins. In this study, 320 Y. enterocolitica biotype 4/O:3 isolates originating in pigs and slaughterhouses were characterized according to the virulence profile, and 61 isolates were typified through SE-AFLP, ERIC-PCR, and PFGE techniques. The majority of the isolates originated from pigs, and the predominant virulence profile was ail+ virF+ rfbC+ ystA+, representing 83.4% of the tested isolates. All of the Y. enterocolitica 4/O:3 isolates were positive for at least ystA gene. The SE-AFLP and ERIC-PCR patterns were highly homogeneous. The SE-AFLP was more discriminative than the ERIC-PCR and tended to cluster isolates according to the slaughterhouse. Despite the limited genetic diversity of Y. enterocolitica 4/O:3, PFGE was shown to be the most discriminative technique considering one band of difference. Fattening pigs proved to be an important reservoir of Y. enterocolitica biotype 4/O:3 carrying virulence genes.

  12. AFLP Approach Reveals Variability in Phragmites australis: Implications for Its Die-Back and Evidence for Genotoxic Effects

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    Andrea Coppi

    2018-03-01

    Full Text Available Phragmites australis is a subcosmopolitan species typical of wetlands being studied in Europe for its disappearance from natural stands, a phenomenon called reed die-back syndrome (RDBS. Although it is conjectured that low genetic variability contributes to RDBS, this aspect remains neglected to this day. Using a molecular fingerprinting approach and a sequence analysis of the trnT-trnL/rbcL-psaI regions of cpDNA, this study aimed to compare the genetic structure of stable vs. RDBS-affected P. australis stands from five wetlands of central Italy. Beforehand, in order to characterize the health condition of reed populations, the occurrence of the main macromorphological descriptors for RDBS was considered on 40 reed stands. Soil samples were also collected to examine the total content of heavy metals. The current study analyzed cpDNA in 19 samples and AFLP profiles in 381 samples to investigate the genetic structure of Phragmites populations. Based on the multinomial-Dirichlet model, an analysis of candidate loci under selective pressure was also performed. The relationships among AFLP data, RDBS descriptors and chemicals were evaluated with the use of Linear Mixed Models. The analysis of the cpDNA shows the occurrence of the haplotypes M (the most widespread, and K here recorded for the first time in Italy. Three new haplotypes were also described. The DNA fingerprinting analysis has produced a total of 322 loci (98% polymorphic and shows the medium-to-high amount of genetic diversity. The significant genetic differentiation among wetlands (Fst = 0.337 suggests either low gene flow or small effective population size. Moreover, the low amount of outlier loci (only 5; l.5% of the total, seems to indicate the scarce occurrence of selective pressure upon the reed’s genome. Genetic diversity increased in relationship to the decrease in diameter and of flowering buds of the reed, two of the trends associated with the die-back. The current study

  13. An AFLP estimation of the outcrossing rate of Spondias tuberosa (Anacardiaceae), an endemic species to the Brazilian semiarid region.

    Science.gov (United States)

    Fernandes Santos, Carlos Antonio; de Souza Gama, Renata Natália Cândido

    2013-06-01

    The umbu tree (Spondias tuberosa) is one of the most important endemic species to the Brazilian tropical semiarid region. The umbu tree has edible fruits with a peculiar flavor that are consumed in natura or in a semi-industrialized form, such as jams, candies and juices. The majority of endemic species to Brazilian semiarid region have not been studied or sampled to form germ-plasm collections, which increases the risk of losing genetic variability of the adapted species to xerophytic conditions. The aim of this study was to estimate outcrossing rates in S. tuberosa using a multilocus mixed model in order to guide genetic resources and breeding programs of this species. DNA samples were extracted from 92 progenies of umbu trees, which were distributed among 12 families. These trees were planted by seed in 1991 in Petrolina, PE, Brazil. The experimental design was a randomized block, with a total of 42 progenies sampled in three regions. The experimental units were composed by five plants and five replications. The outcrossing rate was estimated by the multilocus model, which is available in the MLTR software, and was based on 17 polymorphic AFLP bands obtained from AAA_CTG and AAA_CTC primer combinations. The observed heterozygotes ranged from 0.147 to 0.499, with a maximum frequency estimated for the AAA_CTC 10 amplicon. The multilocus outcrossing estimation (t(m)) was 0.804 +/- 0.072, while the single-locus (t(s)) was 0.841 +/- 0.079, which suggests that S. tuberosa is predominantly an outcrossing species. The difference between t(m) and t(s) was -0.037 +/- 0.029, which indicates that biparental inbreeding was nearly absent. The mean inbreeding coefficient or fixation index (F) among maternal plants was--0.103 +/- 0.045, and the expected F was 0.108, which indicates that there was no excess of heterozygotes in the maternal population. The outcrossing estimates obtained in the present study indicate that S. tuberosa is an open-pollinated species. Biometrical

  14. cDNA-AFLP analysis reveals differential gene expression in compatible interaction of wheat challenged with Puccinia striiformis f. sp. tritici.

    Science.gov (United States)

    Wang, Xiaojie; Tang, Chunlei; Zhang, Gang; Li, Yingchun; Wang, Chenfang; Liu, Bo; Qu, Zhipeng; Zhao, Jie; Han, Qingmei; Huang, Lili; Chen, Xianming; Kang, Zhensheng

    2009-06-30

    Puccinia striiformis f. sp. tritici is a fungal pathogen causing stripe rust, one of the most important wheat diseases worldwide. The fungus is strictly biotrophic and thus, completely dependent on living host cells for its reproduction, which makes it difficult to study genes of the pathogen. In spite of its economic importance, little is known about the molecular basis of compatible interaction between the pathogen and wheat host. In this study, we identified wheat and P. striiformis genes associated with the infection process by conducting a large-scale transcriptomic analysis using cDNA-AFLP. Of the total 54,912 transcript derived fragments (TDFs) obtained using cDNA-AFLP with 64 primer pairs, 2,306 (4.2%) displayed altered expression patterns after inoculation, of which 966 showed up-regulated and 1,340 down-regulated. 186 TDFs produced reliable sequences after sequencing of 208 TDFs selected, of which 74 (40%) had known functions through BLAST searching the GenBank database. Majority of the latter group had predicted gene products involved in energy (13%), signal transduction (5.4%), disease/defence (5.9%) and metabolism (5% of the sequenced TDFs). BLAST searching of the wheat stem rust fungus genome database identified 18 TDFs possibly from the stripe rust pathogen, of which 9 were validated of the pathogen origin using PCR-based assays followed by sequencing confirmation. Of the 186 reliable TDFs, 29 homologous to genes known to play a role in disease/defense, signal transduction or uncharacterized genes were further selected for validation of cDNA-AFLP expression patterns using qRT-PCR analyses. Results confirmed the altered expression patterns of 28 (96.5%) genes revealed by the cDNA-AFLP technique. The results show that cDNA-AFLP is a reliable technique for studying expression patterns of genes involved in the wheat-stripe rust interactions. Genes involved in compatible interactions between wheat and the stripe rust pathogen were identified and their

  15. cDNA-AFLP analysis reveals differential gene expression in compatible interaction of wheat challenged with Puccinia striiformis f. sp. tritici

    Directory of Open Access Journals (Sweden)

    Huang Lili

    2009-06-01

    Full Text Available Abstract Background Puccinia striiformis f. sp. tritici is a fungal pathogen causing stripe rust, one of the most important wheat diseases worldwide. The fungus is strictly biotrophic and thus, completely dependent on living host cells for its reproduction, which makes it difficult to study genes of the pathogen. In spite of its economic importance, little is known about the molecular basis of compatible interaction between the pathogen and wheat host. In this study, we identified wheat and P. striiformis genes associated with the infection process by conducting a large-scale transcriptomic analysis using cDNA-AFLP. Results Of the total 54,912 transcript derived fragments (TDFs obtained using cDNA-AFLP with 64 primer pairs, 2,306 (4.2% displayed altered expression patterns after inoculation, of which 966 showed up-regulated and 1,340 down-regulated. 186 TDFs produced reliable sequences after sequencing of 208 TDFs selected, of which 74 (40% had known functions through BLAST searching the GenBank database. Majority of the latter group had predicted gene products involved in energy (13%, signal transduction (5.4%, disease/defence (5.9% and metabolism (5% of the sequenced TDFs. BLAST searching of the wheat stem rust fungus genome database identified 18 TDFs possibly from the stripe rust pathogen, of which 9 were validated of the pathogen origin using PCR-based assays followed by sequencing confirmation. Of the 186 reliable TDFs, 29 homologous to genes known to play a role in disease/defense, signal transduction or uncharacterized genes were further selected for validation of cDNA-AFLP expression patterns using qRT-PCR analyses. Results confirmed the altered expression patterns of 28 (96.5% genes revealed by the cDNA-AFLP technique. Conclusion The results show that cDNA-AFLP is a reliable technique for studying expression patterns of genes involved in the wheat-stripe rust interactions. Genes involved in compatible interactions between wheat and the

  16. cDNA-AFLP analysis of differential gene expression related to cell chemotactic and encystment of Azospirillum brasilense.

    Science.gov (United States)

    Li, Huamin; Cui, Yanhua; Wu, Lixian; Tu, Ran; Chen, Sanfeng

    2011-12-20

    Our previous study indicated org35 was involved in chemotaxis and interacted with nitrogen fixation transcriptional activator NifA via PAS domain. In order to reveal the role of org35 in nitrogen regulation, the downstream target genes of org35 were identified. We here report differentially expressed genes in org35 mutants comparing with wild type Sp7 by means of cDNA-AFLP. Four up-regulated transcript-derived fragments (TDFs) homologues of chemotaxis transduction proteins were found, including CheW, methyl-accepting chemotaxis protein and response regulator CheY-like receiver. Three distinct TDFs (AB46, AB58 and AB63) were similar to PHB de-polymerase C-terminus, cell shape-determining protein and flagellin domain protein. And 11 TDFs showed similarities with signal transduction proteins, including homologous protein of the nitrogen regulation protein NtrY and nitrate/nitrite response regulator protein NarL. These data suggested that the Azospirillum brasilense org35 was a multi-effecter and involved in chemotaxis, cyst development and regulation of nitrogen fixation. Copyright © 2010 Elsevier GmbH. All rights reserved.

  17. A search for diagnostic AFLP markers in Cichorium species with emphasis on endive and chicory cultivar groups.

    Science.gov (United States)

    Kiers, A M; Mes, T H; van der Meijden, R; Bachmann, K

    2000-06-01

    The genus Cichorium consists of two widely cultivated species C. intybus (chicory) and C. endivia (endive) and four wild species, C. bottae, C. spinosum, C. calvum, and C. pumilum. A multivariate and an UPGMA (unweighted pair group method average) analysis based on AFLP (amplified fragment length polymorphism) markers were used to establish the genetic relationships among the species and cultivar groups of C. intybus and C. endivia. At the species level, the results correspond with previously obtained phylogenetic relationships in that C. bottae is the most divergent species, and C. intybus and C. spinosum, as well as C. endivia, C. pumilum, and C. calvum formed clusters. Based on the congruence between phylogenetic and genetic analyses, unique markers were expected for all species, however, hardly any specific marker was found except for C. bottae. The analysis of cultivar groups of C. intybus resembled the species analysis in two respects: (i) grouping of cultivars according to cultivar groups, and (ii) lack of markers unique to cultivar groups. In contrast to C. intybus, the cultivar series of C. endivia do not form distinct groups, which would reflect that crosses have been made among the various cultivar groups. The relationships among Cichorium species and cultivars will be useful for setting up a core collection of Cichorium, and stress the importance of inclusion of the wild species in the collection.

  18. Cryptococcal meningitis due to Cryptococcus neoformans genotype AFLP1/VNI in Iran: a review of the literature.

    Science.gov (United States)

    Badali, Hamid; Alian, Shahriar; Fakhim, Hamed; Falahatinejad, Mahsa; Moradi, Ali; Mohammad Davoudi, Mehrnaz; Hagen, Ferry; Meis, Jacques F

    2015-12-01

    Cryptococcal meningitis is the most important opportunistic fungal infection with a high mortality in HIV-patients in less developed regions. Here, we report a case of cryptococcal meningitis in a 49-year-old HIV-positive female due to Cryptococcus neoformans (serotype A, mating-type alpha, genotype AFLP1/VNI) in Sari, Iran. In vitro antifungal susceptibility tests showed MICs of isavuconazole (0.016 μg ml(-1) ), voriconazole (0.031 μg ml(-1) ), posaconazole (0.031 μg ml(-1) ), itraconazole (0.063 μg ml(-1) ), amphotericin B (0.125 μg ml(-1) ) and fluconazole (8 μg ml(-1) ). Despite immediate antifungal therapy, the patient died 4 days later due to respiratory failure. Cryptococcal infections have been infrequently reported from Iran and therefore we analysed all published cases of cryptococcosis in Iran since the first reported case from 1969. © 2015 Blackwell Verlag GmbH.

  19. Detection of recent hybridization between sympatric Chilean Puya species (Bromeliaceae) using AFLP markers and reconstruction of complex relationships.

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    Schulte, Katharina; Silvestro, Daniele; Kiehlmann, Elke; Vesely, Sanja; Novoa, Patricio; Zizka, Georg

    2010-12-01

    The Chilean Puya species constitute a monophyletic group, co-occurring in different species combinations within the country and displaying a remarkable morphological variability. Here, we studied the importance of recent hybridization and introgression in the group and reconstructed the complex inter- and intraspecific relationships. Amplified fragment length polymorphism (AFLP) analysis, including 109 accessions of all Chilean Puya species and four putative hybrids, yielded 984 characters. Three main genetic groups were revealed, with the chilensis group (P. chilensis, P. gilmartiniae, P. boliviensis) diverging first, and the alpestris (P. alpestris, P. berteroniana) and coerulea group (P. venusta, P. coerulea) forming sister groups. STRUCTURE analyses confirmed a hybrid origin of morphologically intermediate individuals, and detected several additional hybrids. Hybrids were found between the chilensis and alpestris group, and between the alpestris and coerulea group. Exclusion of hybrids improved phylogenetic reconstructions. The study demonstrates that the detection of hybrids within Bromeliaceae can be difficult based on morphological characters alone and that efficient reproductive barriers may only slowly establish, leading to hybridization between closely related sympatric species. The importance of hybridization for the rapid diversification of Puya is discussed. Copyright © 2010 Elsevier Inc. All rights reserved.

  20. An AFLP marker linked to the Pm-1 gene that confers resistance to Podosphaera xanthii race 1 in Cucumis melo

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    Ana Paula Matoso Teixeira

    2008-01-01

    Full Text Available Brazil produced 330,000 metric tons of melons in 2005, principally in the Northeast region where one of the most important melon pathogens is the powdery mildew fungus Podosphaera xanthii. The disease is controlled mainly by incorporating single dominant resistance genes into commercial hybrids. We report on linkage analysis of the Pm-1 resistance gene, introgressed from the AF125Pm-1 Cantalupensis Charentais-type breeding line into the yellow-fleshed melon (Group Inodorus breeding line AF426-S by backcrossing to produce the resistant line AF426-R, and the amplified fragment length polymorphism (AFLP marker M75/H35_155 reported to be polymorphic between AF426-S and AF426-R. Segregation analysis of M75/H35_155 using a backcross population of 143 plants derived from [AF426-R x AF426-S] x AF426-S and screened for resistance to P. xanthii race 1 produced a recombination frequency of 4.9%, indicating close linkage between M75/H35_155 and Pm-1. Using the same segregating population, the M75/H35_155 marker had previously been reported to be distantly linked to Prv¹, a gene conferring resistance to papaya ringspot virus-type W. Since M75/H35_155 is linked to Prv¹ at a distance of 40.9 cM it is possible that Pm-1 and Prv¹ are also linked.

  1. Chromosomal regions involved in hybrid performance and heterosis: their AFLP(R)-based identification and practical use in prediction models.

    Science.gov (United States)

    Vuylsteke, M; Kuiper, M; Stam, P

    2000-09-01

    In this paper, a novel approach towards the prediction of hybrid performance and heterosis is presented. Here, we describe an approach based on: (i) the assessment of associations between AFLP(R) markers and hybrid performance and specific combining ability (SCA) across a set of hybrids; and (ii) the assumption that the joint effect of genetic factors (loci) determined this way can be obtained by addition. Estimated gene effects for grain yield varied from additive, partial dominance to overdominance. This procedure was applied to 53 interheterotic hybrids out of a 13 by 13 half-diallel among maize inbreds, evaluated for grain yield. The hybrid value, representing the joint effect of the genetic factors, accounted for up to 62.4% of the variation in the hybrid performance observed, whereas the corresponding efficiency of the SCA model was 36.8%. Efficiency of the prediction for hybrid performance was evaluated by means of a cross-validation procedure for grain yield of (i) the 53 interheterotic hybrids and (ii) 16 hybrids partly related to the 13 by 13 half-diallel. Comparisons in prediction efficiency with the 'distance' model were made. Because the map position of the selected markers is known, putative quantitative trait loci (QTL) affecting grain yield, in terms of hybrid performance or heterosis, are identified. Some QTL of grain yield detected in the present study were located in the vicinity of loci reported earlier as having quantitative effects on grain yield.

  2. Identification of Differentially Expressed Genes by cDNA-AFLP Technique in Response to Drought Stress in Triticum durum

    Directory of Open Access Journals (Sweden)

    Marouane Melloul

    2014-01-01

    Full Text Available Drought is the single largest abiotic stress factor leading to reduced crop yields. The identification of diff erentially expressed genes and the understanding of their functions in environmentally stressful conditions are essential to improve drought tolerance. Transcriptomics is a powerful approach for the global analysis of molecular mechanisms under abiotic stress. To identify genes that are important for drought tolerance, we analyzed mRNA populations from untreated and drought-stressed leaves of Triticum durum by cDNA-amplified fragment length polymorphism (cDNA-AFLP technique. Overall, 76 transcript-derived fragments corresponding to differentially induced transcripts were successfully sequenced. Most of the transcripts identified here, using basic local alignment search tool (BLAST database, were genes belonging to different functional categories related to metabolism, energy, cellular biosynthesis, cell defense, signal transduction, transcription regulation, protein degradation and transport. The expression patterns of these genes were confirmed by quantitative reverse transcriptase real-time polymerase chain reaction (qRT-PCR based on ten selected genes representing different patterns. These results could facilitate the understanding of cellular mechanisms involving groups of genes that act in coordination in response to stimuli of water deficit. The identification of novel stress-responsive genes will provide useful data that could help develop breeding strategies aimed at improving durum wheat tolerance to field stress.

  3. Can AFLP genome scans detect small islands of differentiation? The case of shell sculpture variation in the periwinkle Echinolittorina hawaiiensis.

    Science.gov (United States)

    Tice, K A; Carlon, D B

    2011-08-01

    Genome scans have identified candidate regions of the genome undergoing selection in a wide variety of organisms, yet have rarely been applied to broadly dispersing marine organisms experiencing divergent selection pressures, where high recombination rates can reduce the extent of linkage disequilibrium (LD) and the ability to detect genomic regions under selection. The broadly dispersing periwinkle Echinolittorina hawaiiensis exhibits a heritable shell sculpture polymorphism that is correlated with environmental variation. To elucidate the genetic basis of phenotypic variation, a genome scan using over 1000 AFLP loci was conducted on smooth and sculptured snails from divergent habitats at four replicate sites. Approximately 5% of loci were identified as outliers with Dfdist, whereas no outliers were identified by BayeScan. Closer examination of the Dfdist outliers supported the conclusion that these loci were false positives. These results highlight the importance of controlling for Type I error using multiple outlier detection approaches, multitest corrections and replicate population comparisons. Assuming shell phenotypes have a genetic basis, our failure to detect outliers suggests that the life history of the target species needs to be considered when designing a genome scan. © 2011 The Authors. Journal of Evolutionary Biology © 2011 European Society For Evolutionary Biology.

  4. Identification of genes involved in stem rust resistance from wheat mutant D51 with the cDNA-AFLP technique.

    Science.gov (United States)

    Yin, Jing; Wang, Guangjin; Xiao, Jialei; Ma, Fengming; Zhang, Hongji; Sun, Yan; Diao, Yanling; Huang, Jinghua; Guo, Qiang; Liu, Dongjun

    2010-02-01

    Wheat (Triticum aestivum L.) stem rust caused by Puccinia graminis f. sp. tritici is one of the main diseases of wheat worldwide. Wheat mutant line D51, which was derived from the highly susceptible cultivar L6239, shows resistance to the prevailing races 21C3CPH, 21C3CKH, and 21C3CTR of P. graminis f. sp. tritici in China. In this study, we used the cDNA-AFLP technology to identify the genes that are likely involved in the stem rust resistance. EcoRI/MseI selective primers were used to generate approximately 1920 DNA fragments. Seventy five differentially transcribed fragments (3.91%) were identified by comparing the samples of 21C3CPH infected D51 with infected L6239 or uninfected D51. Eleven amplified cDNA fragments were sequenced. Eight showed significant similarity to known genes, including TaLr1 (leaf rust resistance gene), wlm24 (wheat powdery mildew resistance gene), stress response genes and ESTs of environment stress of tall fescue. These identified genes are involved in plant defense response and stem rust resistance and need further research to determine their usefulness in breeding new resistance cultivars.

  5. AFLP genome scan in the black rat (Rattus rattus) from Madagascar: detecting genetic markers undergoing plague-mediated selection.

    Science.gov (United States)

    Tollenaere, C; Duplantier, J-M; Rahalison, L; Ranjalahy, M; Brouat, C

    2011-03-01

    The black rat (Rattus rattus) is the main reservoir of plague (Yersinia pestis infection) in Madagascar's rural zones. Black rats are highly resistant to plague within the plague focus (central highland), whereas they are susceptible where the disease is absent (low altitude zone). To better understand plague wildlife circulation and host evolution in response to a highly virulent pathogen, we attempted to determine genetic markers associated with plague resistance in this species. To this purpose, we combined a population genomics approach and an association study, both performed on 249 AFLP markers, in Malagasy R. rattus. Simulated distributions of genetic differentiation were compared to observed data in four independent pairs, each consisting of one population from the plague focus and one from the plague-free zone. We found 22 loci (9% of 249) with higher differentiation in at least two independent population pairs or with combining P-values over the four pairs significant. Among the 22 outlier loci, 16 presented significant association with plague zone (plague focus vs. plague-free zone). Population genetic structure inferred from outlier loci was structured by plague zone, whereas the neutral loci dataset revealed structure by geography (eastern vs. western populations). A phenotype association study revealed that two of the 22 loci were significantly associated with differentiation between dying and surviving rats following experimental plague challenge. The 22 outlier loci identified in this study may undergo plague selective pressure either directly or more probably indirectly due to hitchhiking with selected loci. © 2010 Blackwell Publishing Ltd.

  6. Diversidade genética entre híbridos de laranja-doce e tangor 'Murcott' avaliada por fAFLP e RAPD Genetic diversity among hybrids of sweet orange and 'Murcott' tangor evaluated by fAFLP and RAPD markers

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    Marinês Bastianel

    2006-05-01

    Full Text Available O objetivo deste trabalho foi avaliar a diversidade genética em uma população de 148 híbridos de tangor 'Murcott' (Citrus reticulata Blanco x C. sinensis L. Osbeck e laranja 'Pêra' (C. sinensis L. Osbeck obtidos por polinização controlada, pelo uso de marcadores fAFLP e RAPD. Marcadores polimórficos (416 marcadores fAFLP e 33 RAPD foram utilizados para avaliar a similaridade genética entre os híbridos, calculada com o coeficiente Jaccard pelo método UPGMA. A consistência de cada agrupamento foi determinada pelo programa BOOD. Houve alta similaridade genética entre os parentais. A laranja 'Pêra' apresentou maior número (132 de loci em heterozigose em relação ao tangor 'Murcott' (105, corroborando a teoria de origem híbrida para a laranja-doce. Observaram-se dois grupos distintos de plantas, e um deles abrangeu 80% dos híbridos com maior similaridade com a laranja 'Pêra'. A análise bootstrap não revelou consistência estatística entre esses grupos. Marcadores fAFLP são mais eficientes na avaliação do polimorfismo, sendo indicados para seleção de indivíduos híbridos mais próximos a um dos parentais.The objective of this work was to evaluate the genetic diversity in a population of 148 hybrids of 'Murcott' tangor (Citrus reticulata Blanco x C. sinensis L. Osbeck and 'Pêra' sweet orange (C. sinensis L. Osbeck, obtained by controlled polination, using fAFLP and RAPD markers. Polymorphic markers (416 fAFLP and 33 RAPD markers were used to evaluate genetic similarity among the hybrids, calculated by the coefficient of Jaccard, using the UPGMA method. The consistency of each group was determined by software BOOD. There was high genetic similarity within the parents. 'Pêra' sweet orange had a higher number of loci in heterozygosis (132 compared to 'Murcott' tangor (105, supporting the theory of hybrid origin for sweet oranges. Two distinct groups of plants were observed: one group had 80% of the hybrids that displayed

  7. Similaridade genética entre cultivares de cebola de diferentes tipos e origens, baseada em marcadores AFLP Genetic similarity among onion cultivars of different types and origins, based on AFLP markers

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    CAF Santos

    2011-03-01

    Full Text Available Foi estimada a similaridade genética entre cultivares de cebola de diferentes tipos e regiões geográficas, de forma a orientar programas de recursos genéticos e melhoramento da espécie no Nordeste brasileiro. Foram analisadas 41 cultivares, adotando-se para a visualização da similaridade genética o fenograma UPGMA gerado da matriz de distâncias genéticas estimadas pelo coeficiente de Jaccard e baseadas em 146 bandas polimórficas de Pst1 e Mse1 de AFLP. A correlação cofenética foi de 0,91, indicando boa confiabilidade da representação gráfica para a interpretação dos resultados. Foram observados dois grupos principais no fenograma, no ponto de corte de 0,55 de similaridade: 1 grupo formado por cultivares predominantemente brasileiras, com algumas inclusões de cultivares estrangeiras; e 2 grupo formado por três cultivares estrangeiras (Mercedes, Perfect e TEG 502 PRR. Rijnsburger Jumbo e IPA 8 apresentaram a maior similaridade (85%, enquanto Madrugada foi a mais divergente em relação às demais cultivares. As cultivares da série IPA se dividiram em subgrupos no grupo das cultivares brasileiras (IPA 8, IPA 10 e IPA 11; IPA 12, IPA 7, IPA 2 e IPA 6; IPA 3, IPA 4 e IPA 9, indicando haver variabilidade genética a ser explorada entre aquelas situadas em subgrupos distintos. Bola Precoce e BRS Cascata apresentaram a maior similaridade entre as cultivares de origem brasileira. Foi observada similaridade superior a 39%, refletindo a alta variabilidade genética da coleção de cebola estudada. A introdução de novos acessos deve considerar procedências outras que não norte americanas, para aumentar a variabilidade de germoplasma de cebola disponível no Nordeste do Brasil.The genetic similarity among onion cultivars of different origins was evaluated, in order to carry out genetic resources and breeding programs for this species on the Brazilian Northeast. Forty-one onion cultivars were analyzed for 146 polymorphic Pst1/Mse1

  8. Variabilidade genética em populações de pitangueira oriundas de autopolinização e polinização livre, acessada por AFLP Genetic variability in surinam cherry populations originated from self-pollination and cross pollination, estimated by AFLP

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    Rodrigo Cezar Franzon

    2010-03-01

    Full Text Available Foram utilizados marcadores AFLP para a avaliação de populações de plantas de pitangueira (Eugenia uniflora oriundas de autopolinização e de polinização livre, com o objetivo de verificar a variabilidade existente entre e dentro dessas populações, visando a fornecer mais informações que ajudem no entendimento do modo de reprodução dessa espécie. O material vegetal utilizado foi oriundo de duas seleções de pitangueira ("Pit 15" e "Pit 52", mantidas na Embrapa Clima Temperado. De cada seleção, foram obtidas duas populações F1, por meio de autopolinização e de polinização livre, totalizando quatro populações. Foram analisados 18 indivíduos de cada população e as duas plantas-mãe, totalizando 74 indivíduos. Foram utilizadas três combinações de primers AFLP e calculada a similaridade genética entre plantas pelo coeficiente de Jaccard. Uma estimativa da variabilidade genética entre e dentro das populações foi estimada pela AMOVA. As três combinações de primers AFLP utilizadas amplificaram um total de 178 locos AFLP, dos quais 114 (64,0% foram polimórficos entre todos os indivíduos. Não houve separação clara entre populações descendentes da mesma planta-mãe. Foi observado maior polimorfismo de marcadores AFLP em populações de polinização livre. A proporção da variabilidade genética total entre populações foi significativa, embora tenha sido menor do que aquela observada dentro das populações. A reprodução da pitangueira é decorrente tanto da autofertilização quanto da polinização cruzada, sendo necessário, no entanto, novos estudos para determinar qual a estratégia de reprodução mais eficiente.AFLP molecular markers were used aiming to study the genetic variability within and between Surinam cherry (Eugenia uniflora populations, originated from self-pollination and open pollination of two selections (Pit 15 and Pit 52 of the Embrapa Clima Temperado collection. The objective was to

  9. Low level of genetic variation within Melica transsilvanica populations from the Kraków-Częstochowa Upland and the Pieniny Mts revealed by AFLPs analysis

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    Magdalena Szczepaniak

    2011-01-01

    Full Text Available Fragmented distribution, the breeding system and effects of genetic drift in small-size populations occurring at edge of the species range play an important role in shaping genetic diversity of such a species. Melica transsilvanica is a plant rare in the flora of Poland, where it reaches the northern limit of its continuous range. Amplified Fragment Length Polymorphism (AFLP DNA profiling method was applied to measure genetic diversity among and within populations of M. transsilvanica. Additionally, genetic relationships between M. transsilvanica and Melica ciliata, two closely related species, were explored. A total of 68 plants from 7 populations of M. transsilvanica and 24 plants from 2 populations of M. ciliata, collected in Poland and outside it, were analyzed. Using 294 AFLP fragments from 3 primer combinations, accessions were grouped into two major clusters associating with M. ciliata and M. transsilvanica, respectively. Further, two subclusters, corresponding to the samples collected from the Pieniny Mts and from the Kraków - Częstochowa Upland were clearly distinguished within the M. transsilvanica group. The hierarchical AMOVA exhibited significant genetic distinction between these geographic regions (60.89%, p < 0.001. The obtained results showed that the most genetic diversity resided between the populations of M. transsilvanica (86.03% while considerably lower genetic variation was found within the populations (13.97%, which is consistent with the results reported for self-plants. The low level of AFLP genetic variation of M. transsilvanica can be caused by the geographic isolation of populations, which preserves the dominant self-mating breeding system of the species. Individual populations of M. transsilvanica are characterized by isolated gene pools differing by a small number of loci.

  10. Morphometric, AFLP and plastid microsatellite variation in populations of Scalesia divisa and S. incisa (Asteraceae) from the Galápagos Islands

    DEFF Research Database (Denmark)

    NIELSEN, LENE ROSTGAARD; Cowan, Robyn S.; SIEGISMUND, HANS R.

    2003-01-01

    Scalesia divisa and S. incisa (Asteraceae), both endemic to the Galápagos Islands, are found only on San Cristóbal, where S. divisa grows in the north-west of the island while S. incisa occurs in the north-east. At localities in between, populations with deviating individuals occur. Here we analyse...... the population structure of S. divisa, S. incisa and two deviating populations based on morphology, AFLP markers and two plastid microsatellite loci. The deviating populations were collected from either side of the island. In a principal components analysis based on morphological characters they appeared...

  11. Differential transcript profiling through cDNA-AFLP showed complexity of rutin biosynthesis and accumulation in seeds of a nutraceutical food crop (Fagopyrum spp.

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    Gupta Nidhi

    2012-06-01

    Full Text Available Abstract Background Buckwheat, consisting of two cultivated species Fagopyrum tataricum and F. esculentum, is the richest source of flavonoid rutin. Vegetative tissues of both the Fagopyrum species contain almost similar amount of rutin; however, rutin content in seed of F. tataricum are ~50 folds of that in seed of F. esculentum. In order to understand the molecular basis of high rutin content in F. tataricum, differential transcript profiling through cDNA-AFLP has been utilized to decipher what genetic factors in addition to flavonoid structural genes contribute to high rutin content of F. tataricum compared to F. esculentum. Results Differential transcript profiling through cDNA-AFLP in seed maturing stages (inflorescence to seed maturation with 32 primer combinations generated total of 509 transcript fragments (TDFs. 167 TDFs were then eluted, cloned and sequenced from F. tataricum and F. esculentum. Categorization of TDFs on the basis of their presence/absence (qualitative variation or differences in the amount of expression (quantitative variation between both the Fagopyrum species showed that majority of variants are quantitative (64%. The TDFs represented genes controlling different biological processes such as basic and secondary metabolism (33%, regulation (18%, signal transduction (14%, transportation (13%, cellular organization (10%, and photosynthesis & energy (4%. Most of the TDFs except belonging to cellular metabolism showed relatively higher transcript abundance in F. tataricum over F. esculentum. Quantitative RT-PCR analysis of nine TDFs representing genes involved in regulation, metabolism, signaling and transport of secondary metabolites showed that all the tested nine TDFs (Ubiquitin protein ligase, ABC transporter, sugar transporter except MYB 118 showed significantly higher expression in early seed formation stage (S7 of F. tataricum compared to F. esculentum. qRT-PCR results were found to be consistent with the cDNA-AFLP

  12. Molecular phylogeny and population structure of the codling moth (Cydia pomonella) in Central Europe: II. AFLP analysis reflects human-aided local adaptation of a global pest species.

    Science.gov (United States)

    Thaler, R; Brandstätter, A; Meraner, A; Chabicovski, M; Parson, W; Zelger, R; Dalla Via, J; Dallinger, R

    2008-09-01

    Originally resident in southeastern Europe, the codling moth (Cydia pomonella L.) (Tortricidae) has achieved a nearly global distribution, being one of the most successful pest insect species known today. As shown in our accompanying study, mitochondrial genetic markers suggest a Pleistocenic splitting of Cydia pomonella into two refugial clades which came into secondary contact after de-glaciation. The actual distribution pattern shows, however, that Central European codling moths have experienced a geographic splitting into many strains and locally adapted populations, which is not reflected by their mitochondrial haplotype distribution. We therefore have applied, in addition to mitochondrial markers, an approach with a higher resolution potential at the population level, based on the analysis of amplification fragment length polymorphisms (AFLPs). As shown in the present study, AFLP markers elucidate the genetic structure of codling moth strains and populations from different Central European apple orchard sites. While individual genetic diversity within codling moth strains and populations was small, a high degree of genetic differentiation was observed between the analyzed strains and populations, even at a small geographic scale. One of the main factors contributing to local differentiation may be limited gene flow among adjacent codling moth populations. In addition, microclimatic, ecological, and geographic constraints also may favour the splitting of Cydia pomonella into many local populations. Lastly, codling moths in Central European fruit orchards may experience considerable selective pressure due to pest control activities. As a consequence of all these selective forces, today in Central Europe we see a patchy distribution of many locally adapted codling moth populations, each of them having its own genetic fingerprint. Because of the complete absence of any correlation between insecticide resistance and geographic or genetic distances among

  13. AFLP and AMP Fingerprints as Markers to Evaluate Genetic Differences between Medicago truncatula Line Jemalong and 2HA, a New Line Produced by in vitro Culture Selection

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    R.R. Irwanto

    2008-09-01

    Full Text Available A new line, Medicago truncatula cv. Jemalong 2HA (herein known as 2HA has been developed via repetitive regeneration and selection of M. truncatula cv. Jemalong. During somatic embryogenesis, 2HA produces 500 times more embryos than its progenitor, Jemalong. It is interesting to study if those two lines are isogenic or has genetic differences. The main objectives of the study was to evaluate the genotypic differences between Jemalong and 2HA also to evaluate the methylation event in 2HA utilized two DNA fingerprinting techniques, i.e AFLP fingerprints (Amplified Length of Polymorphism and AMP (Amplified Methylation Polymorphism. The results showed that AFLP analysis using eight primers combinations could not detect any differences between Jemalong and 2HA. However, using AMP methylation sensitive primers it could detect 15 polymorphisms out of 840 markers. These results lead to a conclusion that Jemalong and 2HA are isogenic lines. 2HA may have higher regeneration capacities due to methylation process which occurs during the production of 2HA through repetitive regeneration cycles.

  14. Profiling of Leptospira interrogans, L. santarosai, L. meyeri and L. borgpetersenii by SE-AFLP, PFGE and susceptibility testing--a continuous attempt at species and serovar differentiation.

    Science.gov (United States)

    Moreno, Luisa Z; Miraglia, Fabiana; Lilenbaum, Walter; Neto, José S F; Freitas, Julio C; Morais, Zenaide M; Hartskeerl, Rudy A; da Costa, Barbara L P; Vasconcellos, Silvio A; Moreno, Andrea M

    2016-03-09

    Leptospirosis is a widespread systemic zoonosis, considered as reemerging in certain developing countries. Although the cross agglutinin absorption test is still considered the standard method for Leptospira identification, it presents several disadvantages. The aim of this study was to characterize Leptospira spp. isolated from various hosts by genotyping and broth microdilution susceptibility testing in an attempt to differentiate Leptospira species, serogroups and serovars. Forty-seven isolates were studied. They were previously serotyped, and species confirmation was performed by 16S rRNA sequencing. Single-enzyme amplified fragment length polymorphism (SE-AFLP) and pulsed-field gel electrophoresis (PFGE) analysis enabled the distinction of L. interrogans from L. santarosai, L. meyeri and L. borgpetersenii in two main clusters. Among L. interrogans, it was possible to differentiate into two new clusters the serogroup Icterohaemorrhagiae from the serogroups Canicola and Pomona. L. santarosai isolates presented higher genetic variation than the other species in both techniques. Interestingly, the minimum inhibitory concentration (MIC) cluster analysis also provided Leptospira serogroup differentiation. Further studies are necessary regarding serovar Bananal isolates, as they presented the highest MIC values for most of the antimicrobials tested. All studied techniques successfully distinguished Leptospira species and serogroups. Despite being library-dependent methods, these approaches are less labor intensive and more economically viable, particularly SE-AFLP, and can be implemented in most reference laboratories worldwide to enable faster Leptospira typing.

