References of "Grubisic, Stana"
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See detailStructuring effects of climate-related environmental factors on Antarctic microbial mat communities
Verleyen, Elie; Sabbe, Koen; Hodgson, Dominic A et al

in Aquatic Microbial Ecology (2010), 59

Both ground-based and satellite data show that parts of Antarctica have entered a period of rapid climate change, which already affects the functioning and productivity of limnetic ecosystems. To predict ... [more ▼]

Both ground-based and satellite data show that parts of Antarctica have entered a period of rapid climate change, which already affects the functioning and productivity of limnetic ecosystems. To predict the consequences of future climate anomalies for lacustrine microbial communities, we not only need better baseline information on their biodiversity but also on the climaterelated environmental factors structuring these communities. Here we applied denaturing gradient gel electrophoresis (DGGE) of the small subunit ribosomal DNA (SSU rDNA) to assess the genetic composition and distribution of Cyanobacteria and eukaryotes in 37 benthic microbial mat samples from east Antarctic lakes. The lakes were selected to span a wide range of environmental gradients governed by differences in lake morphology and chemical limnology across 5 ice-free oases. Sequence analysis of selected DGGE bands revealed a high degree of potential endemism among the Cyanobacteria (mainly represented by Oscillatoriales and Nostocales), and the presence of a variety of protists (alveolates, stramenopiles and green algae), fungi, tardigrades and nematodes, which corroborates previous microscopy-based observations. Variation partitioning analyses revealed that the microbial mat community structure is largely regulated by both geographical and local environmental factors of which salinity (and related variables), lake water depth and nutrient concentrations are of major importance. These 3 groups of environmental variables have previously been shown to change drastically in Antarctica in response to climate change. Together, these results have obvious consequences for predicting the trajectory of biodiversity under changing climate conditions and call for the continued assessment of the biodiversity of these unique ecosystems. [less ▲]

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See detailSeasonal cyanobacterial dynamics in a mesoeutrophic reservoir: microscopic counts and DGGE (Denaturing Gradient Gel Electrophoresis)
Willame, Raphael; Boutte, Christophe; Grubisic, Stana ULg et al

in Algological Studies (2009), 129

The seasonal planktic cyanobacterial dynamics was assessed during the year 2000 by microscopic and DGGE techniques, on the basis of 22 samples collected from the Haute-Sûre reservoir (Grand-Duchy of ... [more ▼]

The seasonal planktic cyanobacterial dynamics was assessed during the year 2000 by microscopic and DGGE techniques, on the basis of 22 samples collected from the Haute-Sûre reservoir (Grand-Duchy of Luxembourg). Microscopic investigations were carried out according to the standard Utermöhl procedure while 16S rRNA gene fragments obtained by semi-nested PCR were subsequently separated by DGGE. Sequencing of selected excised bands was performed to genotypically define the cyanobacterial assemblages. The dynamics of cyanobacterial communities obtained by both approaches were compared. Several discordances were pointed out. The counting procedure failed to detect cyanobacteria with small dimensions or in very low abundances, whereas DGGE had a lower detection limit when cyanobacteria were scarce (e.g. in spring) and performed better for the study of picosized forms. Generally, only the dominant cyanobacteria were revealed by these two methods. Actually, both techniques appeared to be complementary rather than equivalent. This study underlines the necessity to use multidisciplinary approaches to obtain a more complete view of the microbial diversity and of the community structure [less ▲]

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See detailDiversity of planktonic cyanobacteria and microcystin occurrence in Polish water bodies investigated using a polyphasic approach
Boutte, Christophe; Mankiewicz-Boczek, Joanna; Komarkova, Jarka et al

in Aquatic Microbial Ecology (2008), 51

Microscopic measurements of fresh biomass and 16S rRNA gene sequences from clone libraries and denaturing gradient gel electrophoresis (DGGE) were used to investigate cyanobacterial diversity in Polish ... [more ▼]

Microscopic measurements of fresh biomass and 16S rRNA gene sequences from clone libraries and denaturing gradient gel electrophoresis (DGGE) were used to investigate cyanobacterial diversity in Polish water bodies in 2002. In addition, measurements of microcystin (MC) concentrations were made. Thirty water samples were taken from 11 water bodies; of these samples, 18 were obtained from the Sulejow Reservoir during regular monitoring from June to October. Intraand extracellular MC concentrations in Sulejow samples were measured by high performance liquid chromatography (HPLC). The extracellular MC concentration was assessed using a protein phosphatase inhibition assay (PPIA) in additional lakes. Additionally, physicochemical parameters were measured (total nitrogen [TN], total phosphorus [TP], TN:TP ratio, chlorophyll a concentration, temperature). In Sulejow, high intracellular MC concentrations corresponded to large cyanobacterial biovolumes and to low TN:TP ratios. In the other lakes, extracellular MCs were not linked to any measured parameters. The combination of the microscopic and molecular data showed that Aphanizomenon and Microcystis were the dominant genera during the summer period in the Sulejow Reservoir. At the genetic level, there was a succession of 2 different operational taxonomic units (OTUs) belonging to the lineage Anabaena/Aphanizomenon. In the other water bodies, the most frequent populations were Aphanizomenon, Anabaena, Microcystis and Planktothrix. Small populations of Romeria, Snowella, Woronichinia, Limnothrix and Pseudanabaena were observed, and an enigmatic cluster affiliated with Prochlorothrix was genetically retrieved. Anabaena and Microcystis were presumed to be the main genera responsible for the MC production. [less ▲]

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See detailAdsorption Properties of the Penicillin Derivative DTPA on Gold Substrates
Dreesen, Laurent ULg; Silien, Christophe