  15. Overexpression of Aldo-Keto-Reductase in Azole-resistant Clinical Isolates of Candida Glabrata Determined by cDNA-AFLP

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    Mansour Heidari

    2013-01-01

    Full Text Available Background: Candida glabrata causes significant medical problems in immunocompromised patients. Many strains of this yeast are intrinsically resistant to azole antifungal agents, and treatment is problematic, leading to high morbidity and mortality rates in immunosuppressed individuals. The primary goal of this study was to investigate the genes involved in the drug resistance of clinical isolates of C. glabrata.Methods: The clinical isolates of C. glabrata were collected in an epidemiological survey of candidal infection inimmunocompromised patients and consisted of four fluconazole and itraconazole resistant isolates, two fluconazoleand itraconazole sensitive isolates, and C. glabrata CBS 138 as reference strain. Antifungal susceptibility patterns ofthe organisms were determined beforehand by the Clinical and Laboratory Standards Institute (CLSI. The potentialgene(s implicated in antifungal resistance were investigated using complementary DNA- Amplified Fragment Length Polymorphism (cDNA-AFLP. Semi-quantitative RT-PCR was carried out to evaluate the expression of gene(s in resistant isolates as compared to sensitive and reference strains.Results and conclusions: The aldo-keto-reductase superfamily (AKR gene was upregulated in the resistant clinicalisolates as assessed by cDNA-AFLP. Semi-quantitative RT-PCR revealed AKR mRNA expression approximately twice that seen in the sensitive isolates. Overexpression of the AKR gene was associated with increased fluconazole and itraconazole resistance in C. glabrata. The data suggest that upregulation of the AKR gene might give a new insight into the mechanism of azole resistance.

  16. Analysis of somaclonal variation in transgenic and regenerated plants of Arabidopsis thaliana using methylation related metAFLP and TMD markers.

    Science.gov (United States)

    Coronel, Carlos J; González, Ana I; Ruiz, María L; Polanco, Carlos

    2018-01-01

    We provide evidence that nucleotide sequence and methylation status changes occur in the Arabidopsis genome during in vitro tissue culture at a frequency high enough to represent an important source of variation. Somaclonal variation is a general consequence of the tissue culture process that has to be analyzed specifically when regenerated plants are obtained in any plant species. Currently, there are few studies about the variability comprising sequence changes and methylation status at the DNA level, generated by the culture of A. thaliana cells and tissues. In this work, two types of highly reproducible molecular markers, modified methylation sensitive AFLP (metAFLP) and transposon methylation display (TMD) have been used for the first time in this species to analyze the nucleotide and cytosine methylation changes induced by transformation and tissue culture protocols. We found significantly higher average methylation values (7.5%) in regenerated and transgenic plants when compared to values obtained from seed derived plants (3.2%) and that the main component of the somaclonal variation present in Arabidopsis clonal plants is genetic rather than epigenetic. However, we have found that the Arabidopsis regenerated and transgenic plants had a higher number of non-fully methylated sites flanking transposable elements than the control plants, and therefore, their mobilization can be facilitated. These data provide further evidence that changes in nucleotide sequence and methylation status occur in the Arabidopsis genome during in vitro tissue culture frequently enough to be an important source of variation in this species.

  17. AFLP analysis and improved phytoextraction capacity of transgenic gshI-poplar clones (Populus x canescens L.) for copper in vitro

    Energy Technology Data Exchange (ETDEWEB)

    Gyulai, G. [St. Stephanus Univ., Dept. of Genetics and PB (Hungary); HAS-SIU Research Group for Molecular Plant Breeding (Hungary); IGER, Plas Gogerddan, Aberystwyth (United Kingdom); Humphreys, M.; Skoet, K.; Skoet, L.; Heywood, S.; Lovatt, A.; Roderick, H.; Abberton, M. [IGER, Plas Gogerddan, Aberystwyth (United Kingdom); Bittsanszky, A.; Kiss, J.; Szabo, Z. [St. Stephanus Univ., Dept. of Genetics and PB (Hungary); Gullner, G.; Koemives, T. [Plant Protection Inst., Hungarian Academy of Sciences, Budapest (Hungary); Radimszky, L. [Soil Science Inst., Hungarian Academy of Sciences, Budapest (Hungary); Rennenberg, H. [Albert-Ludwigs-Univ., Inst. fuer Forstbotanik und Baumphysiologie, Freiburg (Germany); Heszky, L. [St. Stephanus Univ., Dept. of Genetics and PB (Hungary); HAS-SIU Research Group for Molecular Plant Breeding (Hungary)

    2005-04-01

    Clone stability and in vitro phytoextraction capacity of vegetative clones of P. x canescens (2n = 4x = 38) including two transgenic clones (ggs11 and lgl6) were studied as in vitro leaf disc cultures. Presence of the gshI-transgene in the transformed clones was detected in PCR reactions using gshI-specific primers. Clone stability was determined by fAFLP (fluorescent amplified DNA fragment length polymorphism) analysis. In total, 682 AFLP fragments were identified generated by twelve selective primer pairs after EcoRI-MseI digestion. Four fragments generated by EcoAGT-MseCCC were different (99.4% genetic similarity) which proves an unexpectedly low bud mutation frequency in P. x canescens. For the study of phytoextraction capacity leaf discs (8 mm) were exposed to a concentration series of ZnSO{sub 4} (10{sup -1} to 10{sup -5} M) incubated for 21 days on aseptic tissue culture media WPM containing 1 {mu}M Cu. ZN{sup 2+} caused phytotoxicity only at high concentrations (10{sup -1} to 10{sup -2} M). The transgenic poplar cyt-ECS (ggs11) clone, as stimulated by the presence of Zn, showed elevated heavy metal (Cu) uptake as compared to the non-transformed clone. These results suggest that gshI-transgenic poplars may be suitable for phytoremediation of soils contaminated with zinc and copper. (orig.)

  18. An AFLP marker linked to the leaf rust resistance gene LrBi16 and test of allelism with Lr14a on chromosome arm 7BL

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    Peipei Zhang

    2015-04-01

    Full Text Available Leaf rust (LR, caused by Puccinia triticina, is one of the most widespread diseases of common wheat (Triticum aestivum L. worldwide. The LR resistance gene LrBi16 has been mapped on chromosome arm 7BL in Chinese wheat cultivar Bimai 16 and was closely linked to SSR loci Xcfa2257 and Xgwm344 with genetic distances of 2.8 cM and 2.9 cM, respectively. In the present study, a total of 304 AFLP primer pairs were used to screen Bimai 16 and Thatcher and resistant and susceptible DNA bulks. The polymorphic AFLP marker P-ATT/M-CGC173 bp was used to genotype F2 and F3 populations to identify markers more closely linked to LrBi16. Marker P-ATT/M-CGC173 bp was tightly linked to LrBi16 with a genetic distance of 0.5 cM. As LrBi16 was mapped near the Lr14a locus, 809 F2 plants from the Bimai 16/RL6013 (Lr14a cross were inoculated with the Pt pathotype FHNQ to test the allelism of Lr14a and LrBi16. All of the F2 plants were resistant to FHNQ (IT between; and 2, suggesting that Lr14a and LrBi16 are allelic.

  19. Utilization of AFLP markers for PCR-based identification of Aspergillus carbonarius and indication of its presence in green coffee samples.

    Science.gov (United States)

    Schmidt, H; Taniwaki, M H; Vogel, R F; Niessen, L

    2004-01-01

    The objective of this work was to test whether ochratoxin A (OTA) production of Aspergillus niger and A. carbonarius is linked to a certain genotype and to identify marker sequences with diagnostic value aiding identification of A. carbonarius, a fungus of major concern regarding OTA production in food and food raw materials. Aspergillus niger and A. carbonarius were isolated mainly from Brazilian coffee sources. The ability of isolates to produce OTA was tested by thin layer chromatography (TLC). Strains were genetically characterized by AFLP fingerprinting and compared with each other and with reference strains. Cluster analysis of fingerprints showed clear separation of A. niger from A. carbonarius strains. To obtain marker sequences, AFLP fragments were isolated from silver stained polyacrylamide gels, cloned and sequenced. Sequences obtained were used to develop species- specific PCR primers for the identification of A. carbonarius in pure culture and in artificially and naturally infected samples of green coffee. No clear correlation between genetic similarity of the strains studied and their potential to produce OTA was found. The PCR assays designed are a useful and specific tool for identification and highly sensitive detection of A. carbonarius. The developed PCR assays allow specific and sensitive detection and identification of A. carbonarius, a fungus considered to be one of the major causative agents for OTA in coffee and grape-derived products. Assays may provide powerful tools to improve quality control and consumer safety in the food processing industry.

  20. Use of AFLPS to distinguish landraces of pejibaye (Bactris gasipaes in brazilian Amazonia Uso de AFLPS para discriminar raças primitivas de pupunha (Bactris gasipaes na Amazônia brasileira

    Directory of Open Access Journals (Sweden)

    Charles R. Clement

    2002-12-01

    Full Text Available Although the first inhabitants of western Amazonia domesticated pejibaye (Bactris gasipaes Kunth, Palmae or peach palm for its fruits, today it is widely planted for its heart-of-palm. Like other domesticates, pejibaye presents a complex hierarchy of landraces developed before the conquest of the Americas. The existence of three landraces (Pará, Solimões, Putumayo was proposed along the Amazonas and Solimões Rivers, Brazil, based on morphological characteristics. There are some questions remaining about the intermediate landrace being an artifact of the morphometric analysis. AFLPs were used to evaluate the relationships among samples of these putative landraces. DNA was extracted from 99 plants representing 13 populations maintained in the Pejibaye Germplasm Bank, Manaus, AM; six primer combinations generated 245 markers via PCR, which were scored in an ABI Prism 310 sequencer and analyzed with GeneScan Software; Jaccard similarities were estimated and a dendrogram was generated with UPGMA. Two groups of plants were observed in the dendrogram instead of three, and were similar at 0.795. Each group contained two subgroups, similar at 0.815. One group (n=41 contained 73% Pará landrace plants, with one subgroup (n=22 containing 91% Pará, and the other (n=19 containing 53% Pará. The other group (n=58 contained 53% Solimões and 40% Putumayo landrace plants, with one subgroup (n=21 containing 52% Solimões and 43% Putumayo, and the other (n=35 containing 57% Solimões and 37% Putumayo. The first group confirmed the Pará landrace. The second group suggested that the Solimões landrace does not exist, but that the Putumayo landrace extends along the Solimões River to Central Amazonia.Os primeiros povos da Amazônia ocidental domesticaram a pupunha (Bactris gasipaes Kunth, Palmae por seu fruto, embora hoje seja muito plantada por seu palmito. Como outros cultivos domesticados, a pupunha apresenta uma hierarquia complexa de raças primitivas

  1. Cytogenetic characterization and AFLP-based genetic linkage mapping for the butterfly Bicyclus anynana, covering all 28 karyotyped chromosomes.

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    Arjen E Van't Hof

    Full Text Available BACKGROUND: The chromosome characteristics of the butterfly Bicyclus anynana, have received little attention, despite the scientific importance of this species. This study presents the characterization of chromosomes in this species by means of cytogenetic analysis and linkage mapping. METHODOLOGY/PRINCIPAL FINDINGS: Physical genomic features in the butterfly B. anynana were examined by karyotype analysis and construction of a linkage map. Lepidoptera possess a female heterogametic W-Z sex chromosome system. The WZ-bivalent in pachytene oocytes of B. anynana consists of an abnormally small, heterochromatic W-chromosome with the Z-chromosome wrapped around it. Accordingly, the W-body in interphase nuclei is much smaller than usual in Lepidoptera. This suggests an intermediate stage in the process of secondary loss of the W-chromosome to a ZZ/Z sex determination system. Two nucleoli are present in the pachytene stage associated with an autosome and the WZ-bivalent respectively. Chromosome counts confirmed a haploid number of n = 28. Linkage mapping had to take account of absence of crossing-over in females, and of our use of a full-sib crossing design. We developed a new method to determine and exclude the non-recombinant uninformative female inherited component in offspring. The linkage map was constructed using a novel approach that uses exclusively JOINMAP-software for Lepidoptera linkage mapping. This approach simplifies the mapping procedure, avoids over-estimation of mapping distance and increases the reliability of relative marker positions. A total of 347 AFLP markers, 9 microsatellites and one single-copy nuclear gene covered all 28 chromosomes, with a mapping distance of 1354 cM. Conserved synteny of Tpi on the Z-chromosome in Lepidoptera was confirmed for B. anynana. The results are discussed in relation to other mapping studies in Lepidoptera. CONCLUSIONS/SIGNIFICANCE: This study adds to the knowledge of chromosome structure and

  2. Effects of copper amendment on the bacterial community in agricultural soil analyzed by the T-RFLP technique

    DEFF Research Database (Denmark)

    Tom-Petersen, Andreas; Leser, Thomas D.; Marsh, Terence L.

    2003-01-01

    The impact of copper amendment on the bacterial community in agricultural soil was investigated by a 2-year field experiment complemented by short-term microcosm studies. In the field, the amendments led to total copper contents that were close to the safety limits laid down by European authorities....... In parallel, bioavailable copper was determined with a copper-specific bioluminescent Pseudomonas reporter strain. The amounts of total Cu as well as of bioavailable Cu in the field declined throughout the experiment. Bacterial community structure was examined by terminal restriction fragment length...... the Rhizobium-Agrobacterium group. Comparable Cu effects were observed for microcosms, but in addition an impact on community structure within the Cytophaga group was observed....

  3. Análisis de adnc-aflp para la expresión diferencial de genes en la interacción manihot esculenta grantz (yuca) xanthomonas axonopodis pv. manihotis

    OpenAIRE

    Santaella, M.; Suárez, E.; González, C.; López, C.; Restrepo, S.; Badillo, A.; Verdier, V.

    2011-01-01

    Desarrollar patrones ADNc - AFLP, para identificar fragmentos expresados diferencialmente entre dos variedades de yuca, una resistente y una susceptible a la bacteriosis. Aislar, secuenciar y analizar los fragmentos seleccionados. Corroborar la expresión diferencial de estos fragmentos mediante "northern blots".

  4. Análisis de ADNC-AFLP para la expresión diferencial de genes en la interacción Manihot esculenta Grantz (Yuca Xanthomonas axonopodis pv. Manihotis

    Directory of Open Access Journals (Sweden)

    M. Santaella

    2001-07-01

    Full Text Available Desarrollar patrones ADNc - AFLP, para identificar fragmentos expresados diferencialmente entre dos variedades de yuca, una resistente y una susceptible a la bacteriosis. Aislar, secuenciar y analizar los fragmentos seleccionados. Corroborar la expresión diferencial de estos fragmentos mediante "northern blots".

  5. Análisis de ADNC-AFLP para la expresión diferencial de genes en la interacción Manihot esculenta Grantz (Yuca) Xanthomonas axonopodis pv. Manihotis

    OpenAIRE

    Verdier V.; Badillo A.; López C.; González C.; Suárez E.; Santaella M.; Restrepo S.

    2001-01-01

    Desarrollar patrones ADNc - AFLP, para identificar fragmentos expresados diferencialmente entre dos variedades de yuca, una resistente y una susceptible a la bacteriosis. Aislar, secuenciar y analizar los fragmentos seleccionados. Corroborar la expresión diferencial de estos fragmentos mediante "northern blots".

  6. Highly Informative Single-Copy Nuclear Microsatellite DNA Markers Developed Using an AFLP-SSR Approach in Black Spruce (Picea mariana) and Red Spruce (P. rubens)

    Science.gov (United States)

    Shi, Yong-Zhong; Forneris, Natascha; Rajora, Om P.

    2014-01-01

    Background Microsatellites or simple sequence repeats (SSRs) are highly informative molecular markers for various biological studies in plants. In spruce (Picea) and other conifers, the development of single-copy polymorphic genomic microsatellite markers is quite difficult, owing primarily to the large genome size and predominance of repetitive DNA sequences throughout the genome. We have developed highly informative single-locus genomic microsatellite markers in black spruce (Picea mariana) and red spruce (Picea rubens) using a simple but efficient method based on a combination of AFLP and microsatellite technologies. Principal Findings A microsatellite-enriched library was constructed from genomic AFLP DNA fragments of black spruce. Sequencing of the 108 putative SSR-containing clones provided 94 unique sequences with microsatellites. Twenty-two of the designed 34 primer pairs yielded scorable amplicons, with single-locus patterns. Fourteen of these microsatellite markers were characterized in 30 black spruce and 30 red spruce individuals drawn from many populations. The number of alleles at a polymorphic locus ranged from 2 to 18, with a mean of 9.3 in black spruce, and from 3 to 15, with a mean of 6.2 alleles in red spruce. The polymorphic information content or expected heterozygosity ranged from 0.340 to 0.909 (mean = 0.67) in black spruce and from 0.161 to 0.851 (mean = 0.62) in red spruce. Ten SSR markers showing inter-parental polymorphism inherited in a single-locus Mendelian mode, with two cases of distorted segregation. Primer pairs for almost all polymorphic SSR loci resolved microsatellites of comparable size in Picea glauca, P. engelmannii, P. sitchensis, and P. abies. Significance The AFLP-based microsatellite-enriched library appears to be a rapid, cost-effective approach for isolating and developing single-locus informative genomic microsatellite markers in black spruce. The markers developed should be useful in black spruce, red spruce

  7. Caracterización molecular de introducciones colombianas de caña flecha utilizando la técnica AFLP

    Directory of Open Access Journals (Sweden)

    Hernando Rivera Jiménez

    2008-12-01

    Full Text Available La fibra de la caña flecha Gynerium sagittatum (Aubl. se utiliza como materia prima para fabricar el "sombrero vueltiao", sombrero típico de la costa caribeña colombiana. Se realizó la caracterización molecular con AFLP para estimar variabilidad genética teniendo en cuenta criterios geográficos y morfológicos de 25 introducciones colombianas del banco de germoplasma de la Universidad de Córdoba. El análisis de correspondencia múltiple discriminó las introducciones en cuatro grupos, donde se identificaron características de importancia artesanal (comercial y atributos agronómicos. Se observó escasa correlación entre distancia geográfica y diferenciación genética, lo cual indicó flujos antrópicos por la reproducción asexual del material.

  8. Genetic relatedness among Campylobacter jejuni serotyped isolates of diverse origin as determined by numerical analysis of amplified fragment length polymorphism (AFLP) profiles

    DEFF Research Database (Denmark)

    Siemer, B.L.; Harrington, C.S.; Nielsen, E.M.

    2004-01-01

    health. The remaining 30 groups contained isolates from humans, chickens and associated food products, cattle, sheep, turkeys, ostriches and/or dogs. Strains assigned to serotypes 2, 6/7, 11 and 12 formed major clusters at the 77.6% S-level. Most other serotypes did not form homogeneous clusters......Aims: To use amplified fragment length polymorphism (AFLP) analysis to evaluate the genetic relatedness among 254 Campylobacter jejuni reference and field strains of diverse origin representing all defined 'Penner' serotypes for this species. Methods and Results: Field strains (n = 207) from human...... diarrhoea and diverse animal and environmental sources were collected mainly through a National surveillance programme in Denmark and serotyped by use of the established 'Penner' scheme. Genetic relationships among these isolates, and the archetypal serotype reference strains, were assessed by numerical...

  9. AFLP analysis of genetic diversity in leafy kale (Brassica oleracea L. convar. acephala (DC.) Alef.) landraces, cultivars and wild populations in Europe

    DEFF Research Database (Denmark)

    Christensen, Stina; von Bothmer, Roland; Poulsen, G.

    2011-01-01

    AFLP markers were used to characterize diversity and asses the genetic structure among 17 accessions of kale landraces, cultivars and wild populations from Europe. The range of average gene diversity in accessions was 0.11–0.27. Several landraces showed higher levels of diversity than the wild...... populations and one cultivar had the lowest diversity measures. The landraces that were most genetically diverse were from areas where kales are known to be extensively grown, suggesting in situ conservation in these areas as a supplement to storage of seeds in gene banks. An analysis of molecular variance...... the relationship among them is due to seed dispersal through human interactions. Our results indicate that a kale population found in a natural habitat in Denmark was probably not truly wild but most likely an escape from a cultivated Danish kale that had subsequently become naturalized....

  10. SNP discovery by illumina-based transcriptome sequencing of the olive and the genetic characterization of Turkish olive genotypes revealed by AFLP, SSR and SNP markers.

    Directory of Open Access Journals (Sweden)

    Hilal Betul Kaya

    Full Text Available BACKGROUND: The olive tree (Olea europaea L. is a diploid (2n = 2x = 46 outcrossing species mainly grown in the Mediterranean area, where it is the most important oil-producing crop. Because of its economic, cultural and ecological importance, various DNA markers have been used in the olive to characterize and elucidate homonyms, synonyms and unknown accessions. However, a comprehensive characterization and a full sequence of its transcriptome are unavailable, leading to the importance of an efficient large-scale single nucleotide polymorphism (SNP discovery in olive. The objectives of this study were (1 to discover olive SNPs using next-generation sequencing and to identify SNP primers for cultivar identification and (2 to characterize 96 olive genotypes originating from different regions of Turkey. METHODOLOGY/PRINCIPAL FINDINGS: Next-generation sequencing technology was used with five distinct olive genotypes and generated cDNA, producing 126,542,413 reads using an Illumina Genome Analyzer IIx. Following quality and size trimming, the high-quality reads were assembled into 22,052 contigs with an average length of 1,321 bases and 45 singletons. The SNPs were filtered and 2,987 high-quality putative SNP primers were identified. The assembled sequences and singletons were subjected to BLAST similarity searches and annotated with a Gene Ontology identifier. To identify the 96 olive genotypes, these SNP primers were applied to the genotypes in combination with amplified fragment length polymorphism (AFLP and simple sequence repeats (SSR markers. CONCLUSIONS/SIGNIFICANCE: This study marks the highest number of SNP markers discovered to date from olive genotypes using transcriptome sequencing. The developed SNP markers will provide a useful source for molecular genetic studies, such as genetic diversity and characterization, high density quantitative trait locus (QTL analysis, association mapping and map-based gene cloning in the olive. High levels

  11. Zoo-Risa [Fun at the Zoo].

    Science.gov (United States)

    Galarza, Ernesto

    This Spanish language picture and rhyme book about animals in the zoo was designed for Spanish-speaking students in grades 1 through 5. It is intended to meet the early reading needs of these students and to establish a foundation for the acquisition of reading skills. It may be used in compensatory education classes for Spanish-speaking students,…

  12. Distinct colonization patterns and cDNA-AFLP transcriptome profiles in compatible and incompatible interactions between melon and different races of Fusarium oxysporum f. sp. melonis

    Directory of Open Access Journals (Sweden)

    Delledonne Massimo

    2011-02-01

    Full Text Available Abstract Background Fusarium oxysporum f. sp. melonis Snyd. & Hans. (FOM causes Fusarium wilt, the most important infectious disease of melon (Cucumis melo L.. The four known races of this pathogen can be distinguished only by infection on appropriate cultivars. No molecular tools are available that can discriminate among the races, and the molecular basis of compatibility and disease progression are poorly understood. Resistance to races 1 and 2 is controlled by a single dominant gene, whereas only partial polygenic resistance to race 1,2 has been described. We carried out a large-scale cDNA-AFLP analysis to identify host genes potentially related to resistance and susceptibility as well as fungal genes associated with the infection process. At the same time, a systematic reisolation procedure on infected stems allowed us to monitor fungal colonization in compatible and incompatible host-pathogen combinations. Results Melon plants (cv. Charentais Fom-2, which are susceptible to race 1,2 and resistant to race 1, were artificially infected with a race 1 strain of FOM or one of two race 1,2 w strains. Host colonization of stems was assessed at 1, 2, 4, 8, 14, 16, 18 and 21 days post inoculation (dpi, and the fungus was reisolated from infected plants. Markedly different colonization patterns were observed in compatible and incompatible host-pathogen combinations. Five time points from the symptomless early stage (2 dpi to obvious wilting symptoms (21 dpi were considered for cDNA-AFLP analysis. After successful sequencing of 627 transcript-derived fragments (TDFs differentially expressed in infected plants, homology searching retrieved 305 melon transcripts, 195 FOM transcripts expressed in planta and 127 orphan TDFs. RNA samples from FOM colonies of the three strains grown in vitro were also included in the analysis to facilitate the detection of in planta-specific transcripts and to identify TDFs differentially expressed among races

  13. Distinct colonization patterns and cDNA-AFLP transcriptome profiles in compatible and incompatible interactions between melon and different races of Fusarium oxysporum f. sp. melonis.

    Science.gov (United States)

    Sestili, Sara; Polverari, Annalisa; Luongo, Laura; Ferrarini, Alberto; Scotton, Michele; Hussain, Jamshaid; Delledonne, Massimo; Ficcadenti, Nadia; Belisario, Alessandra

    2011-02-21

    Fusarium oxysporum f. sp. melonis Snyd. & Hans. (FOM) causes Fusarium wilt, the most important infectious disease of melon (Cucumis melo L.). The four known races of this pathogen can be distinguished only by infection on appropriate cultivars. No molecular tools are available that can discriminate among the races, and the molecular basis of compatibility and disease progression are poorly understood. Resistance to races 1 and 2 is controlled by a single dominant gene, whereas only partial polygenic resistance to race 1,2 has been described. We carried out a large-scale cDNA-AFLP analysis to identify host genes potentially related to resistance and susceptibility as well as fungal genes associated with the infection process. At the same time, a systematic reisolation procedure on infected stems allowed us to monitor fungal colonization in compatible and incompatible host-pathogen combinations. Melon plants (cv. Charentais Fom-2), which are susceptible to race 1,2 and resistant to race 1, were artificially infected with a race 1 strain of FOM or one of two race 1,2 w strains. Host colonization of stems was assessed at 1, 2, 4, 8, 14, 16, 18 and 21 days post inoculation (dpi), and the fungus was reisolated from infected plants. Markedly different colonization patterns were observed in compatible and incompatible host-pathogen combinations. Five time points from the symptomless early stage (2 dpi) to obvious wilting symptoms (21 dpi) were considered for cDNA-AFLP analysis. After successful sequencing of 627 transcript-derived fragments (TDFs) differentially expressed in infected plants, homology searching retrieved 305 melon transcripts, 195 FOM transcripts expressed in planta and 127 orphan TDFs. RNA samples from FOM colonies of the three strains grown in vitro were also included in the analysis to facilitate the detection of in planta-specific transcripts and to identify TDFs differentially expressed among races/strains. Our data suggest that resistance against FOM

  14. SNP Discovery by Illumina-Based Transcriptome Sequencing of the Olive and the Genetic Characterization of Turkish Olive Genotypes Revealed by AFLP, SSR and SNP Markers

    Science.gov (United States)

    Kaya, Hilal Betul; Cetin, Oznur; Kaya, Hulya; Sahin, Mustafa; Sefer, Filiz; Kahraman, Abdullah; Tanyolac, Bahattin

    2013-01-01

    Background The olive tree (Olea europaea L.) is a diploid (2n = 2x = 46) outcrossing species mainly grown in the Mediterranean area, where it is the most important oil-producing crop. Because of its economic, cultural and ecological importance, various DNA markers have been used in the olive to characterize and elucidate homonyms, synonyms and unknown accessions. However, a comprehensive characterization and a full sequence of its transcriptome are unavailable, leading to the importance of an efficient large-scale single nucleotide polymorphism (SNP) discovery in olive. The objectives of this study were (1) to discover olive SNPs using next-generation sequencing and to identify SNP primers for cultivar identification and (2) to characterize 96 olive genotypes originating from different regions of Turkey. Methodology/Principal Findings Next-generation sequencing technology was used with five distinct olive genotypes and generated cDNA, producing 126,542,413 reads using an Illumina Genome Analyzer IIx. Following quality and size trimming, the high-quality reads were assembled into 22,052 contigs with an average length of 1,321 bases and 45 singletons. The SNPs were filtered and 2,987 high-quality putative SNP primers were identified. The assembled sequences and singletons were subjected to BLAST similarity searches and annotated with a Gene Ontology identifier. To identify the 96 olive genotypes, these SNP primers were applied to the genotypes in combination with amplified fragment length polymorphism (AFLP) and simple sequence repeats (SSR) markers. Conclusions/Significance This study marks the highest number of SNP markers discovered to date from olive genotypes using transcriptome sequencing. The developed SNP markers will provide a useful source for molecular genetic studies, such as genetic diversity and characterization, high density quantitative trait locus (QTL) analysis, association mapping and map-based gene cloning in the olive. High levels of

  15. Identificação de híbridos de citros resistentes à mancha-marrom-de-alternária por meio de fAFLP e testes de patogenicidade Alternaria brown spot resistant citrus hybrid identification by means of fAFLP and pathogenicity tests

    Directory of Open Access Journals (Sweden)

    Edvan Alves Chagas

    2007-07-01

    Full Text Available O objetivo deste trabalho foi identificar híbridos, oriundos de hibridações controladas entre 'Folha Murcha' x 'Ponkan' e testá-los quanto à resistência a Alternaria alternata f. sp. citri. As plântulas foram obtidas via cultura in vitro de embriões. Utilizou-se o marcador molecular fAFLP para identificação dos híbridos e, em seguida, realizou-se o teste de patogenicidade nos híbridos com isolados de Alternaria alternata f. sp. citri, em condições de laboratório. Os pares de primers EcoRI AAG - MseI CAG e EcoRI ACC - MseI CAA foram os mais eficientes na identificação dos híbridos, os quais identificaram 48,5% de híbridos. Os híbridos F64, F108, F111, F113, F131 e F139 são potencialmente resistentes a Alternaria alternata f. sp. citri.The objective of this work was to identify hybrids obtained from controlled crossings between 'Folha Murcha' x 'Ponkan', and to check their resistance to Alternaria alternata f. sp. citri. The seedlings were obtained by in vitro embryo culture. The fAFLP marker technique was used to identify the hybrids, then laboratory pathogenicity test of the hybrids was accomplished with Alternaria alternata f. sp. citri isolates. The pairs of primers EcoRI AAG - Msel CAG and EcoRI ACC - Msel CAA were the most efficient for hybrids identification, and distinguished 48.5% of hybrids. Hybrids F64, F108, F111, F113, F131 and F139 showed potential resistance to the Alternaria alternata f. sp. citri.

  16. Genetic variation (AFLPs and nuclear microsatellites) in two anagenetically derived endemic species of Myrceugenia (Myrtaceae) on the Juan Fernández Islands, Chile.

    Science.gov (United States)

    López-Sepúlveda, Patricio; Takayama, Koji; Greimler, Josef; Peñailillo, Patricio; Crawford, Daniel J; Baeza, Marcelo; Ruiz, Eduardo; Kohl, Gudrun; Tremetsberger, Karin; Gatica, Alejandro; Letelier, Luis; Novoa, Patricio; Novak, Johannes; Stuessy, Tod F

    2013-04-01

    Anagenesis (or phyletic evolution) is one mode of speciation that occurs in the evolution of plants on oceanic islands. Of two endemic species on the Juan Fernández Islands (Chile), Myrceugenia fernandeziana and M. schulzei (Myrtaceae), believed to have originated anagenetically from different continental progenitors, the first is endemic to Robinson Crusoe Island and has no clear tie to continental relatives; the last is endemic to the younger island, Alejandro Selkirk Island, and has close affinity to M. colchaguensis in mainland Chile. Using AFLPs and six nuclear microsatellites from 381 individuals representing 33 populations, we determined patterns of genetic variation within and among populations on both islands and between those of the islands and mainland. Considerable genetic variation was found within populations on both islands. The level of gene diversity within M. schulzei was equivalent to that of its close continental relative M. colchaguensis. Genetic diversity was not partitioned geographically in M. fernandeziana and was weakly so and nonsignificantly in M. schulzei. The high genetic variation in both taxa is most likely due to anagenetic speciation. Subsidence of the older island Robinson Crusoe, landscape erosion, and restructuring of communities have severely reduced the overall island population to a single panmictic system. On the younger and less modified Alejandro Selkirk Island, slightly stronger patterns of genetic divergence are seen in M. schulzei. Because both species are genetically diverse and number in the thousands of individuals, neither is presently endangered in the archipelago.

  17. Caracterización molecular de introducciones colombianas de caña flecha utilizando la técnica AFLP

    Directory of Open Access Journals (Sweden)

    suarez Padron Isidro

    2008-12-01

    Full Text Available La fibra de la caña flecha Gynerium sagittatum (Aubl. se utiliza como materia prima para fabricar el "sombrero vueltiao", sombrero típico de la costa caribeña colombiana. Se realizó la caracterización molecular con AFLP para estimar variabilidad genética teniendo en cuenta criterios geográficos y morfológicos de 25 introducciones colombianas del banco de germoplasma de la Universidad de Córdoba. El análisis de correspondencia múltiple discriminó las introducciones en cuatro grupos, donde se identificaron características de importancia artesanal (comercial y atributos agronómicos. Se observó escasa correlación entre distancia geográfica y diferenciación genética, lo cual indicó flujos antrópicos por la reproducción asexual del material.

  18. AFLP marker analysis revealing genetic structure of the tree Parapiptadenia rigida (Benth. Brenan (Leguminosae-Mimosoideae in the southern Brazilian Tropical Rainforest

    Directory of Open Access Journals (Sweden)

    Laís Bérgamo de Souza

    2013-01-01

    Full Text Available Parapiptadenia rigida is a tropical early secondary succession tree characteristic of the Tropical Atlantic Rainforest. This species is of great ecological importance in the recovery of degraded areas. In this study we investigated the variability and population genetic structure of eight populations of P. rigida. Five AFLP primer combinations were used in a sample of 159 individuals representing these eight populations, rendering a total of 126 polymorphic fragments. The averages of percentage of polymorphic loci, gene diversity, and Shannon index were 60.45%, 0.217, and 0.322, respectively. A significant correlation between the population genetic variability and the population sizes was observed. The genetic variability within populations (72.20% was higher than between these (22.80%. No perfect correlation was observed between geographic and genetic distances, which might be explained by differences in deforestation intensities that occurred in these areas. A dendrogram constructed by the UPGMA method revealed the formation of two clusters, these also confirmed by Bayesian analysis for the number of K cluster. These results show that it is necessary to develop urgent management strategies for the conservation of certain populations of P. rigida, while other populations still preserve reasonably high levels of genetic variability.

  19. Molecular characterization of Cryptococcus gattii genotype AFLP6/VGII isolated from woody debris of divi-divi (Caesalpinia coriaria), Bonaire, Dutch Caribbean.

    Science.gov (United States)

    Hagen, Ferry; Chowdhary, Anuradha; Prakash, Anupam; Yntema, Jan-Bart; Meis, Jacques F

    2014-01-01

    The basidiomycetous yeast Cryptococcus gattii is an emerging and primary pathogen. There is a lack of information about its environmental spread outside outbreak regions in Mediterranean Europe, North and South America. Environmental sampling for C. gattii and molecular characterization of the obtained isolates will provide an insight into the global spread of the various genotypes. Woody debris of native divi-divi (Caesalpinia coriaria) trees were sampled across Bonaire, Dutch Caribbean. Colonies suspected for Cryptococcus species were subjected to standard mycology investigations and identification by matrix-assisted laser desorption ionization-time of flight mass spectrometry. Isolates identified as C. gattii were subjected to amplified fragment length polymorphism genotyping, mating-type analysis and multi-locus sequence typing. Ten colonies of C. gattii were cultured from different trunk hollows of the same divi-divi tree. Molecular characterization showed that all isolates were genotype AFLP6/VGII and mating-type α. Multi-locus sequence typing revealed that all isolates were genetically indistinguishable from each other. C. gattii is present in the environment of Bonaire, which suggests that this yeast is likely to be present in the environment of other Caribbean islands. Copyright © 2013 Revista Iberoamericana de Micología. Published by Elsevier Espana. All rights reserved.

  20. Leaf cDNA-AFLP analysis reveals novel mechanisms for boron-induced alleviation of aluminum-toxicity in Citrus grandis seedlings.

    Science.gov (United States)

    Wang, Liu-Qing; Yang, Lin-Tong; Guo, Peng; Zhou, Xin-Xing; Ye, Xin; Chen, En-Jun; Chen, Li-Song

    2015-10-01

    Little information is available on the molecular mechanisms of boron (B)-induced alleviation of aluminum (Al)-toxicity. 'Sour pummelo' (Citrus grandis) seedlings were irrigated for 18 weeks with nutrient solution containing different concentrations of B (2.5 or 20μM H3BO3) and Al (0 or 1.2mM AlCl3·6H2O). B alleviated Al-induced inhibition in plant growth accompanied by lower leaf Al. We used cDNA-AFLP to isolate 127 differentially expressed genes from leaves subjected to B and Al interactions. These genes were related to signal transduction, transport, cell wall modification, carbohydrate and energy metabolism, nucleic acid metabolism, amino acid and protein metabolism, lipid metabolism and stress responses. The ameliorative mechanisms of B on Al-toxicity might be related to: (a) triggering multiple signal transduction pathways; (b) improving the expression levels of genes related to transport; (c) activating genes involved in energy production; and (d) increasing amino acid accumulation and protein degradation. Also, genes involved in nucleic acid metabolism, cell wall modification and stress responses might play a role in B-induced alleviation of Al-toxicity. To conclude, our findings reveal some novel mechanisms on B-induced alleviation of Al-toxicity at the transcriptional level in C. grandis leaves. Copyright © 2015 Elsevier Inc. All rights reserved.

  1. DNA barcoding, MALDI-TOF, and AFLP data support Fusarium ficicrescens as a distinct species within the Fusarium fujikuroi species complex.

    Science.gov (United States)

    Al-Hatmi, Abdullah M S; Mirabolfathy, Mansoureh; Hagen, Ferry; Normand, Anne-Cécile; Stielow, J Benjamin; Karami-Osbo, Rouhollah; van Diepeningen, Anne D; Meis, Jacques F; de Hoog, G Sybren

    2016-02-01

    The Fusarium fujikuroi species complex (FFSC) is one of the most common groups of fusaria associated with plant diseases, mycotoxin production and traumatic and disseminated human infections. Here we present the description and taxonomy of a new taxon, Fusarium ficicrescens sp. nov., collected from contaminated fig fruits in Iran. Initially this species was identified as Fusarium andiyazi by morphology. In the present study the species was studied by multilocus sequence analysis, amplified fragment length polymorphism (AFLP), matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) and phenotypic characters. Multilocus analyses were based on translation elongation factor 1α (TEF1), RNA polymerase subunit (RPB2) and beta-tubulin (BT2) and proved F. ficicrescens as a member of the FFSC. Phylogenetic analysis showed that the fungus is closely related to Fusarium lactis, Fusarium ramigenum, and Fusarium napiforme; known plant pathogens, mycotoxin producers, and occasionally occurring multidrug resistant opportunists. The new species differed by being able to grow at 37 °C and by the absence of mycotoxin production. TEF1 was confirmed as an essential barcode for identifying Fusarium species. In addition to TEF1, we evaluated BT2 and RPB2 in order to provide sufficient genetic and species boundaries information for recognition of the novel species. Copyright © 2015 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

  2. High Genetic and Epigenetic Stability in Coffea arabica Plants Derived from Embryogenic Suspensions and Secondary Embryogenesis as Revealed by AFLP, MSAP and the Phenotypic Variation Rate

    Science.gov (United States)

    Bobadilla Landey, Roberto; Cenci, Alberto; Georget, Frédéric; Bertrand, Benoît; Camayo, Gloria; Dechamp, Eveline; Herrera, Juan Carlos; Santoni, Sylvain; Lashermes, Philippe; Simpson, June; Etienne, Hervé

    2013-01-01

    Embryogenic suspensions that involve extensive cell division are risky in respect to genome and epigenome instability. Elevated frequencies of somaclonal variation in embryogenic suspension-derived plants were reported in many species, including coffee. This problem could be overcome by using culture conditions that allow moderate cell proliferation. In view of true-to-type large-scale propagation of C. arabica hybrids, suspension protocols based on low 2,4-D concentrations and short proliferation periods were developed. As mechanisms leading to somaclonal variation are often complex, the phenotypic, genetic and epigenetic changes were jointly assessed so as to accurately evaluate the conformity of suspension-derived plants. The effects of embryogenic suspensions and secondary embryogenesis, used as proliferation systems, on the genetic conformity of somatic embryogenesis-derived plants (emblings) were assessed in two hybrids. When applied over a 6 month period, both systems ensured very low somaclonal variation rates, as observed through massive phenotypic observations in field plots (0.74% from 200 000 plant). Molecular AFLP and MSAP analyses performed on 145 three year-old emblings showed that polymorphism between mother plants and emblings was extremely low, i.e. ranges of 0–0.003% and 0.07–0.18% respectively, with no significant difference between the proliferation systems for the two hybrids. No embling was found to cumulate more than three methylation polymorphisms. No relation was established between the variant phenotype (27 variants studied) and a particular MSAP pattern. Chromosome counting showed that 7 of the 11 variant emblings analyzed were characterized by the loss of 1–3 chromosomes. This work showed that both embryogenic suspensions and secondary embryogenesis are reliable for true-to-type propagation of elite material. Molecular analyses revealed that genetic and epigenetic alterations are particularly limited during coffee somatic

  3. Long-term boron-deficiency-responsive genes revealed by cDNA-AFLP differ between Citrus sinensis roots and leaves

    Science.gov (United States)

    Lu, Yi-Bin; Qi, Yi-Ping; Yang, Lin-Tong; Lee, Jinwook; Guo, Peng; Ye, Xin; Jia, Meng-Yang; Li, Mei-Li; Chen, Li-Song

    2015-01-01

    Seedlings of Citrus sinensis (L.) Osbeck were supplied with boron (B)-deficient (without H3BO3) or -sufficient (10 μM H3BO3) nutrient solution for 15 weeks. We identified 54 (38) and 38 (45) up (down)-regulated cDNA-AFLP bands (transcript-derived fragments, TDFs) from B-deficient leaves and roots, respectively. These TDFs were mainly involved in protein and amino acid metabolism, carbohydrate and energy metabolism, nucleic acid metabolism, cell transport, signal transduction, and stress response and defense. The majority of the differentially expressed TDFs were isolated only from B-deficient roots or leaves, only seven TDFs with the same GenBank ID were isolated from the both. In addition, ATP biosynthesis-related TDFs were induced in B-deficient roots, but unaffected in B-deficient leaves. Most of the differentially expressed TDFs associated with signal transduction and stress defense were down-regulated in roots, but up-regulated in leaves. TDFs related to protein ubiquitination and proteolysis were induced in B-deficient leaves except for one TDF, while only two down-regulated TDFs associated with ubiquitination were detected in B-deficient roots. Thus, many differences existed in long-term B-deficiency-responsive genes between roots and leaves. In conclusion, our findings provided a global picture of the differential responses occurring in B-deficient roots and leaves and revealed new insight into the different adaptive mechanisms of C. sinensis roots and leaves to B-deficiency at the transcriptional level. PMID:26284101

  4. The Possible Physical Barrier and Coastal Dispersal Strategy for Japanese Grenadier Anchovy, Coilia nasus in the East China Sea and Yellow Sea: Evidence from AFLP Markers

    Directory of Open Access Journals (Sweden)

    Zhi-Qiang Han

    2015-02-01

    Full Text Available In order to ascertain the taxonomic status of the Ariake Sea population of Japanese grenadier anchovy, Coilia nasus, and assess the contemporary possible genetic barrier between the west and east coastal waters of the East China Sea, we used amplified fragment length polymorphism (AFLP markers to detect the genetic structure of C. nasus, in the East China Sea and Yellow Sea. Eighty-one individuals of C. nasus were collected from five locations and 12 individuals of Coilia mystus were sampled from the Yangtze River Estuary. A total of 371 loci were detected by five primer combinations, 310 of which were polymorphic (83.56%. Analysis of molecular variation (AMOVA and pairwise fixation index (FST revealed significant genetic differentiation among five samples, indicating limited gene flow among populations. The dendrogram for populations by neighbor-joining (NJ cluster analysis provided evidence of a clear relationship between genetic and geographic patterns, supporting significant genetic differentiation between China coastal populations and Ariake Sea populations. Compared to the genetic divergence between C. nasus and C. mystus, the level of genetic differentiation between China and the Ariake Sea populations of C. nasus is obvious below the species level, indicating isolated populations of C. nasus in the Ariake Sea. Isolation by distance analysis revealed that direct ocean distance with deep-water at the continental slope and high salinity between west and east coastal waters of the East China Sea served as major physical barrier to C. nasus, supporting the coastal dispersal pattern in this estuarine species, and rejecting offshore dispersal strategy.

  5. Mechanisms on Boron-Induced Alleviation of Aluminum-Toxicity in Citrus grandis Seedlings at a Transcriptional Level Revealed by cDNA-AFLP Analysis

    Science.gov (United States)

    Zhou, Xin-Xing; Yang, Lin-Tong; Qi, Yi-Ping; Guo, Peng; Chen, Li-Song

    2015-01-01

    The physiological and biochemical mechanisms on boron (B)-induced alleviation of aluminum (B)-toxicity in plants have been examined in some details, but our understanding of the molecular mechanisms underlying these processes is very limited. In this study, we first used the cDNA-AFLP to investigate the gene expression patterns in Citrus grandis roots responsive to B and Al interactions, and isolated 100 differentially expressed genes. Results showed that genes related to detoxification of reactive oxygen species (ROS) and aldehydes (i.e., glutathione S-transferase zeta class-like isoform X1, thioredoxin M-type 4, and 2-alkenal reductase (NADP+-dependent)-like), metabolism (i.e., carboxylesterases and lecithin-cholesterol acyltransferase-like 4-like, nicotianamine aminotransferase A-like isoform X3, thiosulfate sulfurtransferase 18-like isoform X1, and FNR, root isozyme 2), cell transport (i.e., non-specific lipid-transfer protein-like protein At2g13820-like and major facilitator superfamily protein), Ca signal and hormone (i.e., calcium-binding protein CML19-like and IAA-amino acid hydrolase ILR1-like 4-like), gene regulation (i.e., Gag-pol polyprotein) and cell wall modification (i.e., glycosyl hydrolase family 10 protein) might play a role in B-induced alleviation of Al-toxicity. Our results are useful not only for our understanding of molecular processes associated with B-induced alleviation of Al-toxicity, but also for obtaining key molecular genes to enhance Al-tolerance of plants in the future. PMID:25747450

  6. The Possible Physical Barrier and Coastal Dispersal Strategy for Japanese Grenadier Anchovy, Coilia nasus in the East China Sea and Yellow Sea: Evidence from AFLP Markers

    Science.gov (United States)

    Han, Zhi-Qiang; Han, Gang; Wang, Zhi-Yong; Gao, Tian-Xiang

    2015-01-01

    In order to ascertain the taxonomic status of the Ariake Sea population of Japanese grenadier anchovy, Coilia nasus, and assess the contemporary possible genetic barrier between the west and east coastal waters of the East China Sea, we used amplified fragment length polymorphism (AFLP) markers to detect the genetic structure of C. nasus, in the East China Sea and Yellow Sea. Eighty-one individuals of C. nasus were collected from five locations and 12 individuals of Coilia mystus were sampled from the Yangtze River Estuary. A total of 371 loci were detected by five primer combinations, 310 of which were polymorphic (83.56%). Analysis of molecular variation (AMOVA) and pairwise fixation index (FST) revealed significant genetic differentiation among five samples, indicating limited gene flow among populations. The dendrogram for populations by neighbor-joining (NJ) cluster analysis provided evidence of a clear relationship between genetic and geographic patterns, supporting significant genetic differentiation between China coastal populations and Ariake Sea populations. Compared to the genetic divergence between C. nasus and C. mystus, the level of genetic differentiation between China and the Ariake Sea populations of C. nasus is obvious below the species level, indicating isolated populations of C. nasus in the Ariake Sea. Isolation by distance analysis revealed that direct ocean distance with deep-water at the continental slope and high salinity between west and east coastal waters of the East China Sea served as major physical barrier to C. nasus, supporting the coastal dispersal pattern in this estuarine species, and rejecting offshore dispersal strategy. PMID:25654225

  7. Mechanisms on boron-induced alleviation of aluminum-toxicity in Citrus grandis seedlings at a transcriptional level revealed by cDNA-AFLP analysis.

    Directory of Open Access Journals (Sweden)

    Xin-Xing Zhou

    Full Text Available The physiological and biochemical mechanisms on boron (B-induced alleviation of aluminum (B-toxicity in plants have been examined in some details, but our understanding of the molecular mechanisms underlying these processes is very limited. In this study, we first used the cDNA-AFLP to investigate the gene expression patterns in Citrus grandis roots responsive to B and Al interactions, and isolated 100 differentially expressed genes. Results showed that genes related to detoxification of reactive oxygen species (ROS and aldehydes (i.e., glutathione S-transferase zeta class-like isoform X1, thioredoxin M-type 4, and 2-alkenal reductase (NADP+-dependent-like, metabolism (i.e., carboxylesterases and lecithin-cholesterol acyltransferase-like 4-like, nicotianamine aminotransferase A-like isoform X3, thiosulfate sulfurtransferase 18-like isoform X1, and FNR, root isozyme 2, cell transport (i.e., non-specific lipid-transfer protein-like protein At2g13820-like and major facilitator superfamily protein, Ca signal and hormone (i.e., calcium-binding protein CML19-like and IAA-amino acid hydrolase ILR1-like 4-like, gene regulation (i.e., Gag-pol polyprotein and cell wall modification (i.e., glycosyl hydrolase family 10 protein might play a role in B-induced alleviation of Al-toxicity. Our results are useful not only for our understanding of molecular processes associated with B-induced alleviation of Al-toxicity, but also for obtaining key molecular genes to enhance Al-tolerance of plants in the future.

  8. Mapping of A1 conferring resistance to the aphid Amphorophora idaei and dw (dwarfing habit in red raspberry (Rubus idaeus L. using AFLP and microsatellite markers

    Directory of Open Access Journals (Sweden)

    Knight Victoria H

    2007-03-01

    Full Text Available Abstract Background Raspberry breeding programmes worldwide aim to produce improved cultivars to satisfy market demands and within these programmes there are many targets, including increased fruit quality, yield and season, and improved pest and disease resistance and plant habit. The large raspberry aphid, Amphorophora idaei, transmits four viruses and vector resistance is an objective in raspberry breeding. The development of molecular tools that discriminate between aphid resistance genes from different sources will allow the pyramiding of such genes and the development of raspberry varieties with superior pest resistance. We have raised a red raspberry (Rubus idaeus F1 progeny from the cross 'Malling Jewel' × 'Malling Orion' (MJ × MO, which segregates for resistance to biotype 1 of the aphid Amphorophora idaei and for a second phenotypic trait, dwarf habit. These traits are controlled by single genes, denoted (A1 and (dw respectively. Results The progeny of 94 seedlings was scored for the segregation of 95 AFLP and 22 SSR markers and a linkage map was constructed that covers a total genetic distance of 505 cM over seven linkage groups. The average linkage group length was 72.2 cM and there was an average of 17 markers per linkage group, of which at least two were codominant SSRs, allowing comparisons with previously published maps of raspberry. The two phenotypic traits, A1 and dw, mapped to linkage groups 3 and 6 respectively. Conclusion The mapping of A1 will facilitate the discrimination of resistance genes from different sources and the pyramiding of aphid resistance genes in new raspberry cultivars; the mapping of dw will allow further investigations into the genetics of dwarfing habit in Rubus.

  9. The possible physical barrier and coastal dispersal strategy for Japanese grenadier anchovy, Coilia nasus in the East China Sea and Yellow Sea: evidence from AFLP markers.

    Science.gov (United States)

    Han, Zhi-Qiang; Han, Gang; Wang, Zhi-Yong; Gao, Tian-Xiang

    2015-02-03

    In order to ascertain the taxonomic status of the Ariake Sea population of Japanese grenadier anchovy, Coilia nasus, and assess the contemporary possible genetic barrier between the west and east coastal waters of the East China Sea, we used amplified fragment length polymorphism (AFLP) markers to detect the genetic structure of C. nasus, in the East China Sea and Yellow Sea. Eighty-one individuals of C. nasus were collected from five locations and 12 individuals of Coilia mystus were sampled from the Yangtze River Estuary. A total of 371 loci were detected by five primer combinations, 310 of which were polymorphic (83.56%). Analysis of molecular variation (AMOVA) and pairwise fixation index (FST) revealed significant genetic differentiation among five samples, indicating limited gene flow among populations. The dendrogram for populations by neighbor-joining (NJ) cluster analysis provided evidence of a clear relationship between genetic and geographic patterns, supporting significant genetic differentiation between China coastal populations and Ariake Sea populations. Compared to the genetic divergence between C. nasus and C. mystus, the level of genetic differentiation between China and the Ariake Sea populations of C. nasus is obvious below the species level, indicating isolated populations of C. nasus in the Ariake Sea. Isolation by distance analysis revealed that direct ocean distance with deep-water at the continental slope and high salinity between west and east coastal waters of the East China Sea served as major physical barrier to C. nasus, supporting the coastal dispersal pattern in this estuarine species, and rejecting offshore dispersal strategy.

  10. Genetic map of AFLP markers in the rat (Rattus norvegicus) derived from the H x B/Ipcv and B x H/cub sets of recombinant inbred strains

    Czech Academy of Sciences Publication Activity Database

    Bonné, A. C. M.; den Bieman, M. G.; Gillissen, G. F.; Křen, Vladimír; Křenová, D.; Bílá, V.; Zídek, Václav; Kostka, Vlastimil; Musilová, Alena; Pravenec, Michal; Van Zutphen, B. F. M.; Van Lith, H. A.

    2003-01-01

    Roč. 41, 3-4 (2003), s. 77-89 ISSN 0006-2928 R&D Projects: GA MŠk LN00A079; GA MŠk LN00A079; GA ČR GV204/98/K015; GA ČR GA305/00/1646 Grant - others:European Commission(XE) BIO4CT960562 Institutional research plan: CEZ:AV0Z5011922 Keywords : AFLP technique * rat * recombinant inbred strains Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 0.569, year: 2003

  11. AFLP estimation of the outcrossing rate of Spondias tuberosa (Anacardiaceae, an endemic species to the Brazilian semiarid region Una estimación AFLP de la tasa de fecundación cruzada de Spondias tuberosa (Anacardiaceae, una especie endémica de la región semiárida de Brasil

    Directory of Open Access Journals (Sweden)

    Carlos Antonio Fernandes Santos

    2013-06-01

    Full Text Available The umbu tree (Spondias tuberosa is one of the most important endemic species to the Brazilian tropical semiarid region. The umbu tree has edible fruits with a peculiar flavor that are consumed in natura or in a semi-industrialized form, such as jams, candies and juices. The majority of endemic species to Brazilian semiarid region have not been studied or sampled to form germ- plasm collections, which increases the risk of losing genetic variability of the adapted species to xerophytic conditions. The aim of this study was to estimate outcrossing rates in S. tuberosa using a multilocus mixed model in order to guide genetic resources and breeding programs of this species. DNA samples were extracted from 92 progenies of umbu trees, which were distributed among 12 families. These trees were planted by seed in 1991 in Petrolina, PE, Brazil. The experimental design was a randomized block, with a total of 42 progenies sampled in three regions. The experimental units were composed by five plants and five replications. The out- crossing rate was estimated by the multilocus model, which is available in the MLTR software, and was based on 17 polymorphic AFLP bands obtained from AAA_CTG and AAA_CTC primer combinations. The observed heterozygotes ranged from 0.147 to 0.499, with a maximum frequency estimated for the AAA_CTC_10 ampli- con. The multilocus outcrossing estimation ( was 0.804±0.072, while the single-locus ( was 0.841±0.079, which suggests that S. tuberosa is predominantly an outcrossing species. The difference between and was -0.037±0.029, which indicates that biparental inbreeding was nearly absent. The mean inbreeding coefficient or fixation index ( among maternal plants was - 0.103±0.045, and the expected was 0.108, which indicates that there was no excess of heterozygotes in the maternal population. The outcrossing estimates obtained in the present study indicate that S. tuberosa is an open-pollinated species. Biometrical models applied

  12. Relationships and genetic consequences of contrasting modes of speciation among endemic species of Robinsonia (Asteraceae, Senecioneae) of the Juan Fernández Archipelago, Chile, based on AFLPs and SSRs.

    Science.gov (United States)

    Takayama, Koji; López-Sepúlveda, Patricio; Greimler, Josef; Crawford, Daniel J; Peñailillo, Patricio; Baeza, Marcelo; Ruiz, Eduardo; Kohl, Gudrun; Tremetsberger, Karin; Gatica, Alejandro; Letelier, Luis; Novoa, Patricio; Novak, Johannes; Stuessy, Tod F

    2015-01-01

    This study analyses and compares the genetic signatures of anagenetic and cladogenetic speciation in six species of the genus Robinsonia (Asteraceae, Senecioneae), endemic to the Juan Fernández Islands, Chile. Population genetic structure was analyzed by amplified fragment length polymorphism (AFLP) and microsatellite (simple sequence repeat, SSR) markers from 286 and 320 individuals, respectively, in 28 populations. Each species is genetically distinct. Previous hypotheses of classification among these species into subgenera and sections, via morphological, phytochemical, isozymic and internal transcribed spacer (ITS) data, have been confirmed, except that R. saxatilis appears to be related to R. gayana rather than R. evenia. Analysis of phylogenetic results and biogeographic context suggests that five of these species have originated by cladogenesis and adaptive radiation on the older Robinson Crusoe Island. The sixth species, R. masafuerae, restricted to the younger Alejandro Selkirk Island, is closely related to and an anagenetic derivative of R. evenia from Robinson Crusoe. Microsatellite and AFLP data reveal considerable genetic variation among the cladogenetically derived species of Robinsonia, but within each the genetic variation is lower, highlighting presumptive genetic isolation and rapid radiation. The anagenetically derived R. masafuerae harbors a level of genetic variation similar to that of its progenitor, R. evenia. This is the first direct comparison of the genetic consequences of anagenetic and cladogenetic speciation in plants of an oceanic archipelago. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.

  13. Gene expression profiling by cDNA-AFLP reveals potential candidate genes for partial resistance of 'Président Roulin' against Venturia inaequalis.

    Science.gov (United States)

    Bastiaanse, Héloïse; Muhovski, Yordan; Parisi, Olivier; Paris, Roberta; Mingeot, Dominique; Lateur, Marc

    2014-11-29

    Scab, caused by the fungus Venturia inaequalis, is one of the most important diseases of cultivated apple. While a few scab resistance genes (R genes) governing qualitative resistance have been isolated and characterized, the biological roles of genes governing quantitative resistance, supposed to be more durable, are still unknown. This study aims to investigate the molecular mechanisms involved in the partial resistance of the old Belgian apple cultivar 'Président Roulin' against V. inaequalis. A global gene expression analysis was conducted in 'Président Roulin' (partially resistant) and in 'Gala' (susceptible) challenged by V. inaequalis by using the cDNA-AFLP method (cDNA-Amplified Fragment Length Polymorphism). Transcriptome analysis revealed significant modulation (up- or down-regulation) of 281 out of approximately 20,500 transcript derived fragments (TDFs) in 'Président Roulin' 48 hours after inoculation. Sequence annotation revealed similarities to several genes encoding for proteins belonging to the NBS-LRR and LRR-RLK classes of plant R genes and to other defense-related proteins. Differentially expressed genes were sorted into functional categories according to their gene ontology annotation and this expression signature was compared to published apple cDNA libraries by Gene Enrichment Analysis. The first comparison was made with two cDNA libraries from Malus x domestica uninfected leaves, and revealed in both libraries a signature of enhanced expression in 'Président Roulin' of genes involved in response to stress and photosynthesis. In the second comparison, the pathogen-responsive TDFs from the partially resistant cultivar were compared to the cDNA library from inoculated leaves of Rvi6 (HcrVf2)-transformed 'Gala' lines (complete disease resistance) and revealed both common physiological events, and notably differences in the regulation of defense response, the regulation of hydrolase activity, and response to DNA damage. TDFs were in silico

  14. Charakteristika společenstva hub na opadu smrku ztepilého kultivací a analýzou T-RFLP

    OpenAIRE

    Kolářová, Zuzana

    2012-01-01

    Fungi have a key role in the decomposition of coniferous litter and affect nutrient cycling in forest ecosystems. Therefore, great emphasis is placed on exploring the diversity of these organisms. The aim of this thesis was to describe fungal diversity in spruce litter and revealed temporal development of this community in a forest regenerating after bark beetle outbreak. Another objective was to compare sites with different length of bark beetle damage. The study area was located in the Bohe...

  15. Analysis of the Airway Microbiota of Healthy Individuals and Patients with Chronic Obstructive Pulmonary Disease by T-RFLP and Clone Sequencing

    DEFF Research Database (Denmark)

    Zakharkina, Tetyana; Heinzel, Elke; Koczulla, Rembert A

    2013-01-01

    Chronic obstructive pulmonary disease (COPD) is a progressive, inflammatory lung disease that affects a large number of patients and has significant impact. One hallmark of the disease is the presence of bacteria in the lower airways....

  16. Use of T-RFLP and seven restriction enzymes to compare the faecal microbiota of obese and lean Japanese healthy men.

    Science.gov (United States)

    Kobayashi, T; Osaki, T; Oikawa, S

    2015-01-01

    The composition of the intestinal microbiota of 92 healthy Japanese men was measured following consumption of identical meals for 3 days; terminal restriction fragment length polymorphisms were then used to analyse the DNA content of their faeces. The obtained operational taxonomic units (OTUs) were further analysed using seven restriction enzymes: 516f-BslI and -HaeIII, 27f-MspI and -AluI, and 35f-HhaI, -MspI and -AluI. Subjects were classified by their body mass index (BMI) as lean (25.0). OTUs were then analysed using data mining software. Pearson correlation coefficients on data mining results indicated only a weak relationship between BMI and OTU diversity. Specific OTUs attributed to lean and obese subjects were further examined by data mining with six groups of enzymes and closely related accession numbers for lean and obese subjects were successfully narrowed down. 16S rRNA sequences showed Bacillus spp., Erysipelothrix spp. and Holdemania spp. to be present among 30 bacterial candidates related to the lean group. Fifteen candidates were classified Firmicutes, one was classified as Chloroflexi, and the others were not classified. 45 Microbacteriaceae, 11 uncultured Actinobacterium, and 3 other families were present among the 119 candidate OTUs related to obesity. We conclude that the presence of Firmicutes and Actinobacteria may be related to the BMI of the subject.

  17. The carnivalization of the world as criticism: laughter, political action and subjectivity in social life and speech La carnavalización del mundo como crítica: risa, acción política y subjetividad en la vida social y en el hablar

    Directory of Open Access Journals (Sweden)

    Raúl Ernesto García Rodríguez

    2013-07-01

    Full Text Available Taking the notion of carnival as developed by Mijail Bakhtin as starting point, in this text I evaluate the possibility of vindicating a carnivalization of the world as a practice of social resistance and transformation in the face of the hegemony of an established dialogicity or a dominant, institutionalized discourse. I analyze the resource of parody and the exercise of subversion of the official –solemn– text, as well as the collective insertion of laughter, as means of inaugurating an alternate, or “second”, existence through which any identitary congruence linked to the reiteration of a discursive regime associated with power relations is contradicted. Thus, I conceive of carnivalization as a milieu generator of specific forms of language and communication that, availing itself of grotesque corporality and masking as well, contravene established patterns of functional, ordered conduct, thereby opening a path that leads to other practices of freedom and the production of subjectivity.A partir de la noción de carnaval desarrollada por Mijail Bajtin, en el presente texto valoro críticamente la posibilidad de reivindicar una carnavalización del mundo como práctica de resistencia y transformación social ante la hegemonía de una dialogicidad establecida o discurso dominante e institucionalizado. Se analiza el recurso de la parodia y el ejercicio de subversión del texto oficial o solemne, así como la inserción colectiva de la risa para inaugurar una existencia alterna o “segunda existencia”, en virtud de la cual se contradice cualquier congruencia identitaria vinculada a la reiteración de un régimen discursivo asociado a las relaciones de poder. Pienso entonces la carnavalización como ámbito generador de formas específicas de lenguaje y comunicación que, a través también de la corporalidad grotesca y el enmascaramiento, transgreden pautas establecidas del comportamiento funcional y ordenado y abren por tanto un camino

  18. Les méthodes d'analyse de ségrégation en mélange et d'association marqueur-trait révèlent des marqueurs AFLP communs de résistance à la septoriose chez un ancien blé dur de Tunisie

    Directory of Open Access Journals (Sweden)

    Medini, M.

    2014-01-01

    Full Text Available Bulk segregant analysis and marker-trait association reveal common AFLP markers for resistance to septoria leaf blotch in Tunisian old durum wheat. Septoria tritici blotch (STB caused by the fungus Mycosphaerella graminicola is currently the major foliar disease of durum wheat in Tunisia. Most of the Tunisian elite cultivars show little or no resistance to this pathogen. Recently, some Tunisian landraces including 'Agili' have been identified as highly resistant to the virulent STB pathotype, 'Tun06'. In order to identify amplified fragment length polymorphism (AFLP markers associated with resistance to STB, we used bulk segregant analysis (BSA in two F3 biparental populations derived from crosses between the resistant durum wheat accession 'Agili' and the susceptible cultivars 'Karim' and 'Khiar' and Association Mapping (AM in a collection of 110 old durum wheat landraces. Out of the 24 EcoRI/MseI primer combinations tested, 4 were polymorphic between resistant and susceptible DNA pools. Screened on the parents and 9 to 12 progenies from each bulk, these polymorphic AFLP primer combinations revealed EcoACT/MseCTC-241, EcoACA/MseCTT-128, and EcoAGG/MseCTC-104 as specific alleles to resistant individuals suggesting their linkage to a gene for resistance to STB. Binary logistic regression analysis on the diversity panel showed that two AFLP markers out of the three identified by BSA were significantly associated with the resistance. EcoACT/MseCTC-241 was the significantly associated allele at P < 7.10-8 and was identified at a genetic distance of 1.2 cM to the resistance gene. This result indicates the efficiency of using landrace populations to detect potential markers for qualitative resistance.

  19. Estandarización de la técnica molecular de AFLP en palma de aceite tipo Dura (Elaeis guineensis Jacq. y estudio preliminar de caracterización

    Directory of Open Access Journals (Sweden)

    Galeano Carlos Hernando

    2005-06-01

    Full Text Available

    La palma de aceite (Elaeis guinnensis Jacq. desempeña un importante papel en la econo­mía de algunos países tropicales; Colombia ocupa el primer puesto en producción en América Latina y el quinto lugar a nivel mundial. En esta especie el mejo­ramiento genético busca generar materiales con alta producción de aceite y adaptados a las características edafoclimáticas de las diferentes zonas palmeras. El objetivo del presente trabajo fue estandarizar la téc­nica de AFLP (Amplified Fragment-Length Polymorphisms en materiales Dura del Programa de Fitomejora­miento de CENIPALMA. Al protocolo de AFLP de la casa comercial se le realizaron algunas modificacio­nes, como el aumento de la concentración del ADN (270 ng· μL-1 y la dilución 1:10 del producto de la preamplificación. De igual forma, se determinó que para teñir los geles de poliacrilamida con nitrato de plata es necesario usar agua destilada deionizada (Milli Q. También se realizó un estudio prelimi­nar de caracterización molecular en 12 palmas de los tipos Dura, Ténera y E. oleifera; según los agrupa­mientos hechos según métodos fenéticos y multiva­riados se encontró que la mayoría de palmas Dura se agrupan según el lugar de colecta, mientras la palma de origen americano se ubica de forma distante al compararla con las palmas de origen africano.

  20. Visiones Párodicas: Risas, demonios, jocosidades y caricaturas.

    Directory of Open Access Journals (Sweden)

    Beatriz González.

    2008-08-01

    Full Text Available This article attempts to characterize cartoons by examining topics related to them and parody in four different moments. The frst section addresses the arrival of laughter in the Americas and the present-day territory of Colombia. The relationship between laughter and innocence and maliciousness is noted. In the second section, the demon is presented as a source of evil and as an evangelical teaching tool in the same way that the cartoon is used as a method of teaching. The third section addressses the concepts of Charge and the cartoon in the universal language. It identifes Charge as the literature of manners in New Granada during the nineteenth century The parody of customs and its relationship to Realism in European art and to cartoons is noted. The last section discusses the relationship between cartoon and power: how the myth that cartoons can topple governments becomes, during periods of fun-damentalism, a double-edged weapon for the cartoonist.

  1. Diversidad genética intra e inter-específica de ñame (Dioscorea spp. de la región Caribe de Colombia mediante marcadores AFLP

    Directory of Open Access Journals (Sweden)

    Hernando Javier Rivera-Jiménez

    2011-12-01

    Full Text Available Conocer la variabilidad genética del ñame, Dioscorea spp., permite apoyar estrategias de mejoramiento y conservación de este recurso fitogenético. El objetivo de este estudio fue la caracterización molecular de 20 accesiones de Dioscorea spp. mediante la técnica molecular de AFLP para determinar cómo se distribuye la variabilidad genética de manera intra e inter-específica. Los datos fueron analizados mediante los métodos de agrupación de correspondencia múltiple y análisis de similaridad de Dice, estableciendo los niveles de confiabilidad de los grupos genéticos mediante remuestreos. En términos de diversidad interespecífica, los valores promedios de similitud variaron entre 41.81% entre D. alata L. y D. rotundata Poir., y 33.51% entre D. trifida L.f. y D. esculenta (Lour. Burkill, lo que sugiere alta diversidad genética entre las accesiones estudiadas, que formaron cuatro grupos genéticos: D. alata, D. rotundata, D. esculenta y D. trifida, confirmando correspondencia entre la caracterización morfológica, clasificación botánica y la caracterización molecular. En términos de diversidad intraespecífica para la especie D. alata, el análisis también reveló una composición heterogénea en la región Caribe colombiana. Estos estudios ayudarán a definir una estrategia adecuada para fines de conservación y apoyar los esfuerzos futuros en los programas de mejoramiento genético.

  2. Isolates of Ureplasma diversum genotyped by single-enzyme amplified length polymorphism Tipagem genotípica de estirpes de Ureplasma diversum por meio da amplificação de fragmentos polimórficos com única enzima (SE-AFLP

    Directory of Open Access Journals (Sweden)

    Melissa Buzinhani

    2007-03-01

    Full Text Available Isolates of Ureaplasma diversum recovered from bovines with reproductive disorders and healthy ones of four premises were compared by SE-AFLP. Twenty-eight SE-AFLP profiles without monomorphic fragments were obtained. The ureaplasma studied were divided in clusters A and B. Cluster A was divided in subclusters A1 and A2, while A1 was divided in subclusters A1a and A1b. Cluster B grouped only the reference strains. The clusters obtained were not associated with the reproductive disorders. The dendrogram obtained showed high heterogeneity among the studied ureaplasmas and indicated a low genomic stability as detected in other species of microorganisms of class Mollicutes.Cepas de referência e 30 estirpes de Ureaplasma diversum isoladas do muco vaginal de bovinos apresentando ou não distúrbios reprodutivos, de quatro diferentes propriedades, foram comparadas por meio da metodologia da SE-AFLP (single-enzyme amplified fragment length polymorphism. Foram obtidos 28 perfis, com ausência de fragmentos monomórficos. No dendrograma, as amostras foram divididas em grupos A e B. O grupo A foi subdividido em A1 e A2 e o A1 dividiu-se em A1a e A1b. As amostras de referência formaram o grupo B. Não houve diferenciação entre as estirpes isoladas de animais doentes ou sadios. Evidenciou-se grande heterogeneidade entre os ureaplasmas estudados indicando baixa estabilidade genômica, como detectado em outras espécies dos microrganismos da classe Mollicutes.

  3. AFLP analysis among Ethiopian arabica coffee genotypes

    African Journals Online (AJOL)

    STORAGESEVER

    2008-09-17

    Sep 17, 2008 ... Results of this study will be utilised for germplasm collection, conservation as well as in variety development efforts. Key words: Coffea arabica L., DNA-based markers, fingerprinting, genetic diversity. INTRODUCTION. Coffee, one of the most important beverage crops in the world and a valuable agricultural ...

  4. Amplified fragment length polymorphisms (AFLPs) analysis of ...

    African Journals Online (AJOL)

    The taxonomy of species belonging to Solanum section Solanum (sometimes referred to as the Solanum nigrum complex or black nightshades) is known to be difficult and has resulted in extensive synonymy. Yet, these species play a significant role in nutrition and food security, especially in developing countries.

  5. Terminal restriction fragment length polimorphism (T-RFLP) : una herramienta útil para valorar la dinámica y la diversidad de la población microbiana en aves y cerdos.

    OpenAIRE

    Gómez de Segura, A.

    2007-01-01

    El ecosistema intestinal es un medio complejo y dinámico que puede verse afectado puntualmente por numerosos factores propios del individuo pero también por numerosos factores ambientales o externos (como puede ser la dieta). La necesidad de conocer de una forma rápida y reproducible cómo es la dinámica de la población bacteriana, así como su estructura está siendo posible gracias al desarrollo de técnicas moleculares aplicadas como DGGE (Denaturing Gradient Gel Electrophoresis)1, TGGE (Tempe...

  6. Luis Buñuel: el fantasma de la libertad entre el instinto y la risa

    Directory of Open Access Journals (Sweden)

    Eduardo Peñuela Cañizal

    2008-06-01

    Full Text Available Os temas abordados por Buñuel nos são bem conhecidos, mas o que é importante em seus filmes é a maneira de apresentar esses temas através da mistura de elementos racionais e irracionais. Para o diretor espanhol o cinema é um instrumento de poesia e, nessa perspectiva, ele desenvolve modalidades de escrita destinadas a expressar todo tipo de significações libertárias. Neste artigo se borda uma dessas maneiras de escrita cinematográfica.

  7. Emoción, gesto y actio: la risa en el Ab Urbe Condita (II

    Directory of Open Access Journals (Sweden)

    Moreno Ferrero, Isabel

    2011-10-01

    Full Text Available In the first part of this paper (Talia dixit 5, 2010, 1-24, we analysed the general features of those passages in which Livy used laughter as a main or underlying theme, on the basis of a series of terms (risus /ridere; inridere/risus // arridere whose application could allow us to infer the general concept of this particular emotion and gesture in AVC. Once this aspect has been examined, the main goal of this paper is not only the revision of those characteristics concerning this primary “emotion” within the context of the author’s work itself, but also the comprehensive study of such texts in order to highlight the way in which Livy set both the situation and the characters, creating a certain dramatic actio from which his historiographical and literary project benefitted. Only such an analysis helps us observe the rich spectrum of nuances used by the Paduan historian. Thus, we have intended to show in this paper how Livy obtained new effects by modifying and applying rhetorical theory; how he managed to make some of his characters singularly remembered by hearers or readers thanks to a selection of topics which fitted each of his particular purposes; and finally, how he was able to relate passages in different books and contexts through specific formulas that evoked in the recipient of his work the echo and image sought. Therefore, this paper will show a number of nuances higher than previously expected, since against presumptions, the encomium (praise in Rome still generated lights and shadows.

  8. Entre risas y brumas: un recorrido hipertextual por el mundo artúrico

    Directory of Open Access Journals (Sweden)

    Nieves Martín Rogero

    2012-01-01

    Full Text Available El acercamiento a la tradición resulta fundamental para el desarrollo de la competencia literaria de los más jóvenes. En este trabajo se incide en la pervivencia de la materia artúrica en la literatura infantil y juvenil de acuerdo a un enfoque intertextual. En concreto se profundiza en dos novelas juveniles escritas en castellano, La aventura de sir Karel de Nortumbria, de Manuel Alfonseca, y El rey Arturo cabalga de nuevo, más o menos, de Miguel Ángel Moleón, con objeto de confrontar las referencias a textos precedentes y esclarecer la nueva función que adquieren en la narrativa actual.

  9. AFLP analysis of genetic diversity in main cultivated strains of ...

    African Journals Online (AJOL)

    Ganoderma mushroom is one of the most prescribed traditional medicines, which has been used for medicinal purposes for centuries particularly in China, Japan, Korea and other Asian countries. In this article, the different strains of Ganoderma spp. used in production and their genetic relations of the closely related strains ...

  10. Genetic diversity and identification of variety-specific AFLP markers ...

    African Journals Online (AJOL)

    Fenugreek (Trigonella foenum-graecum), an important spice crop belongs to the family Fabaceae. India is the largest producers as well as the largest exporter of fenugreek. Five common fenugreek varieties of India were included in this study for molecular analysis. For randomly amplified polymorphic DNA (RAPD) analysis ...

  11. Molecular analysis of Albizia species using AFLP markers for ...

    Indian Academy of Sciences (India)

    Department of Agricultural Biotechnology, College of Agriculture, OUAT, Bhubaneshwar 751 003, India. Introduction. Improving commercial and ... The Indian species A. thomsonii are classified as vulnerable (Nayar ..... Sokal R. R. and Sneath P. H. A. 1963 Principles of numerical tax- onomy. Freeman, San Fransisco, USA.

  12. Association of AFLP and SSR markers with agronomic and fibre ...

    Indian Academy of Sciences (India)

    2010-08-04

    Aug 4, 2010 ... Fi- bre yield and quality, and the key factors that determine its economic value, are the most important targets of cotton breeding programmes across ... the seed are not reliable indicators of the performance of the progeny. Further, the fibre quality can be assessed only after the harvest of the crop and hence ...

  13. Application of amplified fragment length polymorphism (AFLPs) for ...

    African Journals Online (AJOL)

    Uapaca kirkiana Muell. Årg is a dioecious fruit tree species for priority domestication in Southern Africa. It reaches reproductive maturity in eight to ten years with male plants making up 50% of breeding populations. Early identification of sex of seedlings is a prerequisite for selection and tree improvement. The amplified ...

  14. Association of AFLP and SSR markers with agronomic and fibre ...

    Indian Academy of Sciences (India)

    2010-08-04

    Aug 4, 2010 ... marker data for each individual markers using Excel data analysis (regression) programe. MRA was conducted using. 'backward' method of 'linear regression analysis' option of. SPSS version 13.0. Markers showing significant regression values were considered as associated with the trait under con-.

  15. Evaluation of interspecific DNA variability in poplars using AFLP and ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-10-19

    Oct 19, 2009 ... Silvae Genetica, 52: 5-6. Klosterman AD, Budowle B, Daselaar P (1993). PCR amplification and detection of human D1S80 VNTR locus. Amplification conditions, population genetics and application in forensic analysis. Int. J. Leg. Med. 105: 257-264. Krauss SL (2000). Patterns and mating in Persoonia ...

  16. Molecular analysis of Albizia species using AFLP markers for ...

    Indian Academy of Sciences (India)

    management strategies for conservation and improvement of the breeding programme for this genus. The genus ... management of this genus. For evaluation of species diver- sity, it is essential that ..... Sokal R. R. and Sneath P. H. A. 1963 Principles of numerical tax- onomy. Freeman, San Fransisco, USA. Singh A. N. ...

  17. Identification of AFLP markers linked with cocoon weight genes in ...

    African Journals Online (AJOL)

    STORAGESEVER

    2010-03-08

    Mar 8, 2010 ... DNA markers used in assisting selection method is a safe method in breeding process, due to deletion of environmental conditions, and it is an important tool in preparing linkage map and QTLs mapping. In mulberry silkworm that is, foundation of world sericulture, its major production- economic.

  18. AFLP fingerprinting analysis of some cultivated varieties of sea ...

    Indian Academy of Sciences (India)

    Chengjiang Ruan1 Diaqiong Li2. Institute of Bio-Resources and Environment of Dalian Nationalities University, Dalian City, Liaoning Province 116600, People's Republic of China; Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Shaanxi 712100, People's Republic ...

  19. (AFLP) analysis of genetic diversity and relationship of Chinese ...

    African Journals Online (AJOL)

    Administrator

    2011-05-30

    May 30, 2011 ... and 25 cultivars that originated from China with fluorescent amplified fragment length polymorphism molecular markers were ... Key words: Rosa rugosa, genetic diversity and relationship, amplified fragment length polymorphism. INTRODUCTION ... northern Japan (Ohwi, 1965), the Korean Peninsula.

  20. Functional Genes of Microorganisms, Comprehending the Dynamics of Agricultural Ecosystems

    Directory of Open Access Journals (Sweden)

    Catiusca Reali

    2017-05-01

    Full Text Available ABSTRACT The microbial composition of different types,in ecosystems (including agro-ecosystems, has been investigated in a rapidly growing number of studies in the past few years. The importance of microorganisms, regarding the maintenance and stability of nutrients in agroecosystems, is a key to maintain the sustainability of a crop. Molecular tools to study microbial communities are possible through many methods such as RISA, DGGE, TGGE, clone libraries, T-RFLP, RAPD, SSCP and more recently NGS (Next-Generation Sequencing. DGGE is widely employed to characterize the diversity and the community dynamics of microorganisms in the environment, making possible to find out specific groups through functional genes, allowing access to data that cannot be obtained by cultural methods. The aim of this paper is to review the functional groups related to agroecosystems and to indicate the critical choice of DNA primers pairs and targeted DNA regions that may be used in PCR-based methods such as the DGGE technique in order to evaluate the microbial communities in a variety of environments.

  1. [Rheumatology - Integration into student training (RISA) : Current structure of clinical rheumatology in German universities (RISA III)].

    Science.gov (United States)

    Riemekasten, G; Aringer, M; Baerwald, C G O; Meyer-Bahlburg, A; Bergner, R; Feuchtenberger, M; Gebhardt, C; Hellmich, B; Keyßer, G; Lorenz, H-M; Kneitz, C; Witte, T; Müller-Ladner, U; Schneider, M; Braun, J; Rautenstrauch, J; Specker, C; Schulze-Koops, H

    2016-06-01

    The German Society of Rheumatology and the Committee for Student Training investigated what effects the structures in university medicine have on student teaching. In February 2014 a questionnaire was sent to the teaching staff and Deans of each of the 37 medical faculties. Of the locations seven were classified as being independent rheumatological university hospitals and nine universities had a W2/W3/C3 grade professor as head of a department of clinical rheumatology but answerable to superiors. In the 37 faculties in Germany the proportion of lecture hours, the proportion of obligatory lecture hours, the number of hours for practical exercises and the number of hours for bedside teaching were distributed very differently and as a rule higher in universities with academic freedom. Not all medical faculties have obligatory teaching in the field of clinical rheumatology. On average medical students see five patients with rheumatological symptoms during their studies. In summary, over the past years it has not been possible to successfully utilize the great importance of rheumatology for society and the innovation potential of this discipline in order to improve the integration of clinical rheumatology into universities.

  2. AFLP studies on downy-mildew-resistant and downy-mildew ...

    Indian Academy of Sciences (India)

    Downy mildew (DM) caused by Peronospora arborescens, is a serious disease in opium poppy (Papaver somniferum), which has a world-wide spread. The establishment of DM-resistant cultivars appears to be a sustainable way to control the disease. In this paper, we present the results of a study aimed at the identification ...

  3. Genetic structure of Indian valerian (Valeriana jatamansi) populations in western Himalaya revealed by AFLP.

    Science.gov (United States)

    Rajkumar, Subramani; Singh, Sunil Kumar; Nag, Akshay; Ahuja, Paramvir S

    2011-10-01

    Valeriana jatamansi Jones is a natural tetraploid species indigenous to the Indian Himalaya. To assess its genetic diversity and population structure, we analyzed six natural populations from the western Himalayan region using amplified fragment length polymorphism. An analysis of molecular variance found that 93% of the genetic variation of V. jatamansi was within populations and 7% among populations. The correlation between genetic and geographic distances (r = 0.14) was not significant. Though the populations are well separated, the lack of distinct genetic variation between populations may be due to either recent rapid fragmentation from a wide and continuous area resulting in genetically similar populations or wide dispersal of seed by wind, since the follicles are feathery. Polyploidy may be the reason for the lack of genetic impoverishment due to fragmentation.

  4. Development of a simple and powerful method, cDNA AFLP-SSPAG ...

    African Journals Online (AJOL)

    AJB SERVER

    2006-12-18

    Dec 18, 2006 ... Using this method, Differential mRNA expression was found between high and low heterosis groups of maize. Differential ... staining polyacrylamide gels provide a novel and very powerful gene cloning method. Key words: Cloning .... diluted 50 fold and 5 µl used as a template for the second amplification ...

  5. Diversity of garlic (Allium sativum L.) using SSR, EST and AFLP markers

    Science.gov (United States)

    Germplasm from the center of origin/diversity is important for the breeding and fingerprinting crop plants. In this study we utilized both dominant and co-dominant markers for the characterization of garlic samples from diverse geographic origins to assess the relative utility of these markers to id...

  6. AFLP/SSR mapping of resistance genes to Alectra vogelii in cowpea ...

    African Journals Online (AJOL)

    user

    ., 1997) to total crop loss of the highly susceptible cultivar Black- eye (Riches, 1990). A. vogelii can produce as ... resistance gene Rac1 (Myers et al., 1996). Ouédraogo et al., (2001) ... RAPD (Garcia-Mas et al., 2000). The SSR technique is ...

  7. AFLP fingerprinting for identification of infra-species groups of Rhizoctonia solani and Waitea circinata

    Science.gov (United States)

    Patch diseases caused by Thanatephorus cucumeris and Waitea circinata varieties (anamorphs: Rhizoctonia species) pose a serious threat to successful maintenance of several important turfgrass species. Reliance on field symptoms to identify Rhizoctonia causal agents can be difficult and misleading. D...

  8. AFLP assisted DNA-Barcoding of mullets (Mugilidae) used in East ...

    African Journals Online (AJOL)

    In this study, we investigated the local genetic structure of juvenile mullets collected from five sites around Bagamoyo (Tanzanian mainland) and Zanzibar Island, East Africa. Fish were caught in low tide using a seine net. The fish were morphologically identified, and then genetically identified using direct sequencing of the ...

  9. AFLP/SSR mapping of resistance genes to Alectra vogelii in cowpea ...

    African Journals Online (AJOL)

    La plante parasite Alectra vogelii (Benth) provoque une réduction significative du rendement de niébé en Afrique. Pour repérer et cartographier le gène de résistance à A. vogelii, une population F2 issue d'un croisement impliquant le cultivar résistant IT81D-994 et le cultivar sensible TVX3236 a été criblée. La technique ...

  10. Revision of Central European taxa of Festuca ser. Psammophilae Pawlus: morphometrical, karyological and AFLP analysis

    Czech Academy of Sciences Publication Activity Database

    Šmarda, P.; Šmerda, J.; Knoll, A.; Bureš, P.; Danihelka, Jiří

    2007-01-01

    Roč. 266, 3-4 (2007), s. 197-232 ISSN 0378-2697 R&D Projects: GA MŠk LC06073; GA ČR(CZ) GD524/05/H536 Grant - others:GA ČR(CZ) GA206/03/0228 Institutional research plan: CEZ:AV0Z60050516 Keywords : taxonomy * evolution * multivariate morphometrics Subject RIV: EF - Botanics Impact factor: 1.492, year: 2007

  11. AFLPs detect low genetic diversity for Phytophthora nemorosa and P. pseudosyringae in the US and Europe

    Science.gov (United States)

    Rachel E. Linzer; David M. Rizzo; Santa Olga Cacciola; Matteo Garbelotto

    2009-01-01

    In California and Oregon, two recently described oomycete forest pathogens, Phytophthora nemorosa and P. pseudosyringae, overlap in their host and geographic ranges with the virulent P. ramorum, causal agent of "sudden oak death." Epidemiological observations, namely broader geographic...

  12. AFLP fingerprinting of Kentucky bluegrass (Poa pratensis L.) from undisturbed Dutch grasslands: implications for conservation

    NARCIS (Netherlands)

    Treuren, van R.

    2008-01-01

    Undisturbed grasslands are considered rich sources of promising genotypes for the development of new varieties of Kentucky bluegrass (Poa pratensis L.). Grasslands that have not been resown with commercial cultivars nor treated with high doses of nitrogen fertilizer have become rare in the

  13. [Rheumatology: Integration into student training--the RISA- Study. Results of a survey exploring the scale of education and training in rheumatology at German universities].

    Science.gov (United States)

    Keysser, G; Zacher, J; Zeidler, H

    2004-04-01

    During the Bone and Joint Decade 2000-2010, national and international rheumatological societies campaign for improvements of undergraduate training in the field of musculoskeletal diseases. In 2002, the Committee for Undergraduate Training of the German Society for Rheumatology (DGRh) performed a survey in order to estimate the extent of rheumatological undergraduate training at German universities. A questionnaire was sent to all university hospitals for internal medicine and for orthopaedics. The items of the survey covered the qualification of the teachers, the number and the time frame of lessons and courses, as well as the items of the curriculum in rheumatology. With 95% of the universities responding, a broad variation of the quality of rheumatological training became obvious, ranging from the absence of competent teaching to a comprehensive curriculum covering theory and practical training. Only a minority of universities fulfilled the recommendations of the DGRh for undergraduate education. The most substantial deficits are found in practical training, caused by insufficiently small numbers of patients seen by the medical students, and by the short duration of the practical courses. The insights described here should lead to the adaptation of the level of education in the field of rheumatology to the demands of a society with growing musculoskeletal problems.

  14. Scientists and Stakeholders in the Chesapeake Bay: How the Mid-Atlantic RISA Strengthens Climate Resilience Through Participatory Decision-Making Processes

    Science.gov (United States)

    Knopman, D.; Berg, N.

    2017-12-01

    The NOAA Mid-Atlantic Regional Integrated Sciences and Assessments (MARISA) program was formed in September 2016 to increase climate resilience in the Mid-Atlantic, with an initial focus on the Chesapeake Bay Watershed. In this talk, we will discuss how the program's unique structure and approach are designed to advance resilience to a changing climate through improved data, place-based decision support, and public engagement. Emphasis will be placed on MARISA's approach to integrating stakeholder perspectives from the onset of decision scoping, through the creation of actionable data sets, and concluding with the co-development of adaptation strategies between the scientific community, decision-makers, and stakeholders. Specific examples of this process involving climate-sensitive decisions and investments regarding water resources, land management, and urban corridors will be discussed.

  15. ¡Huayra huayra pichcamanta!: augurio, risa y regeneración en la política tradicional (Pacota, Huarochirí

    Directory of Open Access Journals (Sweden)

    2002-01-01

    Full Text Available “¡HUAYRA HUAYRA PICHCAMANTA!” : AUGURE, RIRES ET RÉGÉNÉRATION DANS LA POLITIQUE TRADITIONNELLE (PACOTA, HUAROCHIRÍ Une variante du jeu d’oracle pichca, différente de celles décrites par Gentile Lafaille (1998, procure une augure annuelle pour l’agropastoralisme dans la région centrale de Huarochirí (département de Lima, Pérou. L’aspect ludique prédomine, mais les croyances et agissements associés à ce jeu ont également des conséquences pratiques. Aujourd’hui, comme dans le manuscrit quechua de Huarochirí de 1608 [?], un schéma de dualisme alternant sert à régénérer l’ordre politique face aux impondérables climatiques et historiques. Una variante del juego-oráculo de la pichca, diferente de las versiones estudiadas por Gentile Lafaille (1998, facilita el augurio anual para el agropastoralismo en el centro de la provincia de Huarochirí (departamento de Lima, Perú. La nota lúdica predomina, pero las prácticas y creencias en torno al juego también traen consecuencias prácticas. En la actualidad, como en el manuscrito quechua de Huarochirí de 1608 [?], el padrón llamado dualismo alternante sirve para regenerar el orden político frente a los imponderables del clima y de la historia. “¡HUAYRA HUAYRA PICHCAMANTA!” AUGURY, LAUGHTER, AND REGENERATION IN AN ANDEAN POLITICAL REGIME (PACOTA, HUAROCHIRÍ A variant of the oracular game pichca, different from variants described by Gentile Lafaille (1998, provides an annual augury for agropastoralism in central Huarochirí (Department of Lima, Peru. It is playful, but beliefs and practices around it also have practical consequence. Today as in the Huarochirí Quechua manuscript of 1608 [?], a pattern of alternating dualism serves to regenerate political order in the face of climatic and historical imponderables.

  16. Molecular Fingerprints of the Human Fecal Microbiota From 9 to 18 Months Old and the Effect of Fish Oil Supplementation

    DEFF Research Database (Denmark)

    Andersen, Anders Daniel; Mølbak, Lars; Michaelsen, Kim Fleischer

    2011-01-01

    supplementation with 5mL of fish oil (FO) or sunflower oil (SO) from 9 to 18 months of age, stool samples were collected from 132 healthy Danish infants. Molecular fingerprints of the bacterial DNA were obtained by terminal restriction fragment length polymorphism (T-RFLP). Results: The T-RFLP profiles indicated...

  17. AFLP diversity and spatial structure of Calycophyllum candidissimum (Rubiaceae), a dominant tree species of Nicaragua's critically endangered seasonally dry forest.

    Science.gov (United States)

    Dávila-Lara, A; Affenzeller, M; Tribsch, A; Díaz, V; Comes, H P

    2017-10-01

    The Central American seasonally dry tropical (SDT) forest biome is one of the worlds' most endangered ecosystems, yet little is known about the genetic consequences of its recent fragmentation. A prominent constituent of this biome is Calycophyllum candidissimum, an insect-pollinated and wind-dispersed canopy tree of high socio-economic importance, particularly in Nicaragua. Here, we surveyed amplified fragment length polymorphisms across 13 populations of this species in Nicaragua to elucidate the relative roles of contemporary vs historical factors in shaping its genetic variation. Genetic diversity was low in all investigated populations (mean H E =0.125), and negatively correlated with latitude. Overall population differentiation was moderate (Φ ST =0.109, Pforest regions may be genetically resilient to habitat fragmentation due to species-typical dispersal characteristics, the necessity of broad-scale measures for their conservation notwithstanding.

  18. Origin of Spanish invasion by the zebra mussel, Dreissena polymorpha (Pallas, 1771) revealed by amplified fragment length polymorphism (AFLP) fingerprinting

    NARCIS (Netherlands)

    Rajagopal, S.; Pollux, B.J.A.; Peters, J.L.; Cremers, G.; Moon- van der Staay, S.Y.; Alen, van T.; Eygensteyn, J.; Hoek, van A.H.A.M.; Palau, A.; Vaate, de A.B.; Velde, van der G.

    2009-01-01

    The zebra mussel, Dreissena polymorpha is an aquatic nuisance invasive species originally native to the Ponto-Caspian region where it is found in lakes and delta areas of large rivers draining into the Black and Caspian seas. The dispersal of D. polymorpha began at the end of the 18th century, at a

  19. Circumpolar phylogeography of Juncus biglumis (Juncaceae) inferred from AFLP fingerprints, cpDNA sequences, nuclear DNA content and chromosome numbers

    Czech Academy of Sciences Publication Activity Database

    Schönswetter, P.; Suda, Jan; Popp, M.; Weiß-Schneeweiss, H.; Brochmann, C.

    2007-01-01

    Roč. 42, č. 1 (2007), s. 92-103 ISSN 1055-7903 R&D Projects: GA AV ČR(CZ) KSK6005114 Grant - others:-(NO) 150322/720; -(NO) 146515/420 Institutional research plan: CEZ:AV0Z60050516 Keywords : taxonomy * phylogepgraphy * genetics Subject RIV: EF - Botanics Impact factor: 3.994, year: 2007

  20. Significant population genetic structure detected in the rock bream Oplegnathus fasciatus (Temminck & Schlegel, 1844) inferred from fluorescent-AFLP analysis

    Science.gov (United States)

    Xiao, Yongshuang; Ma, Daoyuan; Xu, Shihong; Liu, Qinghua; Wang, Yanfeng; Xiao, Zhizhong; Li, Jun

    2016-05-01

    Oplegnathus fasciatus (rock bream) is a commercial rocky reef fish species in East Asia that has been considered for aquaculture. We estimated the population genetic diversity and population structure of the species along the coastal waters of China using fluorescent-amplified fragment length polymorphisms technology. Using 53 individuals from three populations and four pairs of selective primers, we amplified 1 264 bands, 98.73% of which were polymorphic. The Zhoushan population showed the highest Nei's genetic diversity and Shannon genetic diversity. The results of analysis of molecular variance (AMOVA) showed that 59.55% of genetic variation existed among populations and 40.45% occurred within populations, which indicated that a significant population genetic structure existed in the species. The pairwise fixation index F st ranged from 0.20 to 0.63 and were significant after sequential Bonferroni correction. The topology of an unweighted pair group method with arithmetic mean tree showed two significant genealogical branches corresponding to the sampling locations of North and South China. The AMOVA and STRUCTURE analyses suggested that the O. fasciatus populations examined should comprise two stocks.

  1. Transcriptional profiles of emasculated flowers of black locust (Robinia pseudoacacia) determined using the cDNA-AFLP technique.

    Science.gov (United States)

    Wang, J X; Sun, P; Yuan, C Q; Dai, L; Zhang, Y; Wu, B; Long, C; Sun, Y H; Li, Y

    2015-12-03

    Black locust (Robinia pseudoacacia) is a tree in the subfamily Faboideae, native to North America, that has been naturalized and widely planted in temperate Europe and Asia. Black locust has important ecological and economic value, but its quality needs improvement. Hybridization programs are important for black locust breeding, but the low rate of fruit set after controlled pollination limits both its breeding and that of other monoclinous plant species that share this problem. In this study, we investigated gene expression in emasculated black locust flowers using the cDNA-amplified fragment length polymorphism technique to determine why the rate of fruit set is low after controlled pollination. Flowers that were emasculated after being frozen in liquid nitrogen were used as controls. Changes in the flower transcriptome were more dramatic at 5 h after emasculation than at 48 h. Injury caused by emasculation decreased the expression levels of genes associated with metabolism, growth regulation, signal transduction, and photosynthesis, and it increased the expression of genes related to stress-response metabolism, signal transduction, and promotion of senescence. The changes in the expression levels of these genes had negative effects on sugar metabolism, protein metabolism, lipid metabolism, energy metabolism, matter transport, signal transduction, osmotic regulation, pH regulation, and photosynthesis. Thus, emasculation accelerated flower senescence, resulting in low fruit set.

  2. Distribution of Penicillium commune isolates in cheese dairies mapped using secondary metabolite profiles, morphotypes, RAPD and AFLP fingerprinting

    DEFF Research Database (Denmark)

    Lund, Flemming; Nielsen, A.B.; Skouboe, P.

    2003-01-01

    In an 8-year study of the diversity and distribution of Penicillium commune contaminants in two different cheese dairies, swab and air samples were taken from the production plants, the processing environment and contaminated cheeses. A total of 321 Penicillium commune isolates were characterized...

  3. Revisiting AFLP fingerprinting for an unbiased assessment of genetic structure and differentiation of taurine and zebu cattle

    NARCIS (Netherlands)

    Utsunomiya, Yuri T.; Bomba, Lorenzo; Lucente, Giordana; Colli, Licia; Negrini, Riccardo; Lenstra, Johannes A.; Erhardt, Georg; Garcia, José F.; Ajmone-Marsan, Paolo; Moazami-Goudarzi, K.; Williams, J.; Wiener, P.; Olsaker, I.; Kantanen, J.; Dunner, S.; Cañón, J.; Rodellar, C.; Martín-Burriel, I.; Valentini, A.; Zanotti, M.; Holm, L. E.; Eythorsdottir, E.; Mommens, G.; Polygen, Van Haeringen; Nijman, I. J.; Dolf, G.; Bradley, D. G.

    2014-01-01

    Background: Descendants from the extinct aurochs (Bos primigenius), taurine (Bos taurus) and zebu cattle (Bos indicus) were domesticated 10,000 years ago in Southwestern and Southern Asia, respectively, and colonized the world undergoing complex events of admixture and selection. Molecular data, in

  4. Lyophilization of Spodoptera frugiperda (Lepidoptera: Noctuidae) larvae yields high-quality DNA for use in AFLP genetic studies

    Science.gov (United States)

    Agricultural research in the 21st century has become a collaborative effort. Research on crop pests like Spodoptera frugiperda (J.E. Smith), commonly known as the fall armyworm (FAW), can involve international collaboration because it is a pest not only in the southern United States, but also in La...

  5. Chromosomal regions involved in hybrid performance and heterosis : their AFLP-based identification and practical use in prediction models

    NARCIS (Netherlands)

    Vuylsteke, M.; Kuiper, M.; Stam, P.

    2000-01-01

    In this paper, a novel approach towards the prediction of hybrid performance and heterosis is presented. Here, we describe an approach based on: (i) the assessment of associations between AFLPÒ22 AFLPÒ is a registered trademark of Keygene N.V. ,33 The methylation AFLPÒ method is subject to a patent

  6. AFLP analysis shows high incongruence between genetic differentiation and morphology-based taxonomy in a widely distributed tortoise

    Czech Academy of Sciences Publication Activity Database

    Mikulíček, Peter; Jandzik, D.; Fritz, U.; Schneider, C.; Široký, P.

    2013-01-01

    Roč. 108, č. 1 (2013), s. 151-160 ISSN 0024-4066 Institutional support: RVO:68081766 Keywords : Amplified fragment length polymorphism * morphological plasticity * reptiles * stabilizing selection * Testudines Subject RIV: EG - Zoology Impact factor: 2.535, year: 2013

  7. AFLP markers for the R-gene in the flea beetle, Phyllotreta nemorum, conferring resistance to defenses in Barbarea vulgaris

    NARCIS (Netherlands)

    Breuker, C.J.; Victoir, K.; Jong, de P.W.; Meijden, van der E.; Brakefield, P.M.; Vrieling, K.

    2005-01-01

    A so-called R-gene renders the yellow-striped flea beetle Phyllotreta nemorum L. (Coleoptera: Chrysomelidae: Alticinae) resistant to the defenses of the yellow rocket Barbarea vulgaris R.Br. (Brassicacea) and enables it to use it as a host plant in Denmark. In this study, genetic markers for an

  8. Zebra mussels (Dreissena polymorpha) in Ireland, AFLP-fingerprinting and boat traffic both indicate an origin from Britain

    NARCIS (Netherlands)

    Pollux, B.J.A.; Minchin, D.; Van der Velde, G.; Van Alen, T.; Moon-Van der Staay, S.Y.; Hackstein, J.

    2003-01-01

    The zebra mussel (Dreissena polymorpha) is an aquatic nuisance species that invaded Ireland around 1994. We studied the invasion of the zebra mussel combining field surveys and genetic studies, to determine the origin of invasion and the vector of introduction. Field surveys showed that live zebra

  9. The first genetic linkage map of Eucommia ulmoides

    Indian Academy of Sciences (India)

    AFLP) markers. A total of 22 AFLP primer .... and medicinal components content, strong drought resistance and fast growing. Controlled pollinations ..... (Populus deltoides, P. Nigra and P. Trichocarpa) based on AFLP and microsatellite markers.

  10. Comparison of methods and animal models commonly used for investigation of fecal microbiota: Effects of time, host and gender

    DEFF Research Database (Denmark)

    Bernbom, Nete; Nørrung, Birgit; Saadbye, Peter

    2006-01-01

    Denaturing gradient gel electrophoresis (DGGE), terminal restriction fragment length polymorphism (T-RFLP) and plating on selective agars were used to study variation in the fecal microbiota of rats over time as well as variation between individuals. Investigated rats were either conventional...... and specific pathogen free (SPF). or human flora associated (HFA). A higher variation (p animals. Analysis of DGGE and T-RFLP profiles of fecal microbiota from SPF and HFA rats revealed that variation over time was less significant than...

  11. Covariance of bacterioplankton composition and environmental variables in a temperate delta system

    Science.gov (United States)

    Stepanauskas, R.; Moran, M.A.; Bergamaschi, B.A.; Hollibaugh, J.T.

    2003-01-01

    We examined seasonal and spatial variation in bacterioplankton composition in the Sacramento-San Joaquin River Delta (CA) using terminal restriction fragment length polymorphism (T-RFLP) analysis. Cloned 16S rRNA genes from this system were used for putative identification of taxa dominating the T-RFLP profiles. Both cloning and T-RFLP analysis indicated that Actinobacteria, Verrucomicrobia, Cytophaga-Flavobacterium and Proteobacteria were the most abundant bacterioplankton groups in the Delta. Despite the broad variety of sampled habitats (deep water channels, lakes, marshes, agricultural drains, freshwater and brackish areas), and the spatial and temporal differences in hydrology, temperature and water chemistry among the sampling campaigns, T-RFLP electropherograms from all samples were similar, indicating that the same bacterioplankton phylotypes dominated in the various habitats of the Delta throughout the year. However, principal component analysis (PCA) and partial least-squares regression (PLS) of T-RFLP profiles revealed consistent grouping of samples on a seasonal, but not a spatial, basis. ??-Proteobacteria related to Ralstonia, Actinobacteria related to Microthrix, and ??-Proteobacteria identical to the environmental Clone LD12 had the highest relative abundance in summer/fall T-RFLP profiles and were associated with low river flow, high pH, and a number of optical and chemical characteristics of dissolved organic carbon (DOC) indicative of an increased proportion of phytoplankton-produced organic material as opposed to allochthonous, terrestrially derived organic material. On the other hand, Geobacter-related ??-Proteobacteria showed a relative increase in abundance in T-RFLP analysis during winter/spring, and probably were washed out from watershed soils or sediment. Various phylotypes associated with the same phylogenetic division, based on tentative identification of T-RFLP fragments, exhibited diverse seasonal patterns, suggesting that ecological

  12. An Approach to Command and Control Using Emerging Technologies

    Science.gov (United States)

    2013-06-01

    An Approach To Command and Control Using Emerging Technologies ICCRTS – 044 Dan Carpenter Air Force Research Laboratory / RISA ATTN Dan Carpenter... RISA 525 Brookes Rd Rome, NY 13441 (315) 330-7121 Report Documentation Page Form ApprovedOMB No. 0704-0188 Public reporting burden for the...PROJECT NUMBER 5e. TASK NUMBER 5f. WORK UNIT NUMBER 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) Air Force Research Laboratory / RISA ,525

  13. A Change in the Air: Strategic Innovation and the Combined Bomber Offensive

    Science.gov (United States)

    2011-06-01

    relations interact with other influences of military strategy. Risa Brooks suggests, ―Domestic relations between political and military leaders shape the...Servants : Agency, Oversight, and Civil-Military Relations, 287. 36 Risa Brooks, Shaping Strategy : The Civil-Military Politics of Strategic Assessment...New York, NY: Texere, 2002. Brooks, Risa . Shaping Strategy : The Civil-Military Politics of Strategic Assessment. Princeton, N.J.: Princeton

  14. Application of AFLP molecular markers to genetic characterisation of duck (Anas platyrhyncos, turkey (Meleagris gallopavo and helmeted guinea fowl (Numida meleagris Veneto breeds

    Directory of Open Access Journals (Sweden)

    M. Cassandro

    2010-01-01

    Full Text Available In the last decade, the conservation of local breeds and of their genetic resources has gained more and more importance (Notter, 1999. In fact, the safeguard of animal genetic variability is determinant to maintain ecosystem equilibriums but it is also essential to guarantee future economic potentials of these animal resources. Moreover, biodiversity has a great cultural value and it can be also used for scientific purposes (FAO, 1992.

  15. Analysis of Claviceps africana and C. sorghi from India using AFLPs, EF-1alfa gene intron 4, and Beta-tubulin gene intron 3

    Czech Academy of Sciences Publication Activity Database

    Tooley, P. W.; Bandyopadhyay, R.; Carras, M. M.; Pažoutová, Sylvie

    2006-01-01

    Roč. 101, č. 4 (2006), s. 441-451 ISSN 0953-7562 Institutional research plan: CEZ:AV0Z50200510 Keywords : clavicipitaceae * coevolution * ergot Subject RIV: EE - Microbiology, Virology Impact factor: 1.860, year: 2006

  16. Oidium neolycopersici: Intra-specific variability inferred from AFLP analysis and relationship with closely related powdery mildew fungi infecting various plant species

    NARCIS (Netherlands)

    Jankovics, T.; Bai, Y.; Kovacs, G.M.; Bardin, M.; Nicot, P.C.; Toyoda, H.; Matsuda, Y.; Niks, R.E.; Kiss, L.

    2008-01-01

    Previous works indicated a considerable variation in the pathogenicity, virulence, and host range of Oidium neolycopersici isolates causing tomato powdery mildew epidemics in many parts of the world. In this study, rDNA internal transcribed spacer (ITS) sequences, and amplified fragment length

  17. Phylogeography and molecular diversity analysis of Jatropha curcas L. and the dispersal route revealed by RAPD, AFLP and nrDNA-ITS analysis.

    Science.gov (United States)

    Sudheer Pamidimarri, D V N; Reddy, Muppala P

    2014-05-01

    Jatropha curcas L. (Euphorbiaceae) has acquired a great importance as a renewable source of energy with a number of environmental benefits. Very few attempts were made to understand the extent of genetic diversity and its distribution. This study was aimed to study the diversity and deduce the phylogeography of Jatropha curcas L. which is said to be the most primitive species of the genus Jatropha. Here we studied the intraspecific genetic diversity of the species distributed in different parts of the globe. The study also focused to understand the molecular diversity at reported probable center of origin (Mexico), and to reveal the dispersal route to other regions based on random amplified polymorphic DNA, amplified fragment length polymorphism and nrDNA-ITS sequences data. The overall genetic diversity of J. curcas found in the present study was narrow. The highest genetic diversity was observed in the germplasm collected from Mexico and supports the earlier hypothesis based on morphological data and natural distribution, it is the center for origin of the species. Least genetic diversity found in the Indian germplasm and clustering results revealed that the species was introduced simultaneously by two distinct germplasm and subsequently distributed in different parts of India. The present molecular data further revealed that J. curcas might have spread from the center of the origin to Cape Verde, than to Spain, Portuguese to other neighboring countries and simultaneously to Africa. The molecular evidence supports the Burkill et al. (A dictionary of the economic products of the Malay Peninsula, Governments of Malaysia and Singapore by the Ministry of Agriculture and Co-operatives. Kuala Lumpur, Malaysia, 1966) view of Portuguese might have introduced the species to India. The clustering pattern suggests that the distribution was interfered by human activity.

  18. Identification of DNA sequence variation in Campylobacter jejuni strains associated with the Guillain-Barre syndrome by high-throughput AFLP analysis.

    NARCIS (Netherlands)

    P.C.R. Godschalk (Peggy); M.P. Bergman (Mathijs); R.F.J. Gorkink (Raymond); G. Simons (Guus); N.P.W.C.J. van den Braak (Nicole); A.J. Lastovica (Albert); H.P. Endtz (Hubert); H.A. Verbrugh (Henri); A.F. van Belkum (Alex)

    2006-01-01

    textabstractBACKGROUND: Campylobacter jejuni is the predominant cause of antecedent infection in post-infectious neuropathies such as the Guillain-Barre (GBS) and Miller Fisher syndromes (MFS). GBS and MFS are probably induced by molecular mimicry between human gangliosides and bacterial

  19. Efficiency of RAPD, ISSR, AFLP and ISTR markers for the detection of polymorphisms and genetic relationships in camote de cerro (Dioscorea spp.

    Directory of Open Access Journals (Sweden)

    Ana Paulina Velasco-Ramírez

    2014-03-01

    Conclusion: This indicates an important level of genetic differences despite the fact that the plant is asexually propagated. Based on the diversity statistics, any marker tested in present work can be recommended for use in large-scale genetic studies of populations. However, the low correlations among different molecular marker systems show the importance of the complementarity of the information that is generated by different markers for genetic studies involving estimation of polymorphism and relationships.

  20. DNA barcoding, MALDI-TOF and AFLP data support Fusarium ficicrescens as a distinct species within the F. fujikuroi species complex.

    NARCIS (Netherlands)

    de Hoog, S.; van Diepeningen, A.D.

    2015-01-01

    The Fusarium fujikuroi species complex (FFSC) is one of the most common group of fusaria associated with plant diseases, mycotoxins production and traumatic and disseminated human infections. Here we present the description and taxonomy of a new taxon, Fusarium ficicrescens sp. nov., collected from

  1. Phylogeography and molecular diversity analysis of Jatropha curcas L. and the dispersal route revealed by RAPD, AFLP and nrDNA-ITS analysis

    KAUST Repository

    Sudheer Pamidimarri, D. V N

    2014-01-29

    Jatropha curcas L. (Euphorbiaceae) has acquired a great importance as a renewable source of energy with a number of environmental benefits. Very few attempts were made to understand the extent of genetic diversity and its distribution. This study was aimed to study the diversity and deduce the phylogeography of Jatropha curcas L. which is said to be the most primitive species of the genus Jatropha. Here we studied the intraspecific genetic diversity of the species distributed in different parts of the globe. The study also focused to understand the molecular diversity at reported probable center of origin (Mexico), and to reveal the dispersal route to other regions based on random amplified polymorphic DNA, amplified fragment length polymorphism and nrDNA-ITS sequences data. The overall genetic diversity of J. curcas found in the present study was narrow. The highest genetic diversity was observed in the germplasm collected from Mexico and supports the earlier hypothesis based on morphological data and natural distribution, it is the center for origin of the species. Least genetic diversity found in the Indian germplasm and clustering results revealed that the species was introduced simultaneously by two distinct germplasm and subsequently distributed in different parts of India. The present molecular data further revealed that J. curcas might have spread from the center of the origin to Cape Verde, than to Spain, Portuguese to other neighboring countries and simultaneously to Africa. The molecular evidence supports the Burkill et al. (A dictionary of the economic products of the Malay Peninsula, Governments of Malaysia and Singapore by the Ministry of Agriculture and Co-operatives. Kuala Lumpur, Malaysia, 1966) view of Portuguese might have introduced the species to India. The clustering pattern suggests that the distribution was interfered by human activity. © Springer Science+Business Media 2014.

  2. [Recent advances of amplified fragment length polymorphism and its applications in forensic botany].

    Science.gov (United States)

    Li, Cheng-Tao; Li, Li

    2008-10-01

    Amplified fragment length polymorphism (AFLP) is a new molecular marker to detect genomic polymorphism. This new technology has advantages of high resolution, good stability, and reproducibility. Great achievements have been derived in recent years in AFLP related technologies with several AFLP expanded methodologies available. AFLP technology has been widely used in the fields of plant, animal, and microbes. It has become one of the hotspots in Forensic Botany. This review focuses on the recent advances of AFLP and its applications in forensic biology.

  3. Risk preferences in strategic wildfire decision making: a choice experiment with U.S. wildfire managers.

    Science.gov (United States)

    Wibbenmeyer, Matthew J; Hand, Michael S; Calkin, David E; Venn, Tyron J; Thompson, Matthew P

    2013-06-01

    Federal policy has embraced risa management as an appropriate paradigm for wildfire management. Economic theory suggests that over repeated wildfire events, potential economic costs and risas of ecological damage are optimally balanced when management decisions are free from biases, risa aversion, and risa seeking. Of primary concern in this article is how managers respond to wildfire risa, including the potential effect of wildfires (on ecological values, structures, and safety) and the likelihood of different fire outcomes. We use responses to a choice experiment questionnaire of U.S. federal wildfire managers to measure attitudes toward several components of wildfire risa and to test whether observed risa attitudes are consistent with the efficient allocation of wildfire suppression resources. Our results indicate that fire managers' decisions are consistent with nonexpected utility theories of decisions under risa. Managers may overallocate firefighting resources when the likelihood or potential magnitude of damage from fires is low, and sensitivity to changes in the probability of fire outcomes depends on whether probabilities are close to one or zero and the magnitude of the potential harm. © 2012 Society for Risk Analysis.

  4. An Architecture to Support Information Availability in the Tactical Domain

    Science.gov (United States)

    2012-10-01

    Research Laboratory/Information Directorate Rome Research Site/ RISA 525 Brooks Road Rome NY 13441-4505 8. PERFORMING ORGANIZATION REPORT NUMBER... RISA 525 Brooks Road Rome NY 13441-4505 10. SPONSOR/MONITOR’S ACRONYM(S) N/A 11. SPONSORING/MONITORING AGENCY REPORT NUMBER

  5. Blast Technologies

    Science.gov (United States)

    2011-06-27

    Team Leader Risa Scherer Blast Mitigation Interior and Laboratory Team Leader Blast Technologies POC’s Government Point Of Contacts (POCs): To...to yield injury assessments at higher fidelities and with higher confidence UNCLASSIFIED UNCLASSIFIED Risa Scherer Blast Mitigation Interior and

  6. Smoking in the United States Air Force: Trends, Most Prevalent Diseases and their Association with Cost

    Science.gov (United States)

    2011-09-01

    Talcott, Harry Lando, and Risa J. Stein. “Smoking prevalence and risk factors for smoking in a population of United States Air Force basic trainees...Stein, Risa J., Sara A. Pyle, C. Keith Haddock, W.S. Carlos Poston, Robert Bray, and Jason Williams, “ Reported stress and its relationship to tobacco

  7. Beyond the Resignation Debate: A New Framework for Civil-Military Dialogue

    Science.gov (United States)

    2015-01-01

    recent years. For example, Risa A. Brooks, associate professor of political science at Marquette Uni- versity, considers the potential costs and...Leadership in Wartime (New York: Free Press, 2002), 258–64; Feaver, Armed Servants, 68–75; and Risa A. Brooks, “Militaries and Political Activity in

  8. Arbiters of Social Unrest: Military Responses to the Arab Spring

    Science.gov (United States)

    2011-01-01

    mobilization. 12 Others inferred that military intervention in political affairs was due to military interests and political restraints. Risa ...Comparative Politics 36 (2) (Jan 2004): 144-149. 12 Ibid., 139-157. 13 Risa Brooks, “Political-Military Relations and the Stability of Arab

  9. Civil-Military Relations: A Selected Bibliography

    Science.gov (United States)

    2011-05-01

    2009) Brooks, Risa . Political-Military Relations and the Stability of Arab Regimes. New York: Oxford University Press for the International...Press, 2005. 270pp. (UA23 .B333 2005) Brooks, Risa A. Shaping Strategy: The Civil-Military Politics of Strategic Assessment. Princeton: Princeton

  10. Civil Discourse or Civil War? The Influence of Civil-Military Relations on Iraq and Afghanistan War Strategy

    Science.gov (United States)

    2011-05-04

    Hopkins Univ. Press, 2009), 44. 10 Mackubin T. Owens (professor, Naval War College, Newport, RI), interview by the author, 5 April 2011. 11 Risa A...www.esquire.com/features/fox-fallon (accessed 18 March 2011). Brooks, Risa A. Shaping Strategy: The Civil-Military Politics of Strategic Assessment

  11. Progress Report 1 January 1983 - 31 December 1984. Computer Installation

    DEFF Research Database (Denmark)

    Risø National Laboratory, Roskilde

    This report describes selected parts of the activities at the Computer Installation of Risa National Laboratory in 1983 and 1984. Information given may be preliminary.......This report describes selected parts of the activities at the Computer Installation of Risa National Laboratory in 1983 and 1984. Information given may be preliminary....

  12. Efficacy of Economic Sanctions: North Korea and Iran Case Study

    Science.gov (United States)

    2011-03-08

    by one or more international actors against another, ostensibly with a view to influencing that entity‟s foreign and/or security behavior.”2 Risa ...2 Brendan Taylor, Sanctions as Grand Strategy (London: The International Institute for Strategic Studies, 2010), 12. 3 Risa A. Brooks, “Sanctions

  13. PyroTRF-ID: a novel bioinformatics methodology for the affiliation of terminal-restriction fragments using 16S rRNA gene pyrosequencing data

    Directory of Open Access Journals (Sweden)

    Weissbrodt David G

    2012-12-01

    Full Text Available Abstract Background In molecular microbial ecology, massive sequencing is gradually replacing classical fingerprinting techniques such as terminal-restriction fragment length polymorphism (T-RFLP combined with cloning-sequencing for the characterization of microbiomes. Here, a bioinformatics methodology for pyrosequencing-based T-RF identification (PyroTRF-ID was developed to combine pyrosequencing and T-RFLP approaches for the description of microbial communities. The strength of this methodology relies on the identification of T-RFs by comparison of experimental and digital T-RFLP profiles obtained from the same samples. DNA extracts were subjected to amplification of the 16S rRNA gene pool, T-RFLP with the HaeIII restriction enzyme, 454 tag encoded FLX amplicon pyrosequencing, and PyroTRF-ID analysis. Digital T-RFLP profiles were generated from the denoised full pyrosequencing datasets, and the sequences contributing to each digital T-RF were classified to taxonomic bins using the Greengenes reference database. The method was tested both on bacterial communities found in chloroethene-contaminated groundwater samples and in aerobic granular sludge biofilms originating from wastewater treatment systems. Results PyroTRF-ID was efficient for high-throughput mapping and digital T-RFLP profiling of pyrosequencing datasets. After denoising, a dataset comprising ca. 10′000 reads of 300 to 500 bp was typically processed within ca. 20 minutes on a high-performance computing cluster, running on a Linux-related CentOS 5.5 operating system, enabling parallel processing of multiple samples. Both digital and experimental T-RFLP profiles were aligned with maximum cross-correlation coefficients of 0.71 and 0.92 for high- and low-complexity environments, respectively. On average, 63±18% of all experimental T-RFs (30 to 93 peaks per sample were affiliated to phylotypes. Conclusions PyroTRF-ID profits from complementary advantages of pyrosequencing and T-RFLP

  14. Investigating of yeast species in wine fermentation using terminal restriction fragment length polymorphism method.

    Science.gov (United States)

    Sun, Yue; Liu, Yanlin

    2014-04-01

    The objective of this study was to examine the potential of terminal restriction fragment length polymorphism (T-RFLP) in monitoring yeast communities during wine fermentation and to reveal new information on yeast community of Chinese enology. Firstly, terminal restriction fragment (TRF) lengths database was constructed using 32 pure yeast species. Ten of these species were firstly documented. The species except for Candida vini, Issatchenkia orientalis/Candida krusei, Saccharomyces bayanus, Saccharomyces pastorianus, Saccharomyces cerevisiae, Saccharomyces kudriarzevii and Zygosaccharomyces bisporus could be distinguished by the T-RFLP targeting 5.8S-ITS rDNA. Moreover, the yeast communities in spontaneous fermentation of Chardonnay and Riesling were identified by T-RFLP and traditional methods, including colony morphology on Wallerstein Nutrient (WLN) medium and 5.8S-ITS-RFLP analysis. The result showed that T-RFLP profiles of the yeast community correlated well with that of the results identified by the traditional methods. The TRFs with the highest intensity and present in all the samples corresponded to Saccharomyces sp. Other species detected by both approaches were Hanseniaspora uvarum, Metschnikowia pulcherrima, Pichia minuta var. minuta, Saccharomycodes ludwigii/Torulaspora delbrueckii and Candida zemplinina. This study revealed that T-RFLP technique is a rapid and useful tool for monitoring the composition of yeast species during wine fermentation. Copyright © 2013 Elsevier Ltd. All rights reserved.

  15. Uterine bacterial flora in postpartum Danish Holstein dairy cows determined using DNA-based fingerprinting: Correlation to uterine condition and calving management

    DEFF Research Database (Denmark)

    Elkjær, K.; Ancker, M.-L.; Gustafsson, H.

    2013-01-01

    The overall aim of this study was to describe uterine bacterial flora during the postpartum period in Danish Holstein cows using the Terminal Restriction Fragment Length Polymorphism (T-RFLP) method. This method produces a pattern of nucleic acid fragments from the microorganisms present, reflect......The overall aim of this study was to describe uterine bacterial flora during the postpartum period in Danish Holstein cows using the Terminal Restriction Fragment Length Polymorphism (T-RFLP) method. This method produces a pattern of nucleic acid fragments from the microorganisms present...... included, and for each cow calving management was recorded. Cows were clinically examined on average 8 (range 0–19) and 28 (range 22–38) days after calving, and a uterine sample was taken for bacterial identification using T-RFLP. Milk samples were taken weekly for progesterone analysis. Bacteria were...

  16. Application of fluorescent amplified fragment length polymorphism for comparison of human and animal isolates of Yersinia enterocolitica

    DEFF Research Database (Denmark)

    Fearnley, C.; On, S.L.W.; Kokotovic, Branko

    2005-01-01

    An amplified fragment length polymorphism (AFLP) method, developed to genotype Yersinia enterocolitica, has been used to investigate 70 representative strains isolated from humans, pigs, sheep, and cattle in the United Kingdom. AFLP primarily distinguished Y enterocolitica strains according to th...

  17. Genetic and epigenetic differences associated with environmental gradients in replicate populations of two salt marsh perennials

    NARCIS (Netherlands)

    Foust, C.M.; Preite, V.; Schrey, Aaron W.; Alvarez, M.; Robertson, M.H.; Verhoeven, K.J.F.; Richards, C.L.

    2016-01-01

    While traits and trait plasticity are partly genetically based, investigating epigenetic mechanisms may provide more nuanced understanding of the mechanisms underlying response to environment. Using AFLP and methylation-sensitive AFLP, we tested the hypothesis that differentiation to habitats along

  18. Quantitative comparison of retrosigmoid intradural suprameatal approach and retrosigmoid transtentorial approach: implications for tumors in the petroclival region.

    Science.gov (United States)

    Ambekar, Sudheer; Amene, Chiazo; Sonig, Ashish; Guthikonda, Bharat; Nanda, Anil

    2013-10-01

    Background Retrosigmoid transtentorial (RTT) and retrosigmoid intradural suprameatal (RISA) approaches have been used in the treatment of petroclival tumors. Objective To compare the area of exposure of brainstem and petroclival region obtained through RTT and RISA in cadaveric specimens. Methods Five cadaveric specimens with a total of 10 sides were analyzed. RTT and RISA were performed on five sides each. Brainstem and petroclival surface exposure were measured using both the approaches. These values were compared between the two approaches. Results Brainstem area exposure with RTT was 441 ± 63 mm(2) and that with RISA was 311 ± 61 mm(2). Student's t-test revealed that the difference was significant (p = 0.01). The area of petroclival exposure medial to the Meckel cave through RTT was 696 ± 57 mm(2), and that through RISA was 716 ± 51 mm(2) (p = 0.69). The area of brainstem exposure between V and VII-VII complex through RTT and RISA was 387 ± 86 mm(2) and 378 ± 76 mm(2) (p = 0.87). Conclusion The RTT approach is an excellent approach to ventrolateral brainstem and petroclival region. It provides greater superoventral exposure of the ventrolateral brainstem than RISA and provides similar petroclival exposure.

  19. Assessment of genetic relationships among Spring Dendrobium ...

    African Journals Online (AJOL)

    ajl2

    2012-10-11

    Oct 11, 2012 ... RESULTS. Amplified fragment length polymorphism (AFLP) profiles and analysis. Clear-cut AFLP profiles for 30 Spring Dendrobium culti- vars or varietal materials were generated by the eight primer sets. An example of fluorescent-AFLP profiles for the 30 samples using primer E-AAG/M-CAG is shown in ...

  20. A comparative genetic diversity analysis in mungbean ( Vigna ...

    African Journals Online (AJOL)

    Amplified fragment length polymorphism (AFLP) and inter-simple sequence repeat (ISSR) markers were used to study the DNA polymorphism in elite mungbean genotypes. A total of nine AFLP primer combination and 22 ISSR primers were used. Amplification of genomic DNA of the 30 genotypes, using AFLP analysis, ...

  1. Analytic studies of the hard dumbell fluid

    Science.gov (United States)

    Morriss, G. P.; Cummings, P. T.

    A closed form analytic theory for the structure of the hard dumbell fluid is introduced and evaluated. It is found to be comparable in accuracy to the reference interaction site approximation (RISA) of Chandler and Andersen.

  2. Effect of past agricultural use on the infectivity and composition of a community of arbuscular mycorrhizal fungi

    Czech Academy of Sciences Publication Activity Database

    Voříšková, Alena; Janoušková, Martina; Slavíková, R.; Pánková, Hana; Daniel, Ondřej; Vazačová, Kristýna; Rydlová, Jana; Vosátka, Miroslav; Münzbergová, Zuzana

    2016-01-01

    Roč. 221, APR 01 (2016), s. 28-39 ISSN 0167-8809 R&D Projects: GA ČR GAP504/10/1486 Institutional support: RVO:67985939 Keywords : terminal restriction fragment length polymorfism (T-RFLP) * arbuscular mycorrhizal fungi (AMF) * secondary succession Subject RIV: EF - Botanics Impact factor: 4.099, year: 2016

  3. Bacterial Diversity across Individual Lichens▿ †

    Science.gov (United States)

    Mushegian, Alexandra A.; Peterson, Celeste N.; Baker, Christopher C. M.; Pringle, Anne

    2011-01-01

    Symbioses are unique habitats for bacteria. We surveyed the spatial diversity of bacterial communities across multiple individuals of closely related lichens using terminal restriction fragment length polymorphism (T-RFLP) and pyrosequencing. Centers of lichens house richer, more consistent assemblages than species-poor and compositionally disparate lichen edges, suggesting that ecological succession plays a role in structuring these communities. PMID:21531831

  4. Silver relase from decomposed hyperaccumulating Amanita solitaria fruit-body biomass strongly affects soil microbial community

    Czech Academy of Sciences Publication Activity Database

    Gryndler, M.; Hršelová, H.; Soukupová, L.; Borovička, Jan

    2012-01-01

    Roč. 25, č. 5 (2012), s. 987-993 ISSN 0966-0844 Institutional support: RVO:67985831 Keywords : soil fungi * bacteria * microbiota * heavy metals * toxicity * T-RFLP Subject RIV: DD - Geochemistry Impact factor: 3.284, year: 2012

  5. Bacterial diversity and abundance of a creek valley sites reflected soil pH and season

    Czech Academy of Sciences Publication Activity Database

    Ságová-Marečková, M.; Čermák, L.; Omelka, M.; Kyselková, Martina; Kopecký, J.

    2015-01-01

    Roč. 10, č. 1 (2015), s. 61-70 ISSN 2391-5412 Grant - others:GA AV ČR(CZ) IAA603020901 Program:IA Institutional support: RVO:60077344 Keywords : bacterial communities * actinobacteria * OM quantity and quality * T-RFLP Subject RIV: EE - Microbiology, Virology

  6. Comparison of Bacteroides-Prevotella 16S rRNA genetic markers for fecal samples from different animal species

    Science.gov (United States)

    Fogarty, L.R.; Voytek, M.A.

    2005-01-01

    To effectively manage surface and ground waters it is necessary to improve our ability to detect and identify sources of fecal contamination. We evaluated the use of the anaerobic bacterial group Bacteroides-Prevotella as a potential fecal indicator. Terminal restriction length polymorphism (T-RFLP) of the 16S rRNA genes from this group was used to determine differences in populations and to identify any unique populations in chickens, cows, deer, dogs, geese, horses, humans, pigs, and seagulls. The group appears to be a good potential fecal indicator in all groups tested except for avians. Cluster analysis of Bacteroides-Prevotella community T-RFLP profiles indicates that Bacteroides-Prevotella populations from samples of the same host species are much more similar to each other than to samples from different source species. We were unable to identify unique peaks that were exclusive to any source species; however, for most host species, at least one T-RFLP peak was identified to be more commonly found in that species, and a combination of peaks could be used to identify the source. T-RFLP profiles obtained from water spiked with known-source feces contained the expected diagnostic peaks from the source. These results indicate that the approach of identifying Bacteroides-Prevotella molecular markers associated with host species might be useful in identifying sources of fecal contamination in the environment.

  7. Investigation of the fate and effects of acetyl cedrene on Capitella teleta and sediment bacterial community

    DEFF Research Database (Denmark)

    Ellegaard-Jensen, Lea; Selck, Henriette; Priemé, Anders

    2010-01-01

    /without Capitella teleta (formerly Capitella sp. I)). Furthermore effects of AC on microbial respiration in the system were determined by examining CO(2) flux. T-RFLP (terminal restriction fragment length polymorphism) was used to analyze PCR (polymerase chain reaction) amplified 16S DNA gene fragments from...

  8. Methanogenic community changes, and emissions of methane and other gases, during storage of acidified and untreated pig slurry

    DEFF Research Database (Denmark)

    Petersen, Søren O; Højberg, Ole; Poulsen, Morten

    2014-01-01

    H was nearly constant at values of 5.5 and 6.5. Ammonia losses were reduced by 84 and 49%, respectively, while CH4 emission with both acidification techniques was reduced by >90%. T-RFLP fingerprints showed little effect of acidification or storage time. A major T-RF of 105 bp could represent methanogens...

  9. Increased amount of Bifidobacterium thermacidophilum and Megasphaera elsdenii in the colonic microbiota of pigs fed a swine dysentery preventive diet containing chicory roots and sweet lupine

    DEFF Research Database (Denmark)

    Mølbak, Lars; Thomsen, L.E.; Jensen, Tim Kåre

    2007-01-01

    has previously been shown to prevent swine dysentery caused by Brachyspira hyodysenteriae. The T-RFLP profiling, 16S rRNA gene cloning and in situ hybridization showed that the pigs fed with the fructan-rich diet had a higher proportion of Bifidobacterium thermacidophilum subsp. porcinum...

  10. Terminal restriction fragment length measurement errors are affected mainly by fragment length, G+C nucleotide content and secondary structure melting point

    Czech Academy of Sciences Publication Activity Database

    Bukovská, Petra; Jelínková, Markéta; Hršelová, Hana; Sýkorová, Zuzana; Gryndler, Milan

    2010-01-01

    Roč. 82, č. 3 (2010), s. 223-228 ISSN 0167-7012 R&D Projects: GA MŠk 1M0571 Institutional research plan: CEZ:AV0Z60050516; CEZ:AV0Z50200510 Keywords : T-RFLP * drift * DNA fragment Subject RIV: EF - Botanics Impact factor: 2.018, year: 2010

  11. Fantasías de nubes al viento: primera ronda

    Directory of Open Access Journals (Sweden)

    León de Greiff

    1969-10-01

    Full Text Available Oiga entonces, óye, oíd palabras sin sentido conocido: Las otras son tan huecas si sonoras (dice mi risa como tambor de feria (añejo símil de Perogrullo "profundas", "salomónicas" (torna a decir Mi Risa o Mi Sonrisa. -Tan profundas que no se toca fondo- (símil vetusto asaz, no nada gris, mas sí del buen Monsieur de la Palice...

  12. Endoscope-assisted retrosigmoid intradural suprameatal approach for surgical treatment of trigeminal schwannomas.

    Science.gov (United States)

    Samii, Madjid; Alimohamadi, Maysam; Gerganov, Venelin

    2014-12-01

    Trigeminal schwannomas are the most common intracranial nonvestibular schwannomas, and the dumbbell-shaped subtype is the most challenging. To evaluate the efficiency and safety of the endoscope-assisted retrosigmoid intradural suprameatal approach (EA-RISA) for dumbbell trigeminal schwannomas and to compare EA-RISA with classic RISA. A retrospective study of all patients with trigeminal schwannomas was performed with a focus on dumbbell tumors. Tumors were classified according to a modified Samii classification. Extent of tumor removal, outcome, and morbidity rates in the 2 subgroups were compared. Twenty patients were enrolled: 8 had dumbbell-shaped tumors (type C1), 8 had middle fossa tumors (A1-3), 3 had extracranial extension (D2), and 1 had posterior fossa tumor. Gross total resection was achieved in 15 and near-total resection in 5 patients. In 4 patients with dumbbell tumors, the classic RISA (Samii approach) was used; EA-RISA was used in the other 4 patients. The extent of petrous apex drilling was determined individually on the basis of the anatomic variability of suprameatal tubercle and degree of tumor-induced petrous apex erosion; in 2 patients, only minimal drilling was needed. The endoscope was applied after microsurgical tumor removal and in 3 of 4 patients revealed a significant unrecognized tumor remnant in the anterolateral and superolateral aspects of the Meckel cave. Thus, the EA-RISA technique allowed gross total resection of the tumor. The EA-RISA enlarges the exposure obtained with the classic RISA. Its judicious use can help achieve safe and radical removal of dumbbell-shaped trigeminal schwannomas (C1 type).

  13. XMM-Newton Science Analysis Software: How to Bring New Technologies to Long-life Satellite Missions

    Science.gov (United States)

    Ibarra, A.; Calle, I.; Gabriel, C.; Salgado, J.; Osuna, P.

    2009-09-01

    We present here the beta version of the Remote Interface to SAS Analysis (RISA), a web service-based system that allows users the analysis of XMM-Newton data making use of all of the existing SAS functionalities. RISA takes advantage of GRID architecture to run SAS, achieving high performance in resource management. We are also making the SAS remote analysis compatible with present and future VO standards.

  14. Increased pulmonary vascular permeability as a cause of re-expansion edema in rabbits

    International Nuclear Information System (INIS)

    Pavlin, D.J.; Nessly, M.L.; Cheney, F.W.

    1981-01-01

    In order to study the mechanism(s) underlying re-expansion edema, we measured the concentration of labeled albumin (RISA) in the extravascular, extracellular water (EVECW) of the lung as a measure of pulmonary vascular permeability. Re-expansion edema was first induced by rapid re-expansion of rabbit lungs that had been collapsed for 1 wk by pneumothorax. The RISA in EVECW was expressed as a fraction of its plasma concentration: (RISA)L/(RISA)PL. The volume of EVECW (ml/gm dry lung) was measured using a 24 Na indicator. Results in re-expansion edema were compared with normal control lungs and with oleic acid edema as a model of permeability edema. In re-expanded lungs, EVECW (3.41 +/- SD 1.24 ml/g) and (RISA)L/(RISA)PL 0.84 +/- SD 0.15) were significantly increased when compared with normal control lungs (2.25 +/- 0.41 ml/g and 0.51 +/- 0.20, respectively). Results in oleic acid edema (5.66 +/- 2.23 ml/g and 0.84 +/- 0.23) were similar to re-expansion edema. This suggested that re-expansion edema is due to increased pulmonary vascular permeability caused by mechanical stresses applied to the lung during re-expansion

  15. Molecular research on the genetic diversity of Tunisian date palm ...

    African Journals Online (AJOL)

    Molecular research on the genetic diversity of Tunisian date palm ( Phoenix dactylifera L.) using the random amplified microsatellite polymorphism (RAMPO) and amplified fragment length polymorphism (AFLP) methods.

  16. Amplified restriction fragment length polymorphism in parasite genetics.

    Science.gov (United States)

    Masiga, D K; Tait, A; Turner, C M

    2000-08-01

    The amplified restriction fragment length polymorphism (AFLP) technique is a relatively new method for the analysis of polymorphism that has not yet been widely used in parasitology. In this article, Dan Masiga, Andy Tait and Mike Turner provide a brief introduction to AFLP and illustrate how it can be used in the investigation of marker inheritance in genetic crosses and in the analysis of polymorphism of field populations. They also briefly highlight the strengths and weaknesses of AFLP in comparison with other methods for detecting polymorphism and conclude that AFLP is a very useful addition to the range of techniques available.

  17. Designation of the European Working Group on Legionella Infection (EWGLI) amplified fragment length polymorphism types of Legionella pneumophila serogroup 1 and results of intercentre proficiency testing Using a standard protocol

    DEFF Research Database (Denmark)

    Fry, N K; Bangsborg, Jette Marie; Bergmans, A

    2002-01-01

    Infections (EWGLI) AFLP types, (ii). describes the EWGLI AFLP types identified for the 130 strains in the EWGLI culture collection, and (iii). reports the results of a newly introduced international programme of proficiency testing. Following preliminary analysis of 20 epidemiologically unrelated isolates...... (recorded as AFLP type 001-016 or untypeable) was determined by participants with reference to these 16 AFLP types, either visually or using gel analysis software where available, and reported to the coordinating centre. Nine of the 12 strains, including an epidemiologically related pair and two pairs...

  18. A Comparison between the Kawase and Extended Retrosigmoid Approaches (Retrosigmoid Transtentorial and Retrosigmoid Intradural Suprameatal Approaches) for Accessing the Petroclival Tumors. A Cadaveric Study.

    Science.gov (United States)

    Sharma, Mayur; Ambekar, Sudheer; Guthikonda, Bharat; Nanda, Anil

    2014-06-01

    Background The aim of our study was to compare the area of exposure at the ventral brainstem and petroclival region offered by the Kawase, retrosigmoid transtentorial (RTT), and the retrosigmoid intradural suprameatal (RISA) approaches in cadaveric models. Methods We performed 15 approaches (five each of the Kawase, RISA, and RTT approaches) on silicone-injected adult cadaver heads. Ventral brainstem and petroclival areas of exposure were measured and compared. Results The mean ventral brainstem area exposed by the Kawase approach was 55.00 ± 24.1 mm(2), significantly less than that exposed by RTT (441 ± 63.3 mm(2)) and RISA (311 ± 61 mm(2)) (p RISA (p = 0.01). The mean petroclival area of exposure through the Kawase approach was significantly smaller than that obtained through the RTT and RISA approaches (101.7 ± 545.01 mm(2), 696 ± 57.7 mm(2), and 716.7 ± 51.4 mm(2), respectively). Conclusion Retrosigmoid approaches provide a greater exposure of the brainstem and petroclival areas. The Kawase approach is ideally suited for lesions around the Meckel cave with an extension into the middle fossa. These approaches can be used in conjunction with one another to access petroclival tumors.

  19. Strong incidence of Pseudomonas aeruginosa on bacterial rrs and ITS genetic structures of cystic fibrosis sputa.

    Directory of Open Access Journals (Sweden)

    Laurence Pages-Monteiro

    Full Text Available Cystic fibrosis (CF lungs harbor a complex community of interacting microbes, including pathogens like Pseudomonas aeruginosa. Meta-taxogenomic analysis based on V5-V6 rrs PCR products of 52 P. aeruginosa-positive (Pp and 52 P. aeruginosa-negative (Pn pooled DNA extracts from CF sputa suggested positive associations between P. aeruginosa and Stenotrophomonas and Prevotella, but negative ones with Haemophilus, Neisseria and Burkholderia. Internal Transcribed Spacer analyses (RISA from individual DNA extracts identified three significant genetic structures within the CF cohorts, and indicated an impact of P. aeruginosa. RISA clusters Ip and IIIp contained CF sputa with a P. aeruginosa prevalence above 93%, and of 24.2% in cluster IIp. Clusters Ip and IIIp showed lower RISA genetic diversity and richness than IIp. Highly similar cluster IIp RISA profiles were obtained from two patients harboring isolates of a same P. aeruginosa clone, suggesting convergent evolution in the structure of their microbiota. CF patients of cluster IIp had received significantly less antibiotics than patients of clusters Ip and IIIp but harbored the most resistant P. aeruginosa strains. Patients of cluster IIIp were older than those of Ip. The effects of P. aeruginosa on the RISA structures could not be fully dissociated from the above two confounding factors but several trends in these datasets support the conclusion of a strong incidence of P. aeruginosa on the genetic structure of CF lung microbiota.

  20. Rapid Detection of Emerging Pathogens and Loss of Microbial Diversity Associated with Severe Lung Disease in Cystic Fibrosis.

    Science.gov (United States)

    Flight, William G; Smith, Ann; Paisey, Christopher; Marchesi, Julian R; Bull, Matthew J; Norville, Phillip J; Mutton, Ken J; Webb, A Kevin; Bright-Thomas, Rowland J; Jones, Andrew M; Mahenthiralingam, Eshwar

    2015-07-01

    Respiratory infection in cystic fibrosis (CF) is polymicrobial, but standard sputum microbiology does not account for the lung microbiome or detect changes in microbial diversity associated with disease. As a clinically applicable CF microbiome surveillance scheme, total sputum nucleic acids isolated by a standard high-throughput robotic method for accredited viral diagnosis were profiled for bacterial diversity using ribosomal intergenic spacer analysis (RISA) PCR. Conventional culture and RISA were performed on 200 paired sputum samples from 93 CF adults; pyrosequencing of the 16S rRNA gene was applied to 59 patients to systematically determine bacterial diversity. Compared to the microbiology data, RISA profiles clustered into two groups: the emerging nonfermenting Gram-negative organisms (eNFGN) and Pseudomonas groups. Patients who were culture positive for Burkholderia, Achromobacter, Stenotrophomonas, and Ralstonia clustered within the eNFGN group. Pseudomonas group RISA profiles were associated with Pseudomonas aeruginosa culture-positive patients. Sequence analysis confirmed the abundance of eNFGN genera and Pseudomonas within these respective groups. Low bacterial diversity was associated with severe lung disease (P RISA PCR rapidly detecting the presence of dominant eNFGN pathogens or P. aeruginosa missed by culture (11% of cases). We provide guidance for how this straightforward CF microbiota profiling scheme may be adopted by clinical laboratories. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  1. Vadose zone microbial community structure and activity in metal/radionuclide contaminated sediments. Final technical report

    Energy Technology Data Exchange (ETDEWEB)

    Balkwill, David L.

    2002-08-17

    This final technical report describes the research carried out during the final two months of the no-cost extension ending 11/14/01. The primary goals of the project were (1) to determine the potential for transformation of Cr(VI) (oxidized, mobile) to Cr(III) (reduced, immobile) under unsaturated conditions as a function of different levels and combinations of (a) chromium, (b) nitrate (co-disposed with Cr), and (c) molasses (inexpensive bioremediation substrate), and (2) to determine population structure and activity in experimental treatments by characterization of the microbial community by signature biomarker analysis and by RT-PCR and terminal restriction fragment length polymorphism (T-RFLP) and 16S ribosomal RNA genes. It was determined early in the one-year no-cost extension period that the T-RFLP approach was problematic in regard to providing information on the identities of microorganisms in the samples examined. As a result, it could not provide the detailed information on microbial community structure that was needed to assess the effects of treatments with chromium, nitrate, and/or molasses. Therefore, we decided to obtain the desired information by amplifying (using TR-PCR, with the same primers used for T-RFLP) and cloning 16S rRNA gene sequences from the same RNA extracts that were used for T-RFLP analysis. We also decided to use a restriction enzyme digest procedure (fingerprinting procedure) to place the clones into types. The primary focus of the research carried out during this report period was twofold: (a) to complete the sequencing of the clones, and (b) to analyze the clone sequences phylogenetically in order to determine the relatedness of the bacteria detected in the samples to each other and to previously described genera and species.

  2. Silver release from decomposed hyperaccumulating Amanita solitaria fruit-body biomass strongly affects soil microbial community

    Czech Academy of Sciences Publication Activity Database

    Gryndler, Milan; Hršelová, Hana; Soukupová, Lucie; Borovička, Jan

    2012-01-01

    Roč. 25, č. 5 (2012), s. 987-993 ISSN 0966-0844 R&D Projects: GA ČR(CZ) GAP504/11/0484 Institutional support: RVO:61389005 ; RVO:61388971 ; RVO:67985831 Keywords : soil fungi * bacteria * microbiota * heavy metals * toxicity * T-RFLP Subject RIV: BG - Nuclear, Atomic and Molecular Physics, Colliders; EE - Microbiology, Virology (MBU-M); DD - Geochemistry (GLU-S) Impact factor: 3.284, year: 2012

  3. Temporal assessment of microbial communities in soils of two contrasting mangroves

    OpenAIRE

    Rigonato, Janaina; Kent, Angela D.; Gumiere, Thiago; Branco, Luiz Henrique Zanini; Andreote, Fernando Dini; Fiore, Marli Fátima

    2018-01-01

    ABSTRACT Variations in microbial communities promoted by alterations in environmental conditions are reflected in similarities/differences both at taxonomic and functional levels. Here we used a natural gradient within mangroves from seashore to upland, to contrast the natural variability in bacteria, cyanobacteria and diazotroph assemblages in a pristine area compared to an oil polluted area along a timespan of three years, based on ARISA (bacteria and cyanobacteria) and nifH T-RFLP (diazotr...

  4. Changes in bacterial community structure in the colon of pigs fed different experimental diets and after infection with Brachyspira hyodysenteriae

    DEFF Research Database (Denmark)

    Leser, Thomas D.; Lindecrona, Rikke Hvid; Jensen, Tim Kåre

    2000-01-01

    Bacterial communities in the large intestines of pigs were compared using terminal restriction fragment length polymorphism (T-RFLP) analysis targeting the 16S ribosomal DNA. The pigs were fed different experimental diets based on either modified standard feed or cooked rice supplemented with die...... between two independent but identical experiments. When the animals were experimentally infected with Brachyspira hyodysenteriae, causing swine dysentery, many of the T-RFs fluctuated, suggesting a destabilization of the microbial community....

  5. XMM-Newton Remote Interface to Science Analysis Software: First Public Version

    Science.gov (United States)

    Ibarra, A.; Gabriel, C.

    2011-07-01

    We present the first public beta release of the XMM-Newton Remote Interface to Science Analysis (RISA) software, available through the official XMM-Newton web pages. In a nutshell, RISA is a web based application that encapsulates the XMM-Newton data analysis software. The client identifies observations and creates XMM-Newton workflows. The server processes the client request, creates job templates and sends the jobs to a computer. RISA has been designed to help, at the same time, non-expert and professional XMM-Newton users. Thanks to the predefined threads, non-expert users can easily produce light curves and spectra. And on the other hand, expert user can use the full parameter interface to tune their own analysis. In both cases, the VO compliant client/server design frees the users from having to install any specific software to analyze XMM-Newton data.

  6. Ammonia oxidizing bacteria community dynamics in a pilot-scale wastewater treatment plant.

    Directory of Open Access Journals (Sweden)

    Xiaohui Wang

    Full Text Available BACKGROUND: Chemoautotrophic ammonia oxidizing bacteria (AOB have the metabolic ability to oxidize ammonia to nitrite aerobically. This metabolic feature has been widely used, in combination with denitrification, to remove nitrogen from wastewater in wastewater treatment plants (WWTPs. However, the relative influence of specific deterministic environmental factors to AOB community dynamics in WWTP is uncertain. The ecological principles underlying AOB community dynamics and nitrification stability and how they are related are also poorly understood. METHODOLOGY/PRINCIPAL FINDINGS: The community dynamics of ammonia oxidizing bacteria (AOB in a pilot-scale WWTP were monitored over a one-year period by Terminal Restriction Fragment Length Polymorphism (T-RFLP. During the study period, the effluent ammonia concentrations were almost below 2 mg/L, except for the first 60 days, indicting stable nitrification. T-RFLP results showed that, during the test period with stable nitrification, the AOB community structures were not stable, and the average change rate (every 15 days of AOB community structures was 10% ± 8%. The correlations between T-RFLP profiles and 10 operational and environmental parameters were tested by Canonical Correlation Analysis (CCA and Mantel test. The results indicated that the dynamics of AOB community correlated most strongly with Dissolved Oxygen (DO, effluent ammonia, effluent Biochemical Oxygen Demand (BOD and temperature. CONCLUSIONS/SIGNIFICANCE: This study suggests that nitrification stability is not necessarily accompanied by a stable AOB community, and provides insight into parameters controlling the AOB community dynamics within bioreactors with stable nitrification.

  7. Application of a new PCR primer for terminal restriction fragment length polymorphism analysis of the bacterial communities in plant roots.

    Science.gov (United States)

    Sakai, Masao; Matsuka, Akira; Komura, Taichi; Kanazawa, Shinjiro

    2004-10-01

    Contamination with plastid small subunit (SSU) rDNA is a major drawback when analyzing the bacterial communities of plant roots using culture-independent methods. In this study, a polymerase chain reaction (PCR) primer, 783r, was designed and tested to specifically amplify the SSU rDNA of various bacterial species without amplifying the SSU rDNA of plant plastids. To confirm how useful the community analysis of rhizobacteria is using 783r, the terminal restriction fragment length polymorphism (T-RFLP) method was performed with wheat (Triticum aestivum) and spinach (Spinacea oleracea) root samples. Using the standard T-RFLP method, a large T-RF peak of plant plastid SSU rDNA interfered with the bacterial community analysis. In contrast, the T-RFLP method using the 783r primer was able to detect the bacterial DNA while directly eliminating the influence of the plant-derived DNA extracted from the plant roots. Primer 783r might, therefore, be a useful PCR primer for the culture-independent analysis of bacterial communities in plant roots using SSU rDNA.

  8. Molecular Analysis of Bacterial Communities in Biofilms of a Drinking Water Clearwell

    Science.gov (United States)

    Zhang, Minglu; Liu, Wenjun; Nie, Xuebiao; Li, Cuiping; Gu, Junnong; Zhang, Can

    2012-01-01

    Microbial community structures in biofilms of a clearwell in a drinking water supply system in Beijing, China were examined by clone library, terminal restriction fragment length polymorphism (T-RFLP) and 454 pyrosequencing of the amplified 16S rRNA gene. Six biofilm samples (designated R1–R6) collected from six locations (upper and lower sites of the inlet, middle and outlet) of the clearwell revealed similar bacterial patterns by T-RFLP analysis. With respect to the dominant groups, the phylotypes detected by clone library and T-RFLP generally matched each other. A total of 9,543 reads were obtained from samples located at the lower inlet and the lower outlet sites by pyrosequencing. The bacterial diversity of the two samples was compared at phylum and genus levels. Alphaproteobacteria dominated the communities in both samples and the genus of Sphingomonas constituted 75.1%–99.6% of this phylum. A high level of Sphingomonas sp. was first observed in the drinking water biofilms with 0.6–1.0 mg L−1 of chlorine residual. Disinfectant-resistant microorganisms deserve special attention in drinking water management. This study provides novel insights into the microbial populations in drinking water systems and highlights the important role of Sphingomonas species in biofilm formation. PMID:23059725

  9. Chitinase genes revealed and compared in bacterial isolates, DNA extracts and a metagenomic library from a phytopathogen suppressive soil

    Energy Technology Data Exchange (ETDEWEB)

    Hjort, K.; Bergstrom, M.; Adesina, M.F.; Jansson, J.K.; Smalla, K.; Sjoling, S.

    2009-09-01

    Soil that is suppressive to disease caused by fungal pathogens is an interesting source to target for novel chitinases that might be contributing towards disease suppression. In this study we screened for chitinase genes, in a phytopathogen-suppressive soil in three ways: (1) from a metagenomic library constructed from microbial cells extracted from soil, (2) from directly extracted DNA and (3) from bacterial isolates with antifungal and chitinase activities. Terminal-restriction fragment length polymorphism (T-RFLP) of chitinase genes revealed differences in amplified chitinase genes from the metagenomic library and the directly extracted DNA, but approximately 40% of the identified chitinase terminal-restriction fragments (TRFs) were found in both sources. All of the chitinase TRFs from the isolates were matched to TRFs in the directly extracted DNA and the metagenomic library. The most abundant chitinase TRF in the soil DNA and the metagenomic library corresponded to the TRF{sup 103} of the isolate, Streptomyces mutomycini and/or Streptomyces clavifer. There were good matches between T-RFLP profiles of chitinase gene fragments obtained from different sources of DNA. However, there were also differences in both the chitinase and the 16S rRNA gene T-RFLP patterns depending on the source of DNA, emphasizing the lack of complete coverage of the gene diversity by any of the approaches used.

  10. Bidirectional peritoneal transport of albumin in continuous ambulatory peritoneal dialysis

    DEFF Research Database (Denmark)

    Joffe, P; Henriksen, Jens Henrik Sahl

    1995-01-01

    The present study was undertaken in order to assess bidirectional peritoneal kinetics of albumin after simultaneous i.v. and i.p. injection of radioiodinated albumin tracers (125I-RISA and 131I-RISA) in eight clinically stable uraemic patients undergoing continuous ambulatory peritoneal dialysis...... mass at the end of the dialysis (54 +/- 19 mumol, P peritoneal...... (CAPD). The plasma volume, intravascular albumin mass (IVM), and overall extravasation rate of albumin were not significantly different from that found in healthy controls. Albumin flux from the plasma into the peritoneal cavity was 3.71 +/- 0.82 (SD) mumol/h, which was only 3% of the overall...

  11. Analysis of genetic diversity in accessions of Irvingia gabonensis ...

    African Journals Online (AJOL)

    Amplified fragment length polymorphism (AFLP) was used to assess genetic diversity and relationships among 15 accessions of Irvingia gabonensis collected from Cameroun, Gabon, and Nigeria. Twelve AFLP+3 primers produced 384 polymorphic fragments. Average genetic distance (AGD) between the 15 accessions ...

  12. Genetic and phylogenetic analysis of ten Gobiidae species in China ...

    African Journals Online (AJOL)

    Administrator

    2011-09-07

    Sep 7, 2011 ... The results agreed with the traditional taxonomy of the morphological characters. AFLP fingerprints were ... It allows fast and efficient generation of a large amount of genetic data. Until now, AFLP ..... Hamamatsu C, Sugiyama K, Ikeda Y, Sakamoto K, Fumihito A, Ohno. Han et al. 10535. S, Gojobori T (2000).

  13. Use of genetic markers in Alstroemeria

    NARCIS (Netherlands)

    Han, T.H.

    2001-01-01

    This thesis describes the results of various applications of the AFLP technique in Alstroemeria . The aim of this study was 1) to adapt the AFLP technique for Alstroemeria species which has a large genome size, 2) to

  14. Analysis of DNA methylation variation in sibling tobacco ( Nicotiana ...

    African Journals Online (AJOL)

    Amplified fragment length polymorphism (AFLP) and methylation-sensitive amplification polymorphism (MSAP) analysis were used to investigate the genome of two sibling tobacco cultivars, Yunyan85 and Yunyan87, their parent K326 and the other tobacco cultivar NC89. AFLP analysis indicated that, the genome primary ...

  15. Genetic diversity of Actinobacillus lignieresii isolates from different hosts

    DEFF Research Database (Denmark)

    Kokotovic, Branko; Angen, Øystein; Bisgaard, Magne

    2011-01-01

    Genetic diversity detected by analysis of amplified fragment length polymorphisms (AFLPs) of 54 Actinobacilus lignieresii isolates from different hosts and geographic localities is described. On the basis of variances in AFLP profiles, the strains were grouped in two major clusters; one comprisin...

  16. Population structure of Salmonella investigated by amplified fragment length polymorphism

    DEFF Research Database (Denmark)

    Torpdahl, M.; Ahrens, Peter

    2004-01-01

    Aims: This study was undertaken to investigate the usefulness of amplified fragment length polymorphism (AFLP) in determining the population structure of Salmonella. Methods and Results: A total of 89 strains were subjected to AFLP analysis using the enzymes BglII and BspDI, a combination...

  17. Genetic diversity of taro, Colocasia esculenta (L.) Schott, in Southeast Asia and the Pacific

    NARCIS (Netherlands)

    Kreike, N.; Eck, van H.J.; Lebot, V.

    2004-01-01

    The genetic diversity of 255 taro (Colocasia esculenta) accessions from Vietnam, Thailand, Malaysia, Indonesia, the Philippines, Papua New Guinea and Vanuatu was studied using AFLPs. Three AFLP primer combinations generated a total of 465 scorable amplification products. The 255 accessions were

  18. Phenotypic and molecular characterization of selected tomato ...

    Indian Academy of Sciences (India)

    2011-08-19

    Aug 19, 2011 ... (2001) found new AFLP markers in interspe- cific crosses of wheat, and Marfil et al. (2006) also detected new RAPD and AFLP markers in interspecific hybrids of potatoes, a crop that has a high degree of homosequential- ity and is very close to tomatoes. A different degree of DNA methylation in the hybrid ...

  19. Genetic and phylogenetic analysis of ten Gobiidae species in China ...

    African Journals Online (AJOL)

    To study the genetic and phylogenetic relationship of gobioid fishes in China, the representatives of 10 gobioid fishes from 2 subfamilies in China were examined by amplified fragment length polymorphism (AFLP) analysis. We established 220 AFLP bands for 45 individuals from the 10 species, and the percentage of ...

  20. Genetic diversity of Indonesia milkfish ( Chanos chanos ) using ...

    African Journals Online (AJOL)

    Genetic diversity of milkfish (Chanos chanos) from Indonesia was investigated using amplified fragment length polymorphism (AFLP) markers. A total of 255 loci were detected by combination of seven primers from 130 individuals collected at seven locations. AFLP analysis provided useful information in determining genetic ...

  1. Evolution and genetic population structure of prickly lettuce (Lactuca serriola) and its RGC2 resistance gene cluster

    NARCIS (Netherlands)

    Kuang, H.; Eck, van H.J.; Sicard, D.; Michelmore, R.; Nevo, E.

    2008-01-01

    Genetic structure and diversity of natural populations of prickly lettuce (Lactuca serriola) were studied using AFLP markers and then compared with the diversity of the RGC2 disease resistance gene cluster. Screening of 696 accessions from 41 populations using 319 AFLP markers showed that eastern

  2. Assessment of genetic diversity for some Iraqi date palms ( Phoenix ...

    African Journals Online (AJOL)

    Amplified fragment length polymorphisms (AFLP) were used to evaluate the genetic diversity between 18 date palm (Phoenix dactylifera L.) varieties (11 females and 7 males) collected from the center of Iraq. Six primer pairs were applied to detect polymorphism between varieties. A total of 83 polymorphic AFLP fragments ...

  3. Amplified fragment length polymorphism of Puccinia graminis f. sp ...

    African Journals Online (AJOL)

    The developed AFLP fingerprints for the Ethiopian Pgt isolates reported herein could support the breeding program to develop strategies for the deployment of resistance genes in its continued effort to minimize the impact of stem rust on wheat in Ethiopia. Keywords: AFLP, wheat, stem rust, genetic diversity, population ...

  4. Analysis of genetic diversity in bambara groundnut [ Vigna ...

    African Journals Online (AJOL)

    Amplified fragment length polymorphism (AFLP) was used to assess genetic diversity among 100 selected bambara groundnut [Vigna subterranea (L.) Verdc] landraces from a diverse geographic area of Tanzania. Eleven informative AFLP primer combinations generated a total of 49 scorable polymorphic amplification ...

  5. Molecular marker analysis to differentiate a clonal selection of ...

    African Journals Online (AJOL)

    Lalit Kumar

    2013-04-03

    Apr 3, 2013 ... Microsatellite and amplified fragment length polymorphism (AFLP) markers were used to differentiate. Manjari Naveen, a clonal selection of Centennial Seedless variety of grape. Twenty one (21) microsatellite primers could not detect variation between parent variety and its clone. AFLP analysis.

  6. Genetic differentiation in Japanese flounder in the Yellow Sea and ...

    African Journals Online (AJOL)

    The population structure of Japanese flounder (Paralichthys olivaceus) in the Yellow and East China Seas were analyzed using amplified fragment length polymorphism (AFLP) and cytochrome c oxidase subunit I (COI) gene sequencing. A total of 390 reproducible bands were generated by 10 AFLP primer combinations in ...

  7. Encapsulation dehydration colligative cryoprotective strategies and amplified fragment length polymorphism markers to verify the identity and genetic stability of euglenoids following cryopreservation.

    Science.gov (United States)

    Harding, Keith; Miller, Julia; Timmermann, Hella; Lorenz, Maike; Day, John G; Friedl, Thomas

    2010-01-01

    An encapsulation/dehydration procedure was developed for Euglena gracilis Klebs as a 'model alga' to examine various cryoprotective regimes combined with controlled rate cooling to cryopreserve other Euglenoid taxa. Cryoprotective variables were optimised to enable reproducible growth following a combination of alginate encapsulation, sucrose osmotic dehydration, air desiccation, methanol treatment, cooling to -40 degrees C and plunging into liquid nitrogen (LN). Amplified Fragment Length Polymorphism (AFLP) analysis was adapted to: (i) verify algal identity by discriminating between different Euglenoids and (ii) examine the genetic stability of algal cultures prior to various stages of cryoprotective treatments and following exposure to LN. AFLPs were highly reproducible (> 99%) as reliable diagnostic markers, where a single DNA fragment change accounted for -0.4% of the detectable variation in an AFLP pattern. AFLP changes were detected in cryoprotective treatments following LN exposure. Successive stages of the dehydration and desiccation treatments did not accumulate AFLP changes indicating these are random events.

  8. Microbial community analysis of field-grown soybeans with different nodulation phenotypes.

    Science.gov (United States)

    Ikeda, Seishi; Rallos, Lynn Esther E; Okubo, Takashi; Eda, Shima; Inaba, Shoko; Mitsui, Hisayuki; Minamisawa, Kiwamu

    2008-09-01

    Microorganisms associated with the stems and roots of nonnodulated (Nod(-)), wild-type nodulated (Nod(+)), and hypernodulated (Nod(++)) soybeans [Glycine max (L.) Merril] were analyzed by ribosomal intergenic transcribed spacer analysis (RISA) and automated RISA (ARISA). RISA of stem samples detected no bands specific to the nodulation phenotype, whereas RISA of root samples revealed differential bands for the nodulation phenotypes. Pseudomonas fluorescens was exclusively associated with Nod(+) soybean roots. Fusarium solani was stably associated with nodulated (Nod(+) and Nod(++)) roots and less abundant in Nod(-) soybeans, whereas the abundance of basidiomycetes was just the opposite. The phylogenetic analyses suggested that these basidiomycetous fungi might represent a root-associated group in the Auriculariales. Principal-component analysis of the ARISA results showed that there was no clear relationship between nodulation phenotype and bacterial community structure in the stem. In contrast, both the bacterial and fungal community structures in the roots were related to nodulation phenotype. The principal-component analysis further suggested that bacterial community structure in roots could be classified into three groups according to the nodulation phenotype (Nod(-), Nod(+), or Nod(++)). The analysis of root samples indicated that the microbial community in Nod(-) soybeans was more similar to that in Nod(++) soybeans than to that in Nod(+) soybeans.

  9. Diversity of the skin microbiota of fishes: evidence for host species specificity.

    Science.gov (United States)

    Larsen, Andrea; Tao, Zhen; Bullard, Stephen A; Arias, Covadonga R

    2013-09-01

    Skin microbiota of Gulf of Mexico fishes were investigated by ribosomal internal spacer analysis (RISA) and 16S rRNA gene sequencing. A total of 102 fish specimens representing six species (Mugil cephalus, Lutjanus campechanus, Cynoscion nebulosus, Cynoscion arenarius, Micropogonias undulatus, and Lagodon rhomboides) were sampled at regular intervals throughout a year. The skin microbiota from each individual fish was analyzed by RISA and produced complex profiles with 23 bands on average. Similarities between RISA profiles ranged from 97.5% to 4.0%. At 70% similarity, 11 clusters were defined, each grouping individuals from the same fish species. Multidimensional scaling and analysis of similarity correlated the RISA-defined clusters with geographic locality, date, and fish species. Global R values indicated that fish species was the most indicative variable for group separation. Analysis of 16S rRNA gene sequences (from pooled samples of 10 individual fish for each fish species) showed that the Proteobacteria was the predominant phylum in skin microbiota, followed by the Firmicutes and the Actinobacteria. The distribution and abundance of bacterial sequences were different among all species analyzed. Aeribacillus was found in all fish species representing 19% of all clones sequenced, while some genera were fish species-specific (Neorickettsia in M. cephalus and Microbacterium in L. campechanus). Our data provide evidence for the existence of specific skin microbiota associated with particular fish species. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  10. Ribosomal intergenic spacer analysis as a tool for monitoring methanogenic Archaea changes in an anaerobic digester.

    Science.gov (United States)

    Ciesielski, Slawomir; Bułkowska, Katarzyna; Dabrowska, Dorota; Kaczmarczyk, Dariusz; Kowal, Przemyslaw; Możejko, Justyna

    2013-08-01

    The applicability of a newly-designed PCR primer pair in examination of methanogenic Archaea in a digester treating plant biomass was evaluated by Ribosmal Intergenic Spacer Analysis (RISA). To find a suitable approach, three variants of RISA were tested: (1) standard, polyacrylamide gel-based, (2) automated, utilized capillary electrophoresis (GA-ARISA), and (3) automated microfluidics-based (MF-ARISA). All three techniques yielded a consistent picture of archaeal community structure changes during anaerobic digestion monitored for more than 6 weeks. While automated variants were more practical for handling and rapid analysis of methanogenic Archaea, the gel-based technique was advantageous when micro-organism identification was required. A DNA-sequence analysis of dominant bands extracted from the gel revealed that the main role in methane synthesis was played by micro-organisms affiliated with Methanosarcina barkeri. The obtained results revealed that RISA is a robust method allowing for detailed analysis of archaeal community structure during organic biomass conversion into biogas. In addition, our results showed that GA-ARISA has a higher resolution and reproducibility than other variants of RISA and could be used as a technique for tracking changes in methanogenic Archaea in an anaerobic digester.

  11. Simultaneous determination of extracellular volume and blood volume with the Volemetron

    NARCIS (Netherlands)

    Planque, B.A. de; Geyskes, C.G.; Dongen, R. van; Dorhout Mees, E.J.

    A new instrument, the “Volemetron”***, constructed to measure blood volume with radioactive isotopes, was adapted to determine 82Br distribution volume. Details of the technique arc given. Mean values of both RISA and 82Br distribution volume in normal men and women were determined. They were in

  12. Value of continuous leakage monitoring with radioactive iodine-131-labeled human serum albumin during hyperthermic isolated limb perfusion with tumor necrosis factor-alpha and melphalan

    NARCIS (Netherlands)

    van Ginkel, RJ; Limburg, PC; Piers, DA; Hoekstra, HJ; Schraffordt Koops, H.

    Background: The aim of this study was to analyze the value of continuous leakage monitoring with radioactive iodine-131-labeled human serum albumin (RISA) in patients treated with hyperthermic isolated limb perfusion with tumor necrosis factor-alpha (TNFalpha) and melphalan. Methods: Forty-eight

  13. Clinical studies short-lived isotopes

    International Nuclear Information System (INIS)

    Webber, M.D.; Victery, W.S.; Cragin, M.D.

    1976-01-01

    Progress is reported in the following areas of research: demonstration of intravascular thrombosis using tantalum particles and /sup 99m/Tc; correlation of MAA thrombosis scans with fibrinogen uptake test; RISA and 125 I-fibrinogen accumulation in sites of forming and formed thrombi; and clinicopathologic correlations of the 125 I thyroid scan

  14. Developing a drought early warning information system for coastal ecosystems in the Carolinas

    Science.gov (United States)

    Kirsten Lackstrom; Amanda Brennan; Paul Conrads; Lisa Darby; Kirstin Dow; Daniel Tuford

    2016-01-01

    The National Integrated Drought Information System (NIDIS) and the Carolinas Integrated Sciences and Assessments (CISA), a National Oceanic and Atmospheric Administration (NOAA)- funded Regional Integrated Sciences and Assessments (RISA) program, are partnering to develop and support a Carolinas Drought Early Warning System pilot program. Research and projects focus on...

  15. "Climate Matters Documoments": Enabling Regionally-Specific Climate Awareness

    Science.gov (United States)

    Keener, V. W.; Finucane, M.

    2012-12-01

    The Pacific Regional Integrated Sciences & Assessments (RISA) is a multidisciplinary program that enhances the ability of Pacific Island communities to understand, plan for, and adapt to climate-induced change. Using both social and physical science research methods, the Pacific RISA engages a network of regional decision-makers and stakeholders to help solve climate-related issues. Pacific RISA has a broad audience of local and regional decision-makers (i.e. natural resource managers, community planners, state and federal government agencies) and stakeholders (i.e. farmers and ranchers, fishermen, community and native islander groups). The RISA program engages with this audience through a mixed-method approach of two-way communication, including one-on-one interviews, workshops, consensus discussions and public presentations that allow us to tailor our efforts to the needs of specific stakeholders. A recent Pacific RISA project was the creation and production of four short, educational "documoment" videos that explore the different ways in which climate change in Hawaii affects stakeholders from different sectors. The documoments, generally titled "Climate Matters", start with a quote about why climate matters to each stakeholder: a rancher, a coastal hotel owner, the manager of a landfill, and the local branch of the National Weather Service. The narratives then have each stakeholder discussing how climate impacts their professional and personal lives, and describing the types of climate change they have experienced in the islands. Each video ends with a technical fact about how different climate variables in Hawaii (sea level, precipitation, ENSO) have actually changed within the last century of observational data. Freely available on www.PacificRISA.org, the Documoments have been viewed over 350 times, and have inspired similar video projects and received positive attention from different audiences of stakeholders and scientists. In other assessment work the

  16. AFLPMax: a user-friendly application for computing the optimal number of amplified fragment length polymorphism markers needed in phylogenetic reconstruction.

    Science.gov (United States)

    García-Pereira, M J; Quesada, H; Caballero, A; Carvajal-Rodríguez, A

    2012-05-01

    Amplified fragment length polymorphisms (AFLPs) are widely used for phylogenetic inference especially in non-model species. Frequently, trees obtained with other nuclear or mitochondrial markers or with morphological information need additional resolution, increased branch support, or independent data sources (i.e. unlinked loci). In such cases, the use of AFLPs is a quick and cheap option. Computer simulation has shown that dominant AFLP markers lead to less accurate tree topologies than bi-allelic codominant markers such as SNPs, but this difference becomes negligible for shallow trees when using AFLP data sets that include a sufficiently large number of characters. Thus, determining how many AFLP characters are required to recover a given phylogeny is a key issue regarding the appropriateness of AFLPs for phylogenetic reconstruction. Here, we present a user-friendly, java-based graphical interface, AFLPMax, which executes an automatic pipeline of different programs providing the user with the optimal number of AFLP characters needed to recover a given phylogeny with high accuracy and support. Executables for Windows, linux and MacOS X operating systems, source code and user manual are available from: http://webs.uvigo.es/acraaj/AFLPMax.htm. © 2012 Blackwell Publishing Ltd.

  17. Comparison of different volume markers in peritoneal dialysis

    Energy Technology Data Exchange (ETDEWEB)

    De Paepe, M.; Belpaire, F.; Schelstraete, K.; Lameire, N.

    1988-04-01

    Four peritoneal volume markers (carbon /sup 14/-labeled dextran, dextran blue, radioactive albumin, and hemoglobin) were compared. In six rabbits /sup 14/C-dextran was compared with dextran blue during a 4-hour dwell with a 4.25% dextrose solution. The recovery of /sup 14/C-dextran at the end of the dwell was 71% +/- 3% vs. 92% +/- 1% for dextran blue (P less than 0.001). In six other rabbits, radioactive albumin (RISA) was compared with dextran blue. The recovery of RISA was 78% +/- 4%, compared with 85% +/- 2% for dextran blue (P less than 0.05). The calculated peritoneal volumes, uncorrected for disappearance of the markers, were consistently higher than when correction was made. After correction, the calculated end volumes were similar to actually measured end volumes. In six patients with chronic ambulatory peritoneal dialysis, the intraperitoneal volume during a single dwell of 6 hours was estimated in paired observations with lactated Ringer's solution and 1.5% dextrose dialysate, using simultaneously autologous hemoglobin and RISA. In eight additional patients, a single dwell with 4.25% dextrose dialysate was studied. The recoveries of both markers were related to the osmotic strength of the dialysate. Recoveries were 66.7% +/- 2.3% and 69.6% +/- 0.9% in lactated Ringer's solution, and increased to 81% +/- 3% and 82% +/- 2% in 4.25% dextrose for hemoglobin and RISA, respectively. With each dialysate, after correction for disappearance of the marker, no differences in volume profiles or between calculated or measured end volumes could be found with either hemoglobin or RISA.

  18. Genetic variation in an endemic salamander, Salamandra atra, using amplified fragment length polymorphism.

    Science.gov (United States)

    Riberon, Alexandre; Miaud, Claude; Guyetant, R; Taberlet, P

    2004-06-01

    The pattern of genetic differentiation of the endemic alpine salamander, Salamandra atra, has been studied using amplified fragment length polymorphism (AFLP) from 11 populations throughout the range of the two currently recognized subspecies, atra and aurorae. Five different primer combinations produced 706 bands and were analyzed by constructing a phylogenetic tree using NJ and principal component analysis. Significant genetic variation was revealed by AFLP between and within populations but, our results show a lack of genetic structure. AFLP markers seems to be unsuitable to investigate complex and recent diversification.

  19. Genomic diversity among Danish field strains of Mycoplasma hyosynoviae assessed by amplified fragment length polymorphism analysis

    DEFF Research Database (Denmark)

    Kokotovic, Branko; Friis, Niels F.; Nielsen, Elisabeth O.

    2002-01-01

    Genomic diversity among strains of Mycoplasma hyosynoviae isolated in Denmark was assessed by using amplified fragment length polymorphism (AFLP) analysis. Ninety-six strains, obtained from different specimens and geographical locations during 30 years and the type strain of M. hyosynoviae S16(T......) were concurrently examined for variance in BglII-MfeI and EcoRI-Csp6I-A AFLP markers. A total of 56 different genomic fingerprints having an overall similarity between 77 and 96% were detected. No correlation between AFLP variability and period of isolation or anatomical site of isolation could...

  20. Characterization of gut microbiota profiles in coronary artery disease patients using data mining analysis of terminal restriction fragment length polymorphism: gut microbiota could be a diagnostic marker of coronary artery disease.

    Science.gov (United States)

    Emoto, Takuo; Yamashita, Tomoya; Kobayashi, Toshio; Sasaki, Naoto; Hirota, Yushi; Hayashi, Tomohiro; So, Anna; Kasahara, Kazuyuki; Yodoi, Keiko; Matsumoto, Takuya; Mizoguchi, Taiji; Ogawa, Wataru; Hirata, Ken-Ichi

    2017-01-01

    The association between atherosclerosis and gut microbiota has been attracting increased attention. We previously demonstrated a possible link between gut microbiota and coronary artery disease. Our aim of this study was to clarify the gut microbiota profiles in coronary artery disease patients using data mining analysis of terminal restriction fragment length polymorphism (T-RFLP). This study included 39 coronary artery disease (CAD) patients and 30 age- and sex- matched no-CAD controls (Ctrls) with coronary risk factors. Bacterial DNA was extracted from their fecal samples and analyzed by T-RFLP and data mining analysis using the classification and regression algorithm. Five additional CAD patients were newly recruited to confirm the reliability of this analysis. Data mining analysis could divide the composition of gut microbiota into 2 characteristic nodes. The CAD group was classified into 4 CAD pattern nodes (35/39 = 90 %), while the Ctrl group was classified into 3 Ctrl pattern nodes (28/30 = 93 %). Five additional CAD samples were applied to the same dividing model, which could validate the accuracy to predict the risk of CAD by data mining analysis. We could demonstrate that operational taxonomic unit 853 (OTU853), OTU657, and OTU990 were determined important both by the data mining method and by the usual statistical comparison. We classified the gut microbiota profiles in coronary artery disease patients using data mining analysis of T-RFLP data and demonstrated the possibility that gut microbiota is a diagnostic marker of suffering from CAD.

  1. Rumen bacterial community evaluated by 454 pyrosequencing and terminal restriction fragment length polymorphism analyses in dairy sheep fed marine algae.

    Science.gov (United States)

    Castro-Carrera, T; Toral, P G; Frutos, P; McEwan, N R; Hervás, G; Abecia, L; Pinloche, E; Girdwood, S E; Belenguer, A

    2014-03-01

    Developing novel strategies to increase the content of bioactive unsaturated fatty acids (FA) in ruminant-derived products requires a deeper understanding of rumen biohydrogenation and bacteria involved in this process. Although high-throughput pyrosequencing may allow for a great coverage of bacterial diversity, it has hardly been used to investigate the microbiology of ruminal FA metabolism. In this experiment, 454 pyrosequencing and a molecular fingerprinting technique (terminal restriction fragment length polymorphism; T-RFLP) were used concurrently to assess the effect of diet supplementation with marine algae (MA) on the rumen bacterial community of dairy sheep. Eleven lactating ewes were divided in 2 lots and offered a total mixed ration based on alfalfa hay and concentrate (40:60), supplemented with 0 (control) or 8 (MA) g of MA/kg of dry matter. After 54 d on treatments, animals were slaughtered and samples of rumen content and fluid were collected separately for microbial analysis. Pyrosequencing yielded a greater coverage of bacterial diversity than T-RFLP and allowed the identification of low abundant populations. Conversely, both molecular approaches pointed to similar conclusions and showed that relevant changes due to MA addition were observed within the major ruminal phyla, namely Bacteroidetes, Firmicutes, and Proteobacteria. Decreases in the abundance of unclassified Bacteroidales, Porphyromonadaceae, and Ruminococcaceae and increases in as-yet uncultured species of the family Succinivibrionaceae, might be related to a potential role of these groups in different pathways of rumen FA metabolism. Diet supplementation with MA, however, had no effect on the relative abundance of Butyrivibrio and Pseudobutyrivibrio genera. In addition, results from both 454 pyrosequencing and T-RFLP indicate that the effect of MA was rather consistent in rumen content or fluid samples, despite inherent differences between these fractions in their bacterial composition

  2. Bio-Augmentation of Cupriavidus sp. CY-1 into 2,4-D Contaminated Soil: Microbial Community Analysis by Culture Dependent and Independent Techniques

    Science.gov (United States)

    Chang, Young-Cheol; Reddy, M. Venkateswar; Umemoto, Honoka; Sato, Yuki; Kang, Mi-Hye; Yajima, Yuka; Kikuchi, Shintaro

    2015-01-01

    In the present study, a 2,4-dichlorophenoxyacetic acid (2,4-D) degrading bacterial strain CY-1 was isolated from the forest soil. Based on physiological, biochemical and 16S rRNA gene sequence analysis it was identified as Cupriavidus sp. CY-1. Further 2,4-D degradation experiments at different concentrations (200 to 800 mg l-1) were carried out using CY-1. Effect of NaCl and KNO3 on 2,4-D degradation was also evaluated. Degradation of 2,4-D and the metabolites produced during degradation process were analyzed using high pressure liquid chromatography (HPLC) and GC-MS respectively. The amount of chloride ions produced during the 2,4-D degradation were analyzed by Ion chromatography (IC) and it is stoichiometric with 2,4-D dechlorination. Furthermore two different types of soils collected from two different sources were used for 2,4-D degradation studies. The isolated strain CY-1 was bio-augmented into 2,4-D contaminated soils to analyze its degradation ability. Culture independent methods like denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (T-RFLP), and culture dependent methods like colony forming units (CFU) and most probable number (MPN) were used to analyze the survivability of strain CY-1 in contaminated soil. Results of T-RFLP were coincident with the DGGE analysis. From the DGGE, T-RFLP, MPN and HPLC results it was concluded that strain CY-1 effectively degraded 2,4-D without disturbing the ecosystem of soil indigenous microorganisms. PMID:26710231

  3. Discrimination among individuals using terminal restriction fragment length polymorphism profiling of bacteria derived from forensic evidence.

    Science.gov (United States)

    Nishi, Eiji; Tashiro, Yukihiro; Sakai, Kenji

    2015-05-01

    DNA typing from forensic evidence is commonly used to identify individuals. However, when the quantity of the forensic evidence is insufficient, successful identification using DNA typing is impossible. Such evidence may also contain DNA from bacteria that occur naturally on the skin. In this study, we aimed to establish a profiling method using terminal restriction fragment length polymorphisms (T-RFLPs) of the amplified bacterial 16S ribosomal RNA (rRNA) gene. First, the extraction and digestion processes were investigated, and the T-RFLP profiling method using the 16S rRNA gene amplicon was optimized. We then used this method to compare the profiles of bacterial flora from the hands of 12 different individuals. We found that the T-RFLP profiles from one person on different days displayed higher similarity than those between individuals. In a principal component analysis (PCA), T-RFLPs from each individual were closely clustered in 11 out of 12 cases. The clusters could be distinguished from each other, even when the samples were collected from different conditions. No major change of the profile was observed after six months except in two cases. When handprints on glass plates were compared, 11 of 12 individuals were assigned to a few clusters including the cluster corresponding to the correct individual. In conclusion, a method for reproducible T-RFLP profiling of bacteria from trace amounts of handprints was established. The profiles were obtained for particular individuals clustered in PCA and were experimentally separable from other individuals in most cases. This technique could provide useful information for narrowing down a suspect in a criminal investigation.

  4. Community Structure of Denitrifiers, Bacteria, and Archaea along Redox Gradients in Pacific Northwest Marine Sediments by Terminal Restriction Fragment Length Polymorphism Analysis of Amplified Nitrite Reductase (nirS) and 16S rRNA Genes

    Science.gov (United States)

    Braker, Gesche; Ayala-del-Río, Héctor L.; Devol, Allan H.; Fesefeldt, Andreas; Tiedje, James M.

    2001-01-01

    Steep vertical gradients of oxidants (O2 and NO3−) in Puget Sound and Washington continental margin sediments indicate that aerobic respiration and denitrification occur within the top few millimeters to centimeters. To systematically explore the underlying communities of denitrifiers, Bacteria, and Archaea along redox gradients at distant geographic locations, nitrite reductase (nirS) genes and bacterial and archaeal 16S rRNA genes (rDNAs) were PCR amplified and analyzed by terminal restriction fragment length polymorphism (T-RFLP) analysis. The suitablility of T-RFLP analysis for investigating communities of nirS-containing denitrifiers was established by the correspondence of dominant terminal restriction fragments (T-RFs) of nirS to computer-simulated T-RFs of nirS clones. These clones belonged to clusters II, III, and IV from the same cores and were analyzed in a previous study (G. Braker, J. Zhou, L. Wu, A. H. Devol, and J. M. Tiedje, Appl. Environ. Microbiol. 66:2096–2104, 2000). T-RFLP analysis of nirS and bacterial rDNA revealed a high level of functional and phylogenetic diversity, whereas the level of diversity of Archaea was lower. A comparison of T-RFLPs based on the presence or absence of T-RFs and correspondence analysis based on the frequencies and heights of T-RFs allowed us to group sediment samples according to the sampling location and thus clearly distinguish Puget Sound and the Washington margin populations. However, changes in community structure within sediment core sections during the transition from aerobic to anaerobic conditions were minor. Thus, within the top layers of marine sediments, redox gradients seem to result from the differential metabolic activities of populations of similar communities, probably through mixing by marine invertebrates rather than from the development of distinct communities. PMID:11282647

  5. Use of primer selection and restriction enzymes to assess bacterial community diversity in an agricultural soil used for potato production via terminal restriction fragment length polymorphism.

    Science.gov (United States)

    Fortuna, Ann-Marie; Marsh, Terence L; Honeycutt, C Wayne; Halteman, William A

    2011-08-01

    Terminal restriction fragment length polymorphism (T-RFLP) can be used to assess how land use management changes the dominant members of bacterial communities. We compared T-RFLP profiles obtained via amplification with forward primers (27, 63F) each coupled with the fluorescently labeled reverse primer (1392R) and multiple restriction enzymes to determine the best combination for interrogating soil bacterial populations in an agricultural soil used for potato production. Both primer pairs provide nearly universal recognition of a 1,400-bp sequence of the bacterial domain in the V(1)-V(3) region of the 16S ribosomal RNA (rRNA) gene relative to known sequences. Labeling the reverse primer allowed for direct comparison of each forward primer and the terminal restriction fragments' relative migration units obtained with each primer pair and restriction enzyme. Redundancy analysis (RDA) and nested multivariate analysis of variance (MANOVA) were used to assess the effects of primer pair and choice of restriction enzyme on the measured relative migration units. Our research indicates that the 63F-1392R amplimer pair provides a more complete description with respect to the bacterial communities present in this potato (Solanum tuberosum L.)-barley (Hordeum vulgare L.) rotation over seeded to crimson clover (Trifolium praense L.). Domain-specific 16S rRNA gene primers are rigorously tested to determine their ability to amplify across a target region of the gene. Yet, variability within or between T-RFLP profiles can result from factors independent of the primer pair. Therefore, researchers should use RDA and MANOVA analyses to evaluate the effects that additional laboratory and environmental variables have on bacterial diversity.

  6. Terminal Restriction Fragment Length Polymorphism for the Identification of Spirorchiid Ova in Tissues from the Green Sea Turtle, Chelonia mydas.

    Directory of Open Access Journals (Sweden)

    Phoebe A Chapman

    Full Text Available Blood flukes are among the most common disease causing pathogens infecting vertebrates, including humans and some of the world's most globally endangered fauna. Spirorchiid blood flukes are parasites of marine turtles, and are associated with pathology, strandings and mortalities worldwide. Their ova embolize in tissues and incite significant inflammatory responses, however attempts to draw correlations between species and lesions are frustrated by difficulties in identifying ova beyond the genus level. In this study, a newly developed terminal restriction fragment length polymorphism (T-RFLP method was validated as a tool for differentiating between mixed spirorchiid ova in turtle tissue. Initially, a multiplex PCR was used to differentiate between the five genera of spirorchiid flukes. Following this, PCR was performed using genus/genera-specific fluorescently tagged primer pairs and PCR products digested analysis using restriction endonucleases. Using capillary electrophoresis, this T-RFLP method could differentiate between twelve species and genotypes of spirorchiid flukes in turtles. It was applied to 151 tissue samples and successfully identified the spirorchiid species present. It was found to be more sensitive than visual diagnosis, detecting infections in 28 of 32 tissues that were negative on histology. Spirorchiids were present in 96.7% of tissues tested, with Neospirorchis genotype 2 being the most prevalent, present in 93% of samples. Mixed infections were common, being present in 60.7% of samples tested. The method described here is, to our knowledge, the first use of the T-RFLP technique on host tissues or in an animal ecology context, and describes a significant advancement in the clinical capacity to diagnose a common cause of illness in our environment. It is proven as a sensitive, specific and cost-efficient means of identifying spirorchiid flukes and ova in turtles, with the potential to contribute valuable information to

  7. Authentication of medicinal plant botanical identity by amplified fragmented length polymorphism dominant DNA marker: inferences from the Plectranthus genus.

    Science.gov (United States)

    Passinho-Soares, Helna; Felix, Durvalina; Kaplan, Maria Auxiliadora; Margis-Pinheiro, Marcia; Margis, Rogério

    2006-08-01

    In Brazil, Plectranthus species are known as "boldo" and have been used in popular medicine for analgesic and dyspeptic purposes. Plectranthus need to be well identified in order to be used as commercially genuine medicinal plants. Here we describe AFLP DNA patterns able to distinguish among different Pectranthus species. The genetic variability of P. grandis Cramer, P. barbatus Andr. and P. ornatus Codd was analyzed with two sets of AFLP primers allowing detection of 241 loci. A total of 22 monomorphic loci were identified in P. barbatus, 15 in P. grandis and 30 in P. ornatus. Among these, 5 loci were informative and species-specific to P. barbatus, 3 to P. grandis and 2 loci were unique to P. ornatus. The AFLP pattern analyzed by different clustering methods assembled individuals according to their species. So far, AFLP represents a genuine and strong method to certify medicinal plant materials.

  8. Amplified fragment length polymorphism and pulsed field gel electrophoresis for subspecies differentiation of Serpulina pilosicoli

    DEFF Research Database (Denmark)

    Møller, Kristian; Jensen, Tim Kåre; Boye, Mette

    1999-01-01

    Pulsed field gel electrophoresis (PFGE) and amplified fragment length polymorphism (AFLP) were compared for their ability to differentiate between 50 porcine Serpulina pilosicoli isolates. Both techniques were highly sensitive, dividing the isolates into 36 and 38 groups, respectively. Due...

  9. On indigenous production, genetic diversity and crop ecology of enset (Ensete ventricosum (Welw.) Cheesman)

    NARCIS (Netherlands)

    Tsegaye, A.

    2002-01-01

    Keywords : Enset, staple, indigenous knowledge, genetic diversity, AFLP, characterisation, conservation, Leaf Appearance Rate, Radiation Use Efficiency, yield potential, transplanting, leaf pruning, fermentation, 'kocho', food

  10. DNA Methylation Alterations in Breast Cancer

    National Research Council Canada - National Science Library

    Yamamoto, Fumiichiro

    2002-01-01

    We have performed the NotI-MseI MS-AFLP experiments using normal and tumor DNA from breast cancer patients and determined the identity of bands exhibiting consistent changes in breast cancer DNA fingerprint...

  11. Complementary DNA-amplified fragment length polymorphism ...

    African Journals Online (AJOL)

    Complementary DNA-amplified fragment length polymorphism (AFLP-cDNA) analysis of differential gene expression from the xerophyte Ammopiptanthus mongolicus in response to cold, drought and cold together with drought.

  12. Genetic diversity and relationships among cabbage ( Brassica ...

    African Journals Online (AJOL)

    The integration of our data with historical documents confirmed that traditional cabbage landraces cultivated in North of China were first introduced from Russia. Key words: Amplified fragment length polymorphism (AFLP), genetic diversity, cabbage (Brassica oleracea var. capitata), landraces, population structure.

  13. Relationship between morphological and amplified fragment length ...

    African Journals Online (AJOL)

    Relationship between morphological and amplified fragment length polymorphism (AFLP) marker based genetic distance with heterosis in hot pepper (Capsicum annuum L.) SL Krishnamurthy, A Mohan Rao, K Madhavi Reddy, S Ramesh, Shailaja Hittalmani, Rao M. Gopinath ...

  14. Molecular and genetic study of wheat rusts

    African Journals Online (AJOL)

    Nicholas Le Maitre

    Phylogenetic trees were created for leaf and stem rust pathotypes. Field isolates of ... Key words: Prevalence, microsatellite, amplified fragment length polymorphisms (AFLP), phylogeny, Puccinia. INTRODUCTION. Puccinia triticina Eriks ..... Genetic distances and reconstruction phylogenetic trees from microsatellite DNA.

  15. Natural population dynamics and expansion of pathogenic clones of Staphylococcus aureus

    NARCIS (Netherlands)

    D.C. Melles (Damian); R.F.J. Gorkink (Raymond); H.A.M. Boelens (Hélène); S.V. Snijders (Susan); J.K. Peeters (Justine); M.J. Moorhouse (Michael); P.J. van der Spek (Peter); W.B. van Leeuwen (Willem); G. Simons (Guus); H.A. Verbrugh (Henri); A.F. van Belkum (Alex)

    2004-01-01

    textabstractThe population structure of Staphylococcus aureus carried by healthy humans was determined using a large strain collection of nonclinical origin (n = 829). High-throughput amplified fragment length polymorphism (AFLP) analysis revealed 3 major and 2 minor genetic

  16. Genetic variations among Mycoplasma bovis strains isolated from Danish cattle

    DEFF Research Database (Denmark)

    Kusiluka, L.J.M.; Kokotovic, Branko; Ojeniyi, B.

    2000-01-01

    strain of M. bovis (PG45(T)) were assayed for variations in the BglII and MfeI restriction sites in the chromosomal DNA by using the amplified fragment length polymorphism (AFLP) fingerprinting technique. The obtained genomic fingerprints consisted of 62-68 AFLP fragments in the size range of 50-500 bp....... Among the analyzed strains, 18 different AFLP profiles were detected. The similarity between individual fingerprints, calculated by Dice similarity coefficient, ranged from 0.9 to 1.0. Twenty-five strains, including 23 which were isolated during two outbreaks of M. bovis-induced mastitis which occurred...... homogeneity of Danish strains of M. bovis that were probably epidemiologically related and which have remained stable for a considerable length of time. Furthermore; this study has demonstrated that AFLP can be used for genomic fingerprinting and discrimination of M. bovis strains....

  17. Multiplex-endonuclease genotyping approach (MEGA): a tool for the fine-scale detection of unlinked polymorphic DNA markers.

    NARCIS (Netherlands)

    Agbo, E.C.; Duim, B.; Majiwa, P.A.O.; Buscher, P.; Claassen, E.; Pas, te M.F.W.

    2003-01-01

    Restriction enzyme-detectable polymorphisms have been used for assessing genetic differences and generating informative genetic markers. The most detailed fingerprinting analyses have been obtained using the AFLP (amplified fragment length polymorphism) technique, which accesses subsets of

  18. Multiplex-endonuclease genotyping approach (MEGA): a tool for the fine-scale detection of unlinked polymorphic DNA markers

    NARCIS (Netherlands)

    Agbo, Eddy Chukwura; Duim, Birgitta; Majiwa, Phelix A. O.; Büscher, Philippe; Claassen, Eric; te Pas, Marinus F. W.

    2003-01-01

    Restriction enzyme-detectable polymorphisms have been used for assessing genetic differences and generating informative genetic markers. The most detailed fingerprinting analyses have been obtained using the AFLP (amplified fragment length polymorphism) technique, which accesses subsets of

  19. Molecular bases for parallel evolution of translucent bracts in an alpine "glasshouse" plant Rheum alexandrae (Polygonaceae)

    Czech Academy of Sciences Publication Activity Database

    Liu, B. B.; Opgenoorth, L.; Miehe, G.; Zhang, D.-Y.; Wan, D.-S.; Zhao, C.-M.; Jia, Dong-Rui; Liu, J.-Q.

    2013-01-01

    Roč. 51, č. 2 (2013), s. 134-141 ISSN 1674-4918 Institutional support: RVO:67985939 Keywords : cDNA-AFLPs * parallel evolution * adaptations, mutations, diversity Subject RIV: EF - Botanics Impact factor: 1.648, year: 2013

  20. Assessment of genetic relationships among Spring Dendrobium ...

    African Journals Online (AJOL)

    Assessment of genetic relationships among Spring Dendrobium cultivars and varietal materials using amplified fragment length polymorphism (AFLP) analysis. Zheng Quan, Zheng Yongping, Guo Weiming, Lin Weijun, Wang Guangdong ...

  1. Impact of probiotics on colonic microflora in patients with colitis

    DEFF Research Database (Denmark)

    Reddy, B. S.; Ahmed, J.; Macfie, J.

    2010-01-01

    Background: Probiotics colonise the gut and may exert beneficial effects. The aim of this study was to assess if probiotics change the spectrum of colonic microflora in patients with colitis when taken daily for a period of one month Methods: This is a prospective double blind randomised crossover...... of study. Terminal-restriction fragment length polymorphism technique (T-RFLP) and principal component analysis (PCA) on the bacterial community were used to study the faecal mircoflora. Results: Sixteen patients completed the study, 8 had Crohn’s disease and 8 had ulcerative colitis. Median age was 62...... in patients with colitis. This observation might have clinical implications....

  2. Effects of PAH-Contaminated Soil on Rhizosphere Microbial Communities

    DEFF Research Database (Denmark)

    Pritchina, Olga; Ely, Cairn; Smets, Barth F.

    2011-01-01

    sativa var. Tango), zucchini (Cucurbita pepo spp. pepo var. Black Beauty), and pumpkin (C. pepo spp. pepo var. Howden) 16S rDNA terminal restriction fragment length polymorphism (T-RFLP) profiles of rhizosphere microbial communities from different soil/plant combinations were compared with a pairwise...... Pearson correlation coefficient. Rhizosphere microbial communities of zucchini and pumpkin grown in the media amended with highest degree of contaminated soil clustered separately, whereas communities of these plants grown in unamended or amended with lower concentrations of contaminated soil, grouped...

  3. Global Diversity of Desert Hypolithic Cyanobacteria

    Directory of Open Access Journals (Sweden)

    Donnabella C. Lacap-Bugler

    2017-05-01

    Full Text Available Global patterns in diversity were estimated for cyanobacteria-dominated hypolithic communities that colonize ventral surfaces of quartz stones and are common in desert environments. A total of 64 hypolithic communities were recovered from deserts on every continent plus a tropical moisture sufficient location. Community diversity was estimated using a combined t-RFLP fingerprinting and high throughput sequencing approach. The t-RFLP analysis revealed desert communities were different from the single non-desert location. A striking pattern also emerged where Antarctic desert communities were clearly distinct from all other deserts. Some overlap in community similarity occurred for hot, cold and tundra deserts. A further observation was that the producer-consumer ratio displayed a significant negative correlation with growing season, such that shorter growing seasons supported communities with greater abundance of producers, and this pattern was independent of macroclimate. High-throughput sequencing of 16S rRNA and nifH genes from four representative samples validated the t-RFLP study and revealed patterns of taxonomic and putative diazotrophic diversity for desert communities from the Taklimakan Desert, Tibetan Plateau, Canadian Arctic and Antarctic. All communities were dominated by cyanobacteria and among these 21 taxa were potentially endemic to any given desert location. Some others occurred in all but the most extreme hot and polar deserts suggesting they were relatively less well adapted to environmental stress. The t-RFLP and sequencing data revealed the two most abundant cyanobacterial taxa were Phormidium in Antarctic and Tibetan deserts and Chroococcidiopsis in hot and cold deserts. The Arctic tundra displayed a more heterogenous cyanobacterial assemblage and this was attributed to the maritime-influenced sampling location. The most abundant heterotrophic taxa were ubiquitous among samples and belonged to the Acidobacteria

  4. Genetic Diversity and Sectional Relationships from an Amplified Fragment Length Polymorphism Analysis of Taiwan Bananas

    OpenAIRE

    Chang, Shu-Fen; Chang, Yueh-Long; Yen, Yung-Fu; Miyajima, Ikuo; Huang, Kuang-Liang

    2017-01-01

    Phylogenetic relationships among 19 Musa species or cultivars were examined through DNA fingerprinting with amplified fragment length polymorphism (AFLP) analysis. The AFLP analysis was performed on the Musa species or cultivars with 21 primer combinations, yielding a total of 6,348 DNA bands, among which 6,113 (96.3%) were polymorphic. M. itinerans var. formosana demonstrated 133 monomorphic bands, which is the most among all samples. Unweighted pair–group method with arithmetic averages was...

  5. Application of Amplified Fragment Length Polymorphism Fingerprinting for Taxonomy and Identification of the Soft Rot Bacteria Erwinia carotovora and Erwinia chrysanthemi

    OpenAIRE

    Avrova, Anna O.; Hyman, Lizbeth J.; Toth, Rachel L.; Toth, Ian K.

    2002-01-01

    The soft rot bacteria Erwinia carotovora and Erwinia chrysanthemi are important pathogens of potato and other crops. However, the taxonomy of these pathogens, particularly at subspecies level, is unclear. An investigation using amplified fragment length polymorphism (AFLP) fingerprinting was undertaken to determine the taxonomic relationships within this group based on their genetic relatedness. Following cluster analysis on the similarity matrices derived from the AFLP gels, four clusters (c...

  6. Mesenteric venous thrombosis following vaginal delivery

    Directory of Open Access Journals (Sweden)

    Roopa Sachidananda

    2013-01-01

    Full Text Available Acute abdomen following an uneventful vaginal delivery is a rare occurrence. Diagnosis may be delayed due to pregnancy related comorbid conditions such as preeclampsia, hemolysis elevated, liver enzymes, low platelet (HELLP count syndrome, acute fatty liver of pregnancy (AFLP, etc. We describe a 21-year-old woman with pre-eclampsia, HELLP syndrome and AFLP with acute abdomen that was managed successfully in our intensive care unit.

  7. Genetic diversity in cultivated carioca common beans based on molecular marker analysis

    Directory of Open Access Journals (Sweden)

    Juliana Morini Küpper Cardoso Perseguini

    2011-01-01

    Full Text Available A wide array of molecular markers has been used to investigate the genetic diversity among common bean species. However, the best combination of markers for studying such diversity among common bean cultivars has yet to be determined. Few reports have examined the genetic diversity of the carioca bean, commercially one of the most important common beans in Brazil. In this study, we examined the usefulness of two molecular marker systems (simple sequence repeats - SSRs and amplified fragment length polymorphisms - AFLPs for assessing the genetic diversity of carioca beans. The amount of information provided by Roger's modified genetic distance was used to analyze SSR data and Jaccards similarity coefficient was used for AFLP data. Seventy SSRs were polymorphic and 20 AFLP primer combinations produced 635 polymorphic bands. Molecular analysis showed that carioca genotypes were quite diverse. AFLPs revealed greater genetic differentiation and variation within the carioca genotypes (Gst = 98% and Fst = 0.83, respectively than SSRs and provided better resolution for clustering the carioca genotypes. SSRs and AFLPs were both suitable for assessing the genetic diversity of Brazilian carioca genotypes since the number of markers used in each system provided a low coefficient of variation. However, fingerprint profiles were generated faster with AFLPs, making them a better choice for assessing genetic diversity in the carioca germplasm.

  8. Molecular markers. Amplified fragment length polymorphism

    Directory of Open Access Journals (Sweden)

    Pržulj Novo

    2005-01-01

    Full Text Available Amplified Fragment Length Polymorphism molecular markers (AFLPs has been developed combining procedures of RFLPs and RAPDs molekular markers, i.e. the first step is restriction digestion of the genomic DNA that is followed by selective amplification of the restricted fragments. The advantage of the AFLP technique is that it allows rapid generation of a large number of reproducible markers. The reproducibility of AFLPs markers is assured by the use of restriction site-specific adapters and adapter-specific primers for PCR reaction. Only fragments containing the restriction site sequence plus the additional nucleotides will be amplified and the more selected nucleotides added on the primer sequence the fewer the number of fragments amplified by PCR. The amplified products are normally separated on a sequencing gel and visualized after exposure to X-ray film or by using fluorescent labeled primers. AFLP shave proven to be extremely proficient in revealing diversity at below the species level. A disadvantage of AFLP technique is that AFLPs are essentially a dominant marker system and not able to identify heterozygotes.

  9. Bidirectional peritoneal transport of albumin in continuous ambulatory peritoneal dialysis

    DEFF Research Database (Denmark)

    Joffe, P; Henriksen, Jens Henrik Sahl

    1995-01-01

    The present study was undertaken in order to assess bidirectional peritoneal kinetics of albumin after simultaneous i.v. and i.p. injection of radioiodinated albumin tracers (125I-RISA and 131I-RISA) in eight clinically stable uraemic patients undergoing continuous ambulatory peritoneal dialysis...... (CAPD). The plasma volume, intravascular albumin mass (IVM), and overall extravasation rate of albumin were not significantly different from that found in healthy controls. Albumin flux from the plasma into the peritoneal cavity was 3.71 +/- 0.82 (SD) mumol/h, which was only 3% of the overall...... extravasation rate (137 +/- 52 mumol/h). Albumin flux from the peritoneal cavity into the plasma was substantially lower (0.22 +/- 0.07 mumol/h, P albumin from plasma over 4 h was 14 +/- 3.2 mumol, which was significantly lower than the intraperitoneal albumin...

  10. Application of a clustering-based peak alignment algorithm to analyze various DNA fingerprinting data.

    Science.gov (United States)

    Ishii, Satoshi; Kadota, Koji; Senoo, Keishi

    2009-09-01

    DNA fingerprinting analysis such as amplified ribosomal DNA restriction analysis (ARDRA), repetitive extragenic palindromic PCR (rep-PCR), ribosomal intergenic spacer analysis (RISA), and denaturing gradient gel electrophoresis (DGGE) are frequently used in various fields of microbiology. The major difficulty in DNA fingerprinting data analysis is the alignment of multiple peak sets. We report here an R program for a clustering-based peak alignment algorithm, and its application to analyze various DNA fingerprinting data, such as ARDRA, rep-PCR, RISA, and DGGE data. The results obtained by our clustering algorithm and by BioNumerics software showed high similarity. Since several R packages have been established to statistically analyze various biological data, the distance matrix obtained by our R program can be used for subsequent statistical analyses, some of which were not previously performed but are useful in DNA fingerprinting studies.

  11. Microbial communities along biogeochemical gradients in a hydrocarbon-contaminated aquifer.

    Science.gov (United States)

    Tischer, Karolin; Kleinsteuber, Sabine; Schleinitz, Kathleen M; Fetzer, Ingo; Spott, Oliver; Stange, Florian; Lohse, Ute; Franz, Janett; Neumann, Franziska; Gerling, Sarah; Schmidt, Christian; Hasselwander, Eyk; Harms, Hauke; Wendeberg, Annelie

    2013-09-01

    Micro-organisms are known to degrade a wide range of toxic substances. How the environment shapes microbial communities in polluted ecosystems and thus influences degradation capabilities is not yet fully understood. In this study, we investigated microbial communities in a highly complex environment: the capillary fringe and subjacent sediments in a hydrocarbon-contaminated aquifer. Sixty sediment sections were analysed using terminal restriction fragment length polymorphism (T-RFLP) fingerprinting, cloning and sequencing of bacterial and archaeal 16S rRNA genes, complemented by chemical analyses of petroleum hydrocarbons, methane, oxygen and alternative terminal electron acceptors. Multivariate statistics revealed concentrations of contaminants and the position of the water table as significant factors shaping the microbial community composition. Micro-organisms with highest T-RFLP abundances were related to sulphate reducers belonging to the genus Desulfosporosinus, fermenting bacteria of the genera Sedimentibacter and Smithella, and aerobic hydrocarbon degraders of the genus Acidovorax. Furthermore, the acetoclastic methanogens Methanosaeta, and hydrogenotrophic methanogens Methanocella and Methanoregula were detected. Whereas sulphate and sulphate reducers prevail at the contamination source, the detection of methane, fermenting bacteria and methanogenic archaea further downstream points towards syntrophic hydrocarbon degradation. © 2013 John Wiley & Sons Ltd and Society for Applied Microbiology.

  12. Diversity Profile of Microbes Associated with Anaerobic Sulfur Oxidation in an Upflow Anaerobic Sludge Blanket Reactor Treating Municipal Sewage

    Science.gov (United States)

    Aida, Azrina A.; Kuroda, Kyohei; Yamamoto, Masamitsu; Nakamura, Akinobu; Hatamoto, Masashi; Yamaguchi, Takashi

    2015-01-01

    We herein analyzed the diversity of microbes involved in anaerobic sulfur oxidation in an upflow anaerobic sludge blanket (UASB) reactor used for treating municipal sewage under low-temperature conditions. Anaerobic sulfur oxidation occurred in the absence of oxygen, with nitrite and nitrate as electron acceptors; however, reactor performance parameters demonstrated that anaerobic conditions were maintained. In order to gain insights into the underlying basis of anaerobic sulfur oxidation, the microbial diversity that exists in the UASB sludge was analyzed comprehensively to determine their identities and contribution to sulfur oxidation. Sludge samples were collected from the UASB reactor over a period of 2 years and used for bacterial 16S rRNA gene-based terminal restriction fragment length polymorphism (T-RFLP) and next-generation sequencing analyses. T-RFLP and sequencing results both showed that microbial community patterns changed markedly from day 537 onwards. Bacteria belonging to the genus Desulforhabdus within the phylum Proteobacteria and uncultured bacteria within the phylum Fusobacteria were the main groups observed during the period of anaerobic sulfur oxidation. Their abundance correlated with temperature, suggesting that these bacterial groups played roles in anaerobic sulfur oxidation in UASB reactors. PMID:25817585

  13. Temporal and spatial influences incur reconfiguration of Arctic heathland soil bacterial community structure.

    Science.gov (United States)

    Hill, Richard; Saetnan, Eli R; Scullion, John; Gwynn-Jones, Dylan; Ostle, Nick; Edwards, Arwyn

    2016-06-01

    Microbial responses to Arctic climate change could radically alter the stability of major stores of soil carbon. However, the sensitivity of plot-scale experiments simulating climate change effects on Arctic heathland soils to potential confounding effects of spatial and temporal changes in soil microbial communities is unknown. Here, the variation in heathland soil bacterial communities at two survey sites in Sweden between spring and summer 2013 and at scales between 0-1 m and, 1-100 m and between sites (> 100 m) were investigated in parallel using 16S rRNA gene T-RFLP and amplicon sequencing. T-RFLP did not reveal spatial structuring of communities at scales structuring effects may not confound comparison between plot-scale treatments, temporal change is a significant influence. Moreover, the prominence of two temporally exclusive keystone taxa suggests that the stability of Arctic heathland soil bacterial communities could be disproportionally influenced by seasonal perturbations affecting individual taxa. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

  14. Molecular characterization of the stomach microbiota in patients with gastric cancer and controls

    Energy Technology Data Exchange (ETDEWEB)

    Dicksved, J.; Lindberg, M.; Rosenquist, M.; Enroth, H.; Jansson, J.K.; Engstrand, L.

    2009-01-15

    Persistent infection of the gastric mucosa by Helicobacter pylori, can initiate an inflammatory cascade that progresses into atrophic gastritis, a condition associated with reduced capacity for secretion of gastric acid and an increased risk in developing gastric cancer. The role of H. pylori as an initiator of inflammation is evident but the mechanism for development into gastric cancer has not yet been proven. A reduced capacity for gastric acid secretion allows survival and proliferation of other microbes that normally are killed by the acidic environment. It has been postulated that some of these species may be involved in the development of gastric cancer, however their identities are poorly defined. In this study, the gastric microbiota from ten patients with gastric cancer was characterized and compared with five dyspeptic controls using the molecular profiling approach, terminal-restriction fragment length polymorphism (T-RFLP), in combination with 16S rRNA gene cloning and sequencing. T-RFLP analysis revealed a complex bacterial community in the cancer patients that was not significantly different from the controls. Sequencing of 140 clones revealed 102 phylotypes, with representatives from five bacterial phyla (Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria and Fusobacteria). The data revealed a relatively low abundance of H. pylori and showed that the gastric cancer microbiota was instead dominated by different species of the genera Streptococcus, Lactobacillus, Veillonella and Prevotella. The respective role of these species in development of gastric cancer remains to be determined.

  15. The effect of high-fat diet on the composition of the gut microbiota in cloned and non-cloned pigs of lean and obese phenotype

    DEFF Research Database (Denmark)

    Pedersen, Rebecca; Andersen, Anders Daniel; Hermann-Bank, Marie Louise

    2013-01-01

    The aim of this study was to investigate the effect of high-far-high-energy diet on cloned and non-cloned domestic pigs of both lean and obese phenotype and to evaluate if the lean cloned pigs had a lower inter-individual variation as compared with non-cloned pigs. The microbiota of colon...... and terminal ileum was investigated in cloned and non-cloned pigs that received a high-far-high-energy diet with either restricted or ad libitum access to feed, resulting in lean and obese phenotypes, respectively. The fecal microbiota of lean pigs was investigated by terminal restriction fragment length...... polymorphism (T-RFLP). The intestinal microbiota of lean and obese cloned and non-cloned pigs was analyzed by quantitative real time PCR and a novel high-throughput qPCR platform (Fluidigm). Principal component analysis (PCA) of the T-RFLP profiles revealed that lean cloned and non-cloned pigs had a different...

  16. Active bacterial community structure along vertical redox gradients in Baltic Sea sediment

    Energy Technology Data Exchange (ETDEWEB)

    Jansson, Janet; Edlund, Anna; Hardeman, Fredrik; Jansson, Janet K.; Sjoling, Sara

    2008-05-15

    Community structures of active bacterial populations were investigated along a vertical redox profile in coastal Baltic Sea sediments by terminal-restriction fragment length polymorphism (T-RFLP) and clone library analysis. According to correspondence analysis of T-RFLP results and sequencing of cloned 16S rRNA genes, the microbial community structures at three redox depths (179 mV, -64 mV and -337 mV) differed significantly. The bacterial communities in the community DNA differed from those in bromodeoxyuridine (BrdU)-labeled DNA, indicating that the growing members of the community that incorporated BrdU were not necessarily the most dominant members. The structures of the actively growing bacterial communities were most strongly correlated to organic carbon followed by total nitrogen and redox potentials. Bacterial identification by sequencing of 16S rRNA genes from clones of BrdU-labeled DNA and DNA from reverse transcription PCR (rt-PCR) showed that bacterial taxa involved in nitrogen and sulfur cycling were metabolically active along the redox profiles. Several sequences had low similarities to previously detected sequences indicating that novel lineages of bacteria are present in Baltic Sea sediments. Also, a high number of different 16S rRNA gene sequences representing different phyla were detected at all sampling depths.

  17. Identical genotypes of an ericoid mycorrhiza-forming fungus occur in roots of Epacris pulchella (Ericaceae) and Leptospermum polygalifolium (Myrtaceae) in an Australian sclerophyll forest.

    Science.gov (United States)

    Curlevski, Nathalie J A; Chambers, Susan M; Anderson, Ian C; Cairney, John W G

    2009-03-01

    Assemblages of fungi associated with roots of cooccurring Epacris pulchella (Ericaceae) and Leptospermum polygalifolium (Myrtaceae) seedlings at a sclerophyll forest site in New South Wales, Australia, were investigated by direct DNA extraction and analysis of rRNA gene internal transcribed spacer (ITS) products by denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (T-RFLP) analyses. While ordination of the DGGE data suggested that the assemblages did not differ significantly between the two plant taxa, T-RFLP data provided marginal statistical support for the presence of different assemblages. Fungi isolated from roots of both plants were identified by ITS sequence comparisons largely as ascomycetes, several of which had close sequence identity to Helotiales ericoid mycorrhizal (ERM) fungi. One isolate morphotype from E. pulchella had close sequence similarity to ectomycorrhizal fungi in the Cenococcum geophilum complex, and neighbour-joining analysis grouped this strongly with other Australian C. geophilum-like sequences. Distribution of genotypes of an ERM Helotiales ascomycete in root systems of the two plant taxa was also investigated using inter-simple sequence repeat (ISSR)-PCR. Nineteen ISSR genotypes were identified, two of which were present in roots of both plant taxa. The results are discussed in the context of potential mycelial connections between Ericaceae and non-Ericaceae plants.

  18. Bacterial diversity in fumarole environments of the Paricutín volcano, Michoacán (Mexico).

    Science.gov (United States)

    Medrano-Santillana, Miguel; Souza-Brito, Elcia Margaret; Duran, Robert; Gutierrez-Corona, Felix; Reyna-López, Georgina Elena

    2017-05-01

    Active volcanoes are among the most extreme environments on Earth. The extreme temperatures, presence of toxic heavy metals and low nutrient bioavailability favor the development of extremophiles. We characterized the physical-chemical parameters of and bacterial communities (T-RFLP and 16S rRNA gene libraries) inhabiting fumarole niches of the Paricutín volcano located in Michoacán (Mexico). This volcano, which surged in 1943, is one of the youngest volcanoes on Earth and the microbial diversity in this area is yet to be characterized. The sampling stations were characterized in a pH range from 5.34 to 7.89 and showed different temperatures (soil, 27-87 °C; air, 13.6-56 °C) with high concentrations of metals such as iron and arsenic. The most abundant bacterial populations, confirmed by T-RFLP and 16S rRNA gene libraries, were related to members of Firmicutes and Proteobacteria phyla including sequences associated with thermophiles and sulfate reducing bacteria. Overall, the Paricutín volcano showed low bacterial diversity and its prokaryotic diversity was characterized by the impossibility of amplifying Archaea-related sequences.

  19. Characterization of the bacterial community associated with the surface and mucus layer of whiting (Merlangius merlangus).

    Science.gov (United States)

    Smith, Cindy J; Danilowicz, Bret S; Meijer, Wim G

    2007-10-01

    The bacterial community inhabiting the mucus layer and surface of whiting was examined to determine whether the bacteria present are a reflection of the surrounding water or an indigenous bacterial flora is present. The outer mucus, mouth mucus and gut of four whiting harvested from a site in the Irish Sea and the surrounding water were examined by terminal restriction fragment length polymorphism (tRFLP) analysis of the 16S rRNA gene and clone library construction. The water community was the most diverse, with only a small number of shared water-mucus phylotypes present. The bacterial flora associated with the outer mucus layer were more diverse than that of the mouth mucus and gut. All three mucus layers were characterized by the presence of a dominant phylotype, identified as clone wom-1, highly similar to Photobacterium iliopiscarium. In addition to other Photobacterium phylotypes, members of the CFB and Clostridia groups were also detected. Subsequently, whiting from 11 different sites along the east and south coast of Ireland were compared by tRFLP analysis. Strikingly, the mucus layer of whiting at all sites was characterized by the presence and dominance of a TRF corresponding to the clone wom-1 which was virtually absent from the water column.

  20. Spatial distribution of ammonia-oxidizing archaea and bacteria across eight freshwater lakes in sediments from Jiangsu of China

    Directory of Open Access Journals (Sweden)

    Xu Sun

    2014-03-01

    Full Text Available Ammonia-oxidizingarchaea (AOA and ammonia-oxidizing bacteria (AOB play an important role innitrogen transformation in freshwater sediments. However, it is still unclear towhat extent the distribution patterns of these microorganisms are affected bythe freshwater sediment across a large geographical scale. This study wasdesigned to gain insight into the heterogeneity distribution of AOA and AOB in32 freshwater sediments from a wide range of ecologic types. Real-time quantitative polymerasechain reaction PCR(qPCR combined with the terminal restrictionfragment length polymorphism(T-RFLP were employed to characterize the abundance, diversity, and communitystructure of the AOA and AOB in 32 freshwater sediments. AOA and AOB wereubiquitous in all sediments, and archaeal amoA far outnumbered bacterial amoA inmost sediments with lower organic matters. The abundance of AOA and AOB did notvary with the freshwater ecological type (macrophyte dominated region and algaedominated region. Based on  the T-RFLP of an amoA gene, this research found that organicmatters in pore water rather than other factors affect the AOA communitystructure in sediments, while the AOB were not significantly different in thefreshwater sediments. Phylogenetic analysis showed that all archaeal amoAsequences fell within either the Crenarchaeotal Group (CG I.1b or the CGI.1asubgroup, and all AOB clustered with genus Nitrosomonas or Nitrosospira. The data obtained inthis study elucidates the role of ammonia-oxidizing archaea andammonia-oxidizing bacteria in the nitrogen cycle of freshwater ecosystems.

  1. Response of bacterioplankton community structure to an artificial gradient of pCO2 in the Arctic Ocean

    Directory of Open Access Journals (Sweden)

    R. Zhang

    2013-06-01

    Full Text Available In order to test the influences of ocean acidification on the ocean pelagic ecosystem, so far the largest CO2 manipulation mesocosm study (European Project on Ocean Acidification, EPOCA was performed in Kings Bay (Kongsfjorden, Spitsbergen. During a 30 day incubation, bacterial diversity was investigated using DNA fingerprinting and clone library analysis of bacterioplankton samples. Terminal restriction fragment length polymorphism (T-RFLP analysis of the PCR amplicons of the 16S rRNA genes revealed that general bacterial diversity, taxonomic richness and community structure were influenced by the variation of productivity during the time of incubation, but not the degree of ocean acidification. A BIOENV analysis suggested a complex control of bacterial community structure by various biological and chemical environmental parameters. The maximum apparent diversity of bacterioplankton (i.e., the number of T-RFs in high and low pCO2 treatments differed significantly. A negative relationship between the relative abundance of Bacteroidetes and pCO2 levels was observed for samples at the end of the experiment by the combination of T-RFLP and clone library analysis. Our study suggests that ocean acidification affects the development of bacterial assemblages and potentially impacts the ecological function of the bacterioplankton in the marine ecosystem.

  2. Response of bacterioplankton community structure to an artificial gradient of pCO2 in the Arctic Ocean

    Science.gov (United States)

    Zhang, R.; Xia, X.; Lau, S. C. K.; Motegi, C.; Weinbauer, M. G.; Jiao, N.

    2013-06-01

    In order to test the influences of ocean acidification on the ocean pelagic ecosystem, so far the largest CO2 manipulation mesocosm study (European Project on Ocean Acidification, EPOCA) was performed in Kings Bay (Kongsfjorden), Spitsbergen. During a 30 day incubation, bacterial diversity was investigated using DNA fingerprinting and clone library analysis of bacterioplankton samples. Terminal restriction fragment length polymorphism (T-RFLP) analysis of the PCR amplicons of the 16S rRNA genes revealed that general bacterial diversity, taxonomic richness and community structure were influenced by the variation of productivity during the time of incubation, but not the degree of ocean acidification. A BIOENV analysis suggested a complex control of bacterial community structure by various biological and chemical environmental parameters. The maximum apparent diversity of bacterioplankton (i.e., the number of T-RFs) in high and low pCO2 treatments differed significantly. A negative relationship between the relative abundance of Bacteroidetes and pCO2 levels was observed for samples at the end of the experiment by the combination of T-RFLP and clone library analysis. Our study suggests that ocean acidification affects the development of bacterial assemblages and potentially impacts the ecological function of the bacterioplankton in the marine ecosystem.

  3. Temporal variation of coastal surface sediment bacterial communities along an environmental pollution gradient.

    Science.gov (United States)

    Thiyagarajan, V; Tsoi, M M Y; Zhang, W; Qian, P Y

    2010-07-01

    Terminal restriction fragment length polymorphism analysis (T-RFLP) was used to track the changes of bacterial community compositions (BCC) in coastal surface sediments along an environmental pollution gradient between 2004 and 2006. BCC in the chronically contaminated sites showed the largest deviation from those in the adjacent sites. Surprisingly, BCC at two contrasting environments (oceanic vs. river-influenced) were more similar. Unexpectedly, the BCC did not recover (when compared to oceanic control site) even after 5 years of pollution abatement initiatives in Victoria Harbour, Hong Kong. On the other hand, disposal of treated sewage for 5 years in one of the sites did not significantly affect the BCC. A striking seasonal variation in the BCC was observed at only the polluted sites. Although factors other than pollution gradients may explain the observed BCC patterns, the information presented here can be useful in predicting long-term effects of pollution on BCC. Furthermore, this study suggests that BCC analysis using T-RFLP is a faster, reliable and easier approach to monitor microbenthic community response to environmental pollution gradient in coastal sediments. 2010 Elsevier Ltd. All rights reserved.

  4. Impact of silver nanoparticles on benthic prokaryotes in heavy metal-contaminated estuarine sediments in a tropical environment.

    Science.gov (United States)

    Antizar-Ladislao, B; Bhattacharya, B D; Ray Chaudhuri, S; Sarkar, S K

    2015-10-15

    Little knowledge is available about the potential impact of commercial silver nanoparticles (Ag-NPs) on estuarine microbial communities. The Hugli river estuary, India, is susceptible to heavy metals pollution through boat traffic, and there is the potential for Ag-NP exposure via effluent discharged from ongoing municipal and industrial activities located in close proximity. This study investigated the effects of commercial Ag-NPs on native microbial communities in estuarine sediments collected from five stations, using terminal restriction fragment length polymorphism (T-RFLP) technique. An increase in the number of bacteria in consortium in sediments was observed following exposure to Ag-NPs. In general microbial communities may be resistant in estuarine systems to the antimicrobial effects of commercial Ag-NPs, but key microorganisms, such as Pelobacter propionicus, disappeared following exposure to Ag-NPs. In conclusion, the T-RFLP analysis indicated that Ag-NPs have the potential to shape estuarine sediment bacterial community structure. Copyright © 2015 Elsevier Ltd. All rights reserved.

  5. Fine-scale distribution of ectomycorrhizal fungi colonizing Tsuga diversifolia seedlings growing on rocks in a subalpine Abies veitchii forest.

    Science.gov (United States)

    Yoshida, Naohiro; Son, Joung A; Matsushita, Norihisa; Iwamoto, Kojiro; Hogetsu, Taizo

    2014-05-01

    Numerous species of ectomycorrhizal (ECM) fungi coexist under the forest floor. To explore the mechanisms of coexistence, we investigated the fine-scale distribution of ECM fungal species colonizing root tips in the root system of Tsuga diversifolia seedlings in a subalpine forest. ECM root tips of three seedlings growing on the flat top surface of rocks were sampled after recording their positions in the root system. After the root tips were grouped by terminal-restriction fragment length polymorphism (T-RFLP) analysis of ITS rDNA, the fungal species representing each T-RFLP group were identified using DNA sequencing. Based on the fungal species identification, the distribution of root tips colonized by each ECM fungus was mapped. Significant clustering of root tips was estimated for each fungal species by comparing actual and randomly simulated distributions. In total, the three seedlings were colonized by 40 ECM fungal species. The composition of colonizing fungal species was quite different among the seedlings. Twelve of the 15 major ECM fungal species clustered significantly within a few centimeters. Some clusters overlapped or intermingled, while others were unique. Areas with high fungal species diversity were also identified in the root system. In this report, the mechanisms underlying generation of these ECM root tip clusters in the root system are discussed.

  6. Arbuscular mycorrhizal fungi community structure, abundance and species richness changes in soil by different levels of heavy metal and metalloid concentration.

    Directory of Open Access Journals (Sweden)

    Ramasamy Krishnamoorthy

    Full Text Available Arbuscular Mycorrhizal Fungi (AMF play major roles in ecosystem functioning such as carbon sequestration, nutrient cycling, and plant growth promotion. It is important to know how this ecologically important soil microbial player is affected by soil abiotic factors particularly heavy metal and metalloid (HMM. The objective of this study was to understand the impact of soil HMM concentration on AMF abundance and community structure in the contaminated sites of South Korea. Soil samples were collected from the vicinity of an abandoned smelter and the samples were subjected to three complementary methods such as spore morphology, terminal restriction fragment length polymorphism (T-RFLP and denaturing gradient gel electrophoresis (DGGE for diversity analysis. Spore density was found to be significantly higher in highly contaminated soil compared to less contaminated soil. Spore morphological study revealed that Glomeraceae family was more abundant followed by Acaulosporaceae and Gigasporaceae in the vicinity of the smelter. T-RFLP and DGGE analysis confirmed the dominance of Funneliformis mosseae and Rhizophagus intraradices in all the study sites. Claroideoglomus claroideum, Funneliformis caledonium, Rhizophagus clarus and Funneliformis constrictum were found to be sensitive to high concentration of soil HMM. Richness and diversity of Glomeraceae family increased with significant increase in soil arsenic, cadmium and zinc concentrations. Our results revealed that the soil HMM has a vital impact on AMF community structure, especially with Glomeraceae family abundance, richness and diversity.

  7. Analysis of soil microbial community structure and enzyme activities associated with negative effects of pseudostellaria heterophylla consecutive monoculture on yield

    International Nuclear Information System (INIS)

    Lin, S.; Lin, W.X.

    2015-01-01

    Pseudostellaria heterophylla is an important medicinal plant in China. However, cultivation of P. heterophylla using consecutive monoculture results in significant reductions in yield and quality. In this study, terminal-restriction fragment length polymorphism (T-RFLP) analysis and measurement of soil enzyme activities were used to investigate the regulation of soil micro-ecology to identify ways to overcome the negative effects of P. heterophylla consecutive monoculture. T-RFLP analysis showed that rice/P. heterophylla (RP) and bean/P. heterophylla (BP) crop rotation systems increased the number and diversity of microbial groups in P. heterophylla rhizosphere soil. In particular, the RP and BP crop rotations increased the number and abundance of beneficial bacterial species compared with two-year consecutive monoculture of P. heterophylla. The presence of these beneficial bacteria was positively correlated with soil enzyme activities which increased in rhizosphere soils of the RP and BP crop rotation systems. The results indicated that crop rotation systems could increase activities of key soil enzymes and beneficial microbial groups and improve soil health. This study could provide a theoretical basis to resolve the problems associated with P. heterophylla consecutive monoculture. (author)

  8. Effects of pesticides on community composition and activity of sediment microbes - responses at various levels of microbial community organization

    International Nuclear Information System (INIS)

    Widenfalk, Anneli; Bertilsson, Stefan; Sundh, Ingvar; Goedkoop, Willem

    2008-01-01

    A freshwater sediment was exposed to the pesticides captan, glyphosate, isoproturon, and pirimicarb at environmentally relevant and high concentrations. Effects on sediment microorganisms were studied by measuring bacterial activity, fungal and total microbial biomass as community-level endpoints. At the sub-community level, microbial community structure was analysed (PLFA composition and bacterial 16S rRNA genotyping, T-RFLP). Community-level endpoints were not affected by pesticide exposure. At lower levels of microbial community organization, however, molecular methods revealed treatment-induced changes in community composition. Captan and glyphosate exposure caused significant shifts in bacterial community composition (as T-RFLP) at environmentally relevant concentrations. Furthermore, differences in microbial community composition among pesticide treatments were found, indicating that test compounds and exposure concentrations induced multidirectional shifts. Our study showed that community-level end points failed to detect these changes, underpinning the need for application of molecular techniques in aquatic ecotoxicology. - Molecular techniques revealed pesticide-induced changes at lower levels of microbial community organization that were not detected by community-level end points

  9. Alteration of a human intestinal microbiota under extreme life environment in the Antarctica.

    Science.gov (United States)

    Jin, Jong-Sik; Touyama, Mutsumi; Yamada, Shin; Yamazaki, Takashi; Benno, Yoshimi

    2014-01-01

    The human intestinal microbiota (HIM) settles from birth and continues to change phenotype by some factors (e.g. host's diet) throughout life. However, the effect of extreme life environment on human HIM composition is not well known. To understand HIM fluctuation under extreme life environment in humans, fecal samples were collected from six Japanese men on a long Antarctic expedition. They explored Antarctica for 3 months and collected their fecal samples at once-monthly intervals. Using terminal restriction fragment length polymorphism (T-RFLP) and real time polymerase chain reaction (PCR) analysis, the composition of HIM in six subjects was investigated. Three subjects presented restoration of HIM after the expedition compared versus before and during the expedition. Two thirds samples collected during the expedition belonged to the same cluster in dendrogram. However, all through the expedition, T-RFLP patterns showed interindividual variability. Especially, Bifidobacterium spp. showed a tendency to decrease during and restore after the expedition. A reduction of Bifidobacterium spp. was observed in five subjects the first 1 month of the expedition. Bacteroides thetaiotaomicron, which is thought to proliferate during emotional stress, significantly decreased in one subject, indicating that other factors in addition to emotional stress may affect the composition of HIM in this study. These findings could be helpful to understand the effect of extreme life environment on HIM.

  10. Amazonian dark Earth and plant species from the Amazon region contribute to shape rhizosphere bacterial communities.

    Science.gov (United States)

    Barbosa Lima, Amanda; Cannavan, Fabiana Souza; Navarrete, Acacio Aparecido; Teixeira, Wenceslau Geraldes; Kuramae, Eiko Eurya; Tsai, Siu Mui

    2015-05-01

    Amazonian Dark Earths (ADE) or Terra Preta de Índio formed in the past by pre-Columbian populations are highly sustained fertile soils supported by microbial communities that differ from those extant in adjacent soils. These soils are found in the Amazon region and are considered as a model soil when compared to the surrounding and background soils. The aim of this study was to assess the effects of ADE and its surrounding soil on the rhizosphere bacterial communities of two leguminous plant species that frequently occur in the Amazon region in forest sites (Mimosa debilis) and open areas (Senna alata). Bacterial community structure was evaluated using terminal restriction fragment length polymorphism (T-RFLP) and bacterial community composition by V4 16S rRNA gene region pyrosequencing. T-RFLP analysis showed effect of soil types and plant species on rhizosphere bacterial community structure. Differential abundance of bacterial phyla, such as Acidobacteria, Actinobacteria, Verrucomicrobia, and Firmicutes, revealed that soil type contributes to shape the bacterial communities. Furthermore, bacterial phyla such as Firmicutes and Nitrospira were mostly influenced by plant species. Plant roots influenced several soil chemical properties, especially when plants were grown in ADE. These results showed that differences observed in rhizosphere bacterial community structure and composition can be influenced by plant species and soil fertility due to variation in soil attributes.

  11. Similarity of permeabilities for Ficoll, pullulan, charge-modified albumin and native albumin across the rat peritoneal membrane.

    Science.gov (United States)

    Asgeirsson, D; Axelsson, J; Rippe, C; Rippe, B

    2009-08-01

    Compared to neutral globular proteins, neutral polysaccharides, such as dextran, pullulan and Ficoll, appear hyperpermeable across the glomerular filtration barrier. This has been attributed to an increased flexibility and/or asymmetry of polysaccharides. The present study investigates whether polysaccharides are hyperpermeable also across the continuous capillaries in the rat peritoneum. In anaesthetized Wistar rats, FITC-Ficoll or FITC-pullulan together with (125)I-human serum albumin (RISA) or neutralized (125)I-bovine serum albumin (nBSA) were given intravenously, after which peritoneal dialysis (PD) using conventional PD fluid (Gambrosol 1.5%) was performed for 120 min. Concentrations of FITC-polysaccharides and radioactive albumin species in plasma and dialysis fluid were analysed with high-performance size exclusion chromatography and a gamma counter respectively. Transperitoneal clearance values were calculated for polysaccharides in the molecular radius range 36-150 A, and for RISA and nBSA. Ficoll and pullulan showed more or less identical permeabilities, compared to RISA and nBSA, across the peritoneal membrane. Although RISA-clearance, 5.50 +/- 0.28 (microL min(-1); +/-SEM), tended to be lower than the clearances of Ficoll(36A) (6.55 +/- 0.25), pullulan(36A) (6.08 +/- 0.22) and nBSA (6.56 +/- 0.23), the difference was not statistically significant. This is in contrast to the hyperpermeability exhibited by polysaccharides across the glomerular filtration barrier and also contrasts with the charge selectivity of the latter. The phenomenon of molecular flexibility is more important for a macromolecule's permeability through the glomerular filter than across the continuous peritoneal capillary endothelium. Furthermore, it seems that charge plays a subordinate role in the steady-state transport across the combined peritoneal capillary-interstitial barrier.

  12. How effective is bronchial thermoplasty for severe asthma in clinical practice?

    OpenAIRE

    Thomson, Neil C.; Chanez, Pascal

    2017-01-01

    Bronchial thermoplasty is an intervention developed for the treatment of asthma through the delivery of radio frequency energy to the airways [1, 2]. Evidence for the efficacy and safety of bronchial thermoplasty in severe asthma is based on the results of three randomised controlled trials [3?5]. Two trials compared bronchial thermoplasty with usual care, the Asthma Intervention Research (AIR) trial [3] and the Research in Severe Asthma (RISA) trial [4], whereas the third trial (AIR2) compar...

  13. Profanación del otoño

    OpenAIRE

    Ruiz, Guillermo Augusto

    2014-01-01

    A mis hijos El agua asombrola piel asombrola hierba asombro el cielo asombro Éxtasis de los pasosprofanando descalzosmás allá de estas manos el templo del espacio Perderse por otras líneasque traza la sangre marchitade octubre. Manchar de huellas nocturnas la piel de la luz,de risas la sombra. Fundar íntimo fuego en el centro de las ruinas.

  14. Synergistic benefits between stormwater management measures and a new pricing system for stormwater in the City of Hamburg.

    Science.gov (United States)

    Bertram, N P; Waldhoff, A; Bischoff, G; Ziegler, J; Meinzinger, F; Skambraks, A-K

    2017-09-01

    Hamburg is a growing metropolitan city. The increase in sealed surfaces of about 0.36% per year and the subsequent increased runoff impacts on the city's wastewater infrastructure. Further potential risks to the drainage infrastructure arise also from effects of climate change, e.g. increased intensity and frequency of heavy rainfalls. These challenges were addressed in the Rain InfraStructure Adaption (RISA) project conducted 2009-2015 by HAMBURG WASSER and the State Ministry for Environment and Energy, supported by several municipal stakeholders. RISA addressed intensifying conflicts in the context of urban development and stormwater management at that time. Major results of the project are improvements and recommendations for adequate consideration of stormwater management issues during urban planning as well as new funding mechanisms for stormwater management measures. The latter topic resulted in the introduction of a separated stormwater charge based on the amount of sealed area connected to the sewer system of each property. For both undertakings - the RISA project and the introduction of the separated stormwater charge - a novel, comprehensive, digital database was built. Today, these geographical information system (GIS)-based data offer various scale-independent analysis and information opportunities, which facilitate the day-to-day business of HAMBURG WASSER and stormwater management practice in Hamburg.

  15. Mechanism of Hydrophilicity by Radiation-Induced Surface Activation

    Science.gov (United States)

    Honjo, Yoshio; Furuya, Masahiro; Takamasa, Tomoji; Okamoto, Koji

    When a metal oxide is irradiated by gamma rays, the irradiated surface becomes hydrophilic. This surface phenomenon is called as radiation-induced surface activation (RISA) hydrophilicity. In order to investigate gamma ray-induced and photoinduced hydrophilicity, the contact angles of water droplets on a titanium dioxide surface were measured in terms of irradiation intensity and time for gamma rays of cobalt-60 and for ultraviolet rays. Reciprocals of the contact angles increased in proportion to the irradiation time before the contact angles reached its super-hydrophilic state. The irradiation time dependency is equal to each other qualitatively. In addition, an effect of ambient gas was investigated. In pure argon gas, the contact angle remains the same against the irradiation time. This clearly indicates that certain humidity is required in ambient gas to take place of RISA hydrophilicity. A single crystal titanium dioxide (100) surface was analyzed by X-ray photoelectron spectrometry (XPS). After irradiation with gamma rays, a peak was found in the O1s spectrum, which indicates the adsorption of dissociative water to a surface 5-fold coordinate titanium site, and the formation of a surface hydroxyl group. We conclude that the RISA hydrophilicity is caused by chemisorption of the hydroxyl group on the surface.

  16. Population typing of the causal agent of cassava bacterial blight in the Eastern Plains of Colombia using two types of molecular markers.

    Science.gov (United States)

    Trujillo, César A; Arias-Rojas, Nathalia; Poulin, Lucie; Medina, César A; Tapiero, Anibal; Restrepo, Silvia; Koebnik, Ralf; Bernal, Adriana J

    2014-06-19

    Molecular typing of pathogen populations is an important tool for the development of effective strategies for disease control. Diverse molecular markers have been used to characterize populations of Xanthomonas axonopodis pv. manihotis (Xam), the main bacterial pathogen of cassava. Recently, diversity and population dynamics of Xam in the Colombian Caribbean coast were estimated using AFLPs, where populations were found to be dynamic, diverse and with haplotypes unstable across time. Aiming to examine the current state of pathogen populations located in the Colombian Eastern Plains, we also used AFLP markers and we evaluated the usefulness of Variable Number Tandem Repeats (VNTRs) as new molecular markers for the study of Xam populations. The population analyses showed that AFLP and VNTR provide a detailed and congruent description of Xam populations from the Colombian Eastern Plains. These two typing strategies clearly separated strains from the Colombian Eastern Plains into distinct populations probably because of geographical distance. Although the majority of analyses were congruent between typing markers, fewer VNTRs were needed to detect a higher number of genetic populations of the pathogen as well as a higher genetic flow among sampled locations than those detected by AFLPs. This study shows the advantages of VNTRs over AFLPs in the surveillance of pathogen populations and suggests the implementation of VNTRs in studies that involve large numbers of Xam isolates in order to obtain a more detailed overview of the pathogen to improve the strategies for disease control.

  17. Molecular analysis of field strains of Mycoplasma capricolum subspecies capripneumoniae and Mycoplasma mycoides subspecies mycoides, small colony type isolated from goats in Tanzania

    DEFF Research Database (Denmark)

    Kusiluka, L.J.M.; Ojeniyi, B.; Friis, N.F.

    2001-01-01

    A molecular analysis of strains of Mycoplasma capricolum subsp, capripneumoniae (M. capripneumoniae) and Mycoplasma mycoides subsp. mycoides, small colony type (M. mycoides SQ isolated from goats was performed using the amplified fragment length polymorphism (AFLP) and pulsed-field gel electropho......A molecular analysis of strains of Mycoplasma capricolum subsp, capripneumoniae (M. capripneumoniae) and Mycoplasma mycoides subsp. mycoides, small colony type (M. mycoides SQ isolated from goats was performed using the amplified fragment length polymorphism (AFLP) and pulsed-field gel...... electrophoresis (PFGE) fingerprinting techniques. Among the 11 field strains of M. capripneumoniae from Tanzanian goats, two AFLP patterns were demonstrated, with 10 of the strains showing indistinguishable patterns. Five Kenyan strains of M. capripneumoniae produced three AFLP patterns, with two of them being...... identical PFGE profiles, which were, however, different from the type strain. The AFLP and PFGE profiles of M. mycoides SC strains from goats were identical to those of six strains isolated from cattle affected with contagious bovine pleuropneumonia (CBPP) in the same areas. The results of this study...

  18. Prevalence of avian pathogenic Escherichia coli (APEC) clone harboring sfa gene in Brazil.

    Science.gov (United States)

    Knöbl, Terezinha; Moreno, Andrea Micke; Paixão, Renata; Gomes, Tânia Aparecida Tardelli; Vieira, Mônica Aparecida Midolli; da Silva Leite, Domingos; Blanco, Jesus E; Ferreira, Antônio José Piantino

    2012-01-01

    Escherichia coli sfa+ strains isolated from poultry were serotyped and characterized by polymerase chain reaction (PCR) and amplified fragment length polymorphism (AFLP). Isolates collected from 12 Brazilian poultry farms mostly belonged to serogroup O6, followed by serogroups O2, O8, O21, O46, O78, O88, O106, O111, and O143. Virulence genes associated were: iuc 90%, fim 86% neuS 60%, hly 34%, tsh 28%, crl/csg 26%, iss 26%, pap 18%, and 14% cnf. Strains from the same farm presented more than one genotypic pattern belonging to different profiles in AFLP. AFLP showed a clonal relation between Escherichia coli sfa+ serogroup O6. The virulence genes found in these strains reveal some similarity with extraintestinal E. coli (ExPEC), thus alerting for potential zoonotic risk.

  19. Chronic pancreatitis: a sequela of acute fatty liver of pregnancy.

    Science.gov (United States)

    Apiratpracha, Wichian; Yoshida, Eric M; Scudamore, Charles H; Charles, Scudamore H; Weiss, Alan A; Byrne, Michael F

    2008-02-01

    Chronic pancreatitis following acute fatty liver of pregnancy is rarely reported. We treated a 34-year-old woman who developed acute fatty liver of pregnancy (AFLP) after delivery by caesarean section at 32 weeks of gestation. AFLP was complicated by acute pancreatitis and multiple organ failure. The management of the disease was primarily supportive. She recovered from acute fulminant liver failure and multi-organ failure, apart from the development of symptomatic chronic pancreatitis thereafter. Investigations failed to identify any other causes of chronic pancreatitis. The patient responded very well to pancreatic enzyme supplement for the treatment of steatorrhoea. To our knowledge, this is the first report of chronic pancreatitis as a consequence of multi-organ dysfunction caused by AFLP.

  20. Durable resistance to net blotch and agronomic performance in some barley mutants [Hordeum vulgare L.; Syria

    International Nuclear Information System (INIS)

    Arabi, M.I.E.

    2004-01-01

    Seeds from the net blotch (Pyrenophora teres) susceptible cultivar Thibaut were treated by gamma ray radiation and subsequently evaluated for reaction to the pathogen in the M2-M5 generations. Grain yield and agronomic characteristics of putative mutants were compared with Thibaut in two different locations. Genetic variation among some mutant lines/cv Thibaut was estimated using Amplified Fragment Length Polymorphism (AFLP) markers. Sixteen mutant lines and their mother cultivar Thibaut were analyzed with 14 EcoR1-Mse1 primer combinations. A total number of 504 AFLP bands were analyzed for each pair mutant/Thibaut. Narrow genetic variation among all genotypes was detected with an average of genetic similarity of 0.96. Cluster analysis with the entire AFLP data divided all genotypes into two major groups. The resistant mutant lines were grouped in one subcluster with 0.98 similarity index. Some resistant mutant lines to net blotch with good agronomic performances were produced [it

  1. Nuclear markers reveal that inter-lake cichlids' similar morphologies do not reflect similar genealogy.

    Science.gov (United States)

    Kassam, Daud; Seki, Shingo; Horic, Michio; Yamaoka, Kosaku

    2006-08-01

    The apparent inter-lake morphological similarity among East African Great Lakes' cichlid species/genera has left evolutionary biologists asking whether such similarity is due to sharing of common ancestor or mere convergent evolution. In order to answer such question, we first used Geometric Morphometrics, GM, to quantify morphological similarity and then subsequently used Amplified Fragment Length Polymorphism, AFLP, to determine if similar morphologies imply shared ancestry or convergent evolution. GM revealed that not all presumed morphological similar pairs were indeed similar, and the dendrogram generated from AFLP data indicated distinct clusters corresponding to each lake and not inter-lake morphological similar pairs. Such results imply that the morphological similarity is due to convergent evolution and not shared ancestry. The congruency of GM and AFLP generated dendrograms imply that GM is capable of picking up phylogenetic signal, and thus GM can be potential tool in phylogenetic systematics.

  2. High-resolution genotyping of Listeria monocytogenes by fluorescent amplified fragment length polymorphism analysis compared to pulsed-field gel electrophoresis, random amplified polymorphic DNA analysis, ribotyping, and PCR-restriction fragment length polymorphism analysis

    DEFF Research Database (Denmark)

    Vogel, Birte Fonnesbech; Fussing, V.; Ojeniyi, B.

    2004-01-01

    The purpose of this study was to evaluate fluorescent amplified fragment length polymorphism (AFLP) analysis for the inter- and intraspecies differentiation of a collection of 96 strains of Listeria monocytogenes and 10 non- L. monocytogenes strains representing six other Listeria species...... of different origin. The AFLP technique was compared with three other molecular typing methods - ribotyping, random amplified polymorphic DNA analysis (RAPD), and pulsed-field gel electrophoresis (PFGE) - in terms of discriminatory ability. PCR-restriction fragment length polymorphism was included....... Isolates with identical DNA profiles were distributed across the spectrum of origin. It was not possible to associate certain types with specific food sectors or clinical cases, which is indicative of the spread of L. monocytogenes clones across species. Overall, AFLP fingerprinting was suitable...

  3. Molecular epidemiological analysis of Mycoplasma bovis isolates from the United Kingdom shows two genetically distinct clusters

    DEFF Research Database (Denmark)

    McAuliffe, Laura; Kokotovic, Branko; Ayling, Roger D.

    2004-01-01

    polymorphism (AFLP), and random amplified polymorphic DNA (RAPD) analysis. In addition, the influence of variable surface protein (Vsp) profiles on the profiles generated with molecular typing techniques was studied. Both AFLP and RAPD separated the isolates into two distinct groups, but PFGE showed less......Mycoplasma bovis is an important veterinary pathogen causing pneumonia, arthritis, and mastitis in infected cattle. We investigated the genetic diversity of 53 isolates collected in the United Kingdom between 1996 and 2002 with pulsed-field gel electrophoresis (PFGE), amplified fragment length...... congruence with the other techniques. There was no clear relationship between the geographic origin or year of isolation of the isolates and the profiles produced. No correlation between Vsp profiles and any of the molecular typing techniques was observed. We propose that RAPD and AFLP provide valuable tools...

  4. Prevalence of Avian Pathogenic Escherichia coli (APEC Clone Harboring sfa Gene in Brazil

    Directory of Open Access Journals (Sweden)

    Terezinha Knöbl

    2012-01-01

    Full Text Available Escherichia coli sfa+ strains isolated from poultry were serotyped and characterized by polymerase chain reaction (PCR and amplified fragment length polymorphism (AFLP. Isolates collected from 12 Brazilian poultry farms mostly belonged to serogroup O6, followed by serogroups O2, O8, O21, O46, O78, O88, O106, O111, and O143. Virulence genes associated were: iuc 90%, fim 86% neuS 60%, hly 34%, tsh 28%, crl/csg 26%, iss 26%, pap 18%, and 14% cnf. Strains from the same farm presented more than one genotypic pattern belonging to different profiles in AFLP. AFLP showed a clonal relation between Escherichia coli sfa+ serogroup O6. The virulence genes found in these strains reveal some similarity with extraintestinal E. coli (ExPEC, thus alerting for potential zoonotic risk.

  5. Genetic diversity and relationship of Hedychium from Northeast India as dissected using PCA analysis and hierarchical clustering.

    Science.gov (United States)

    Basak, Supriyo; Ramesh, Aadi Moolam; Kesari, Vigya; Parida, Ajay; Mitra, Sudip; Rangan, Latha

    2014-12-01

    Molecular genetic fingerprints of eleven Hedychium species from Northeast India were developed using PCR based markers. Fifteen inter-simple sequence repeats (ISSRs) and five amplified fragment length polymorphism (AFLP) primers produced 547 polymorphic fragments. Positive correlation (r = 0.46) was observed between the mean genetic similarity and genetic diversity parameters at the inter-species level. AFLP and ISSR markers were able to group the species according to its altitude and intensity of flower aroma. Cophenetic correlation coefficients between the dendrogram and the original similarity matrix were significant for ISSR (r = 0.89) compared to AFLP (r = 0.83) markers. This genetic characterization of Hedychium from Northeast India contributes to the knowledge of genetic structure of the species and can be used to define strategies for their conservation and management.

  6. Using high-throughput DNA sequencing, genetic fingerprinting, and quantitative PCR as tools for monitoring bloom-forming and toxigenic cyanobacteria in Upper Klamath Lake, Oregon, 2013 and 2014

    Science.gov (United States)

    Caldwell Eldridge, Sara L.; Driscoll, Conner; Dreher, Theo W.

    2017-06-05

    Monitoring the community structure and metabolic activities of cyanobacterial blooms in Upper Klamath Lake, Oregon, is critical to lake management because these blooms degrade water quality and produce toxic microcystins that are harmful to humans, domestic animals, and wildlife. Genetic tools, such as DNA fingerprinting by terminal restriction fragment length polymorphism (T-RFLP) analysis, high-throughput DNA sequencing (HTS), and real-time, quantitative polymerase chain reaction (qPCR), provide more sensitive and rapid assessments of bloom ecology than traditional techniques. The objectives of this study were (1) to characterize the microbial community at one site in Upper Klamath Lake and determine changes in the cyanobacterial community through time using T-RFLP and HTS in comparison with traditional light microscopy; (2) to determine relative abundances and changes in abundance over time of toxigenic Microcystis using qPCR; and (3) to determine relative abundances and changes in abundance over time of Aphanizomenon, Microcystis, and total cyanobacteria using qPCR. T-RFLP analysis of total cyanobacteria showed a dominance of only one or two distinct genotypes in samples from 2013, but results of HTS in 2013 and 2014 showed more variations in the bloom cycle that fit with the previous understanding of bloom dynamics in Upper Klamath Lake and indicated that potentially toxigenic Microcystis was more prevalent in 2014 than in years prior. The qPCR-estimated copy numbers of all target genes were higher in 2014 than in 2013, when microcystin concentrations also were higher. Total Microcystis density was shown with qPCR to be a better predictor of late-season increases in microcystin concentrations than the relative proportions of potentially toxigenic cells. In addition, qPCR targeting Aphanizomenon at one site in Upper Klamath Lake indicated a moderate bloom of this species (corresponding to chlorophyll a concentrations between approximately 75 and 200 micrograms

  7. Changes in the rumen bacterial community in response to sunflower oil and fish oil supplements in the diet of dairy sheep.

    Science.gov (United States)

    Belenguer, A; Toral, P G; Frutos, P; Hervás, G

    2010-07-01

    Rumen microbial biohydrogenation of dietary unsaturated fatty acids has a major effect on the process of developing healthier dairy products. This study aimed to investigate in vivo the effect of diet supplementation with sunflower (SO) and fish (FO) oils on the rumen bacterial community in dairy sheep. First, 32 lactating ewes, divided in 8 lots of 4 animals each (2 lots per treatment), were fed a high-concentrate total mixed ration supplemented with 0, 2% SO, 1% FO, or 2% SO plus 1% FO. After 21 d, rumen fluid samples were taken from each lot for DNA extraction and fluorescence in situ hybridization (FISH) analysis. In a second experiment, 5 cannulated ewes were first fed the same TMR, with the exception of a higher forage level, and then changed to the same diet supplemented with 2% SO plus 1% FO. After 0, 3, and 10 d, rumen content samples were taken for DNA extraction and FISH analysis (fluid). Total bacteria and the Butyrivibrio group were studied in microbial DNA by terminal RFLP analysis (T-RFLP), and real-time PCR was used to quantify Butyrivibrio bacteria that produce vaccenic acid or stearic acid. In rumen fluid samples, total bacteria and clostridial clusters IX and XIV were analyzed by FISH. Dietary supplementation with SO plus FO seemed to induce important changes in the total bacteria and Butyrivibrio populations, and a high interindividual variation was observed, and the speed of the effect of the lipid supplementation depended on the individual microbial composition. Analysis by T-RFLP and FISH showed increases in cluster IX bacteria with SO plus FO supplementation, presumably Quinella-like microorganisms. The abundances of vaccenic acid- and stearic acid-producing Butyrivibrio relative to total bacteria, estimated by real time PCR, were low (0.28 and 0.18%, respectively, in rumen fluid, and 0.86 and 0.81% in rumen contents) and only that of SA-producing bacteria seemed to be reduced by diets containing FO, although differences were only

  8. Molecular genetics and diversity of primary biogenic aerosol particles in urban, rural, and high-alpine air

    Science.gov (United States)

    Després, V.; Nowoisky, J.; Klose, M.; Conrad, R.; Andreae, M. O.; Pöschl, U.

    2007-02-01

    This study explores the applicability of molecular methods for the characterization of primary biogenic aerosol (PBA) particles in the atmosphere. Samples of fine particulate matter (PM2.5) and total suspended particulates (TSP) have been collected on different types of filter materials at urban, rural, and high-alpine locations along an altitude transect in the south of Germany (Munich, Hohenpeissenberg, Mt. Zugspitze). From filter aliquots loaded with about one milligram of air particulate matter, DNA could be extracted and DNA sequences could be determined for bacteria, fungi, plants and animals. Sequence analyses were used to determine the identity of biological organisms, and terminal restriction length polymorphism analyses (T-RFLP) were applied to estimate diversities and relative abundances of bacteria. Investigations of blank and background samples showed that filter materials have to be decontaminated prior to use, and that the sampling and handling procedures have to be carefully controlled to avoid artifacts in the analyses. Mass fractions of DNA in PM2.5 were found to be around 0.05% in urban, rural, and high alpine aerosols. The average concentration of DNA determined for urban air was on the order of ~7 ng m-3, indicating that human adults may inhale about one microgram of DNA per day (corresponding to ~105 haploid human genomes). Most of the bacterial sequences found in PM2.5 were from Proteobacteria (42) and some from Actinobacteria (10) and Firmicutes (1). The fungal sequences were characteristic for Ascomycota (3) and Basidiomycetes (1), which are known to actively discharge spores into the atmosphere. The plant sequences could be attributed to green plants (2) and moss spores (2), while animal DNA was found only for one unicellular eukaryote (protist). Over 80% of the 53 bacterial sequences could be matched with about 40% of the 19 T-RF peaks (58 to 494 base pair length) found in the investigated PM2.5 samples. The results demonstrate that the T-RFLP

  9. Characterization of primary biogenic aerosol particles in urban, rural, and high-alpine air by DNA sequence and restriction fragment analysis of ribosomal RNA genes

    Science.gov (United States)

    Després, V. R.; Nowoisky, J. F.; Klose, M.; Conrad, R.; Andreae, M. O.; Pöschl, U.

    2007-12-01

    This study explores the applicability of DNA analyses for the characterization of primary biogenic aerosol (PBA) particles in the atmosphere. Samples of fine particulate matter (PM2.5) and total suspended particulates (TSP) have been collected on different types of filter materials at urban, rural, and high-alpine locations along an altitude transect in the south of Germany (Munich, Hohenpeissenberg, Mt. Zugspitze). From filter segments loaded with about one milligram of air particulate matter, DNA could be extracted and DNA sequences could be determined for bacteria, fungi, plants and animals. Sequence analyses were used to determine the identity of biological organisms, and terminal restriction fragment length polymorphism analyses (T-RFLP) were applied to estimate diversities and relative abundances of bacteria. Investigations of blank and background samples showed that filter materials have to be decontaminated prior to use, and that the sampling and handling procedures have to be carefully controlled to avoid artifacts in the analyses. Mass fractions of DNA in PM2.5 were found to be around 0.05% in urban, rural, and high-alpine aerosols. The average concentration of DNA determined for urban air was on the order of ~7 ng m-3, indicating that human adults may inhale about one microgram of DNA per day (corresponding to ~108 haploid bacterial genomes or ~105 haploid human genomes, respectively). Most of the bacterial sequences found in PM2.5 were from Proteobacteria (42) and some from Actinobacteria (10) and Firmicutes (1). The fungal sequences were characteristic for Ascomycota (3) and Basidiomycota (1), which are known to actively discharge spores into the atmosphere. The plant sequences could be attributed to green plants (2) and moss spores (2), while animal DNA was found only for one unicellular eukaryote (protist). Over 80% of the 53 bacterial sequences could be matched to one of the 19 T-RF peaks found in the PM2.5 samples, but only 40% of the T-RF peaks

  10. Selection of a seed orchard of Eucalyptus dunnii based on genetic diversity criteria calculated using molecular markers.

    Science.gov (United States)

    Marcucci Poltri, S N; Zelener, N; Rodriguez Traverso, J; Gelid, P; Hopp, H E

    2003-06-01

    A Eucalyptus dunnii Maiden breeding population of 46 accessions originated in Australia and selected for fitness to subtropical and cold environments was screened by Amplified Fragment Length Polymorphism (AFLP) and microsatellite markers to obtain quantitative estimates of genetic diversity. A randomly chosen group of AFLP primers generated 205 AFLP bands that were used to fingerprint the genotypes and to evaluate genetic relationships among accessions. Sixty-eight percent (140) of the bands were polymorphic markers. The mean diversity index (DI) was 0.33 and about 52% of the loci had values greater than 0.4. Cluster analysis derived from similarity indices (SI) revealed no particular grouping among accessions suggesting the absence of closely related genotypes, except for five pairs of genotypes. Bootstrap analysis results confirmed the suitability of AFLP to describe genetic relationships in this breeding population. In addition, four highly informative microsatellites were used to construct an identification matrix that discriminated nearly all of the genotypes. Mean values for the number of alleles per locus, DI and SI among accessions were 13, 0.78 and 0.19, respectively, indicating that the breeding population has high genetic diversity. However, several genotypes showed the presence of single microsatellite bands suggesting a putatively important degree of homozygosity. Molecular data were used to design a clonal seed orchard. To achieve this aim, the nine most divergent pairs of genotypes were chosen, thereby retaining 95.2% of the total number of alleles from the 140 polymorphic AFLP loci and the four microsatellite loci analyzed. Mean DI and SI for AFLP and microsatellites showed no significant differences between the original breeding population and the selected seed orchard, confirming that a seed orchard can be designed with a limited number of individuals, which allows similar accessions to be discarded and avoids inbreeding.

  11. Cryptococcus neoformans population diversity and clinical outcomes of HIV-associated cryptococcal meningitis patients in Zimbabwe.

    Science.gov (United States)

    Nyazika, Tinashe K; Hagen, Ferry; Machiridza, Tendai; Kutepa, Melody; Masanganise, Faith; Hendrickx, Marijke; Boekhout, Teun; Magombei-Majinjiwa, Tricia; Siziba, Nonthokozo; Chin'ombe, Nyasha; Mateveke, Kudzanai; Meis, Jacques F; Robertson, Valerie J

    2016-11-01

    HIV and cryptococcal meningitis co-infection is a major public health problem in most developing countries. Cryptococcus neoformans sensu stricto is responsible for the majority of HIV-associated cryptococcosis cases in sub-Saharan Africa. Despite the available information, little is known about cryptococcal population diversity and its association with clinical outcomes in patients with HIV-associated cryptococcal meningitis in sub-Saharan Africa. In a prospective cohort, we investigated the prevalence and clinical outcome of Cryptococcusneoformans sensu stricto meningitis among HIV-infected patients in Harare, Zimbabwe, and compared the genotypic diversity of the isolates with those collected from other parts of Africa. Molecular typing was done using amplified fragment length polymorphism genotyping and microsatellite typing. The majority of patients with HIV-associated Cryptococcusneoformans sensu stricto meningitis in this cohort were males (n=33/55; 60.0 %). The predominant Cryptococcus neoformans sensu stricto genotype among the Zimbabwean isolates was genotype AFLP1/VNI (n=40; 72.7 %), followed by AFLP1A/VNB/VNII (n=8; 14.6 %), and AFLP1B/VNII was the least isolated (n=7; 12.7 %). Most of the isolates were mating-type α (n=51; 92.7 %), and only four (7.3 %) were mating-type a. Overall in-hospital mortality was 55.6 % (n=30), and no difference between infecting genotype and clinical outcome of patient (P=0.73) or CD4+ counts (P=0.79) was observed. Zimbabwean Cryptococcusneoformans sensu stricto genotypes demonstrated a high level of genetic diversity by microsatellite typing, and 51 genotypes within the main molecular types AFLP1/VNI, AFLP1A/VNB/VNII and AFLP1B/VNII were identified. This study demonstrates that Cryptococcusneoformans sensu stricto in Zimbabwe has a high level of genetic diversity when compared to other regional isolates.

  12. DNA methylation increases throughout Arabidopsis development.

    Science.gov (United States)

    Ruiz-García, L; Cervera, M T; Martínez-Zapater, J M

    2005-10-01

    We used amplified fragment length polymorphisms (AFLP) to analyze the stability of DNA methylation throughout Arabidopsis development. AFLP can detect genome-wide changes in cytosine methylation produced by DNA demethylation agents, such as 5-azacytidine, or specific mutations at the DDM1 locus. In both cases, cytosine demethylation is associated with a general increase in the presence of amplified fragments. Using this approach, we followed DNA methylation at methylation sensitive restriction sites throughout Arabidopsis development. The results show a progressive DNA methylation trend from cotyledons to vegetative organs to reproductive organs.

  13. Amplified-fragment length polymorphism fingerprinting of Mycoplasma species

    DEFF Research Database (Denmark)

    Kokotovic, Branko; Friis, N.F.; Jensen, J.S.

    1999-01-01

    Amplified-fragment length polymorphism (AFLP) is a whole-genome fingerprinting method based on selective amplification of restriction fragments. The potential of the method for the characterization of mycoplasmas was investigated in a total of 50 strains of human and animal origin, including......I restriction endonucleases and subsequent ligation of corresponding site-specific adapters. The amplification of AFLP templates with a single set of nonselective primers resulted in reproducible fingerprints of approximately 60 to 80 fragments in the size range of 50 to 500 bp, The method was able...

  14. High-resolution genotyping of Listeria monocytogenes by fluorescent amplified fragment length polymorphism analysis compared to pulsed-field gel electrophoresis, random amplified polymorphic DNA analysis, ribotyping, and PCR-restriction fragment length polymorphism analysis

    DEFF Research Database (Denmark)

    Vogel, Birte Fonnesbech; Fussing, V.; Ojeniyi, B.

    2004-01-01

    of different origin. The AFLP technique was compared with three other molecular typing methods - ribotyping, random amplified polymorphic DNA analysis (RAPD), and pulsed-field gel electrophoresis (PFGE) - in terms of discriminatory ability. PCR-restriction fragment length polymorphism was included...... for virulence gene allele characterization. The 96 L. monocytogenes strains were divided into two major clusters by AFLP fingerprinting at a similarity level of 82% in concordance with the results of PFGE, RAPD, and ribotyping. One main cluster consisted of all of the 24 L. monocytogenes hly allele 1 strains...

  15. Methane emission and community composition patterns of rumen bacteria and methanogens in Holstein dairy cows as affected by silage type and dietary fat

    DEFF Research Database (Denmark)

    Poulsen, Morten; Højberg, Ole; Canibe, Nuria

    Silage type and dietary fat supplementation can affect enteric methane (CH4) emissions from dairy cows. However, the impact of dietary interventions on the rumen microbiota is still not fully understood. The present study used six rumen cannulated Holstein cows (6x4 incomplete Latin Square......) to investigate effects of silages with different methanogenic potential (early grass, late grass, and maize) combined with a CH4-reducing feed additive (crushed rapeseed) on bacterial and methanogenic communities in the rumen. Bacterial and methanogenic community patterns were evaluated by T-RFLP analysis of 16S...... rRNA and methyl co-enzyme M reductase (mcrA) genes, respectively. Methanogen abundances were evaluated by qPCR using two mcrA-targeting primer sets. Silage type significantly affected CH4 emissions and rumen acetate:propionate ratios, being highest for late grass and lowest for maize. Dietary fat...

  16. Effect of β-glucanase and xylanase supplementation of barley- and rye-based diets on caecal microbiota of broiler chickens

    DEFF Research Database (Denmark)

    Josefiak, Damian; Rutkowski, A; Kaczmarek, S

    2010-01-01

    fragment-length polymorphism (T-RFLP)). 2. Plate counting revealed higher total numbers of anaerobic bacteria, lactic acid bacteria and yeasts in caecal contents of birds fed with rye-based diets than in birds fed with barley-based diets. 3. As assessed by FISH analysis, the most abundant bacterial groups......1. The aim was to investigate the effect of grain type (barley or rye) and exogenous enzymes (β-glucanase or xylanase) on the composition of chicken caecal microbiota as examined by classical culturing and molecular techniques (fluorescent in-situ hybridisation (FISH) and terminal-restriction......-RFLP profiles indicated that the caecal microbiota of birds receiving rye-based diets was more diverse than that of birds fed on barley-based diets. 5. Irrespective of the method applied, the results indicate that the cereal type as well as the exogenous enzyme supplementation influence the microbiota...

  17. Impact of chloride on denitrification potential in roadside wetlands.

    Science.gov (United States)

    Lancaster, Nakita A; Bushey, Joseph T; Tobias, Craig R; Song, Bongkeun; Vadas, Timothy M

    2016-05-01

    Developed landscapes are exposed to changes in hydrology and water chemistry that limit their ability to mitigate detrimental impacts to coastal water bodies, particularly those that result from stormwater runoff. The elevated level of impervious cover increases not only runoff but also contaminant loading of nutrients, metals, and road salt used for deicing to water bodies. Here we investigate the impact that road salt has on denitrification in roadside environments. Sediments were collected from a series of forested and roadside wetlands and acclimated with a range of Cl(-) concentrations from 0 to 5000 mg L(-1) for 96 h. Denitrification rates were measured by the isotope pairing technique using (15)N-NO3(-), while denitrifying community structures were compared using terminal restriction fragment length polymorphism (T-RFLP) of nitrous oxide reductase genes (nosZ). Chloride significantly (p removal rates. Copyright © 2016 Elsevier Ltd. All rights reserved.

  18. A new assay based on terminal restriction fragment length polymorphism of homocitrate synthase gene fragments for Candida species identification.

    Science.gov (United States)

    Szemiako, Kasjan; Śledzińska, Anna; Krawczyk, Beata

    2017-08-01

    Candida sp. have been responsible for an increasing number of infections, especially in patients with immunodeficiency. Species-specific differentiation of Candida sp. is difficult in routine diagnosis. This identification can have a highly significant association in therapy and prophylaxis. This work has shown a new application of the terminal restriction fragment length polymorphism (t-RFLP) method in the molecular identification of six species of Candida, which are the most common causes of fungal infections. Specific for fungi homocitrate synthase gene was chosen as a molecular target for amplification. The use of three restriction enzymes, DraI, RsaI, and BglII, for amplicon digestion can generate species-specific fluorescence labeled DNA fragment profiles, which can be used to determine the diagnostic algorithm. The designed method can be a cost-efficient high-throughput molecular technique for the identification of six clinically important Candida species.

  19. Antimicrobial drimane sesquiterpenes and their effect on endophyte communities in the medical tree Warburgia ugandensis

    Directory of Open Access Journals (Sweden)

    Sigrid eDrage

    2014-02-01

    Full Text Available Metabolite profiles (GC–MS, drimane sesquiterpenes, sugars and sugar alcohols, were compared with bacterial and fungal endophyte communities (T-RFLP, DNA clones, qPCR in leaves and roots of the pepper bark tree, Warburgia ugandensis (Canellaceae. Ten individuals each were assessed from two locations east and west of the Great Rift Valley, Kenya, Africa, which differed in humidity and vegetation, closed forest versus open savannah. Despite organ- and partially site-specific variation of drimane sesquiterpenes, no clear effects on bacterial and fungal endophyte communities could be detected. The former were dominated by gram-negative Gammaproteobacteria, Pseudomonadaceae and Enterobacteriaceae, as well as gram-positive Firmicutes; the fungal endophyte communities were more diverse but no specific groups dominated. Despite initial expectations, the endophyte community of the pepper bark tree did not differ from other trees that much.

  20. Bioremediation strategies of hydrocarbons and microbial diversity in the Trindade Island shoreline--Brazil.

    Science.gov (United States)

    Rodrigues, Edmo M; Kalks, Karlos H M; Fernandes, Péricles L; Tótola, Marcos R

    2015-12-30

    This study analyzed the microbial diversity colonizing the surface of an oil sample during its contact with water, off the Trindade Island coast and simulated the efficiency of eight different bioremediation strategies for this environment. The diversity analysis was performed using acrylic coupons that served as the support for an oil inclusion at sea. The coupons were sampled over 30 days, and T-RFLP multiplex was employed to access the diversity of fungi, Bacteria and Archaea present on the oil surface. The bioremediation strategies were simulated in a respirometer. The results showed that the bacterial domain was the most dominant in oil colonization and that the richness of the species attached to the oil gradually increases with the exposure time of the coupons. The combination of biostimulation and bioaugmentation with a native population was proven to be an effective strategy for the remediation of oil off the Trindade Island shoreline. Copyright © 2015 Elsevier Ltd. All rights reserved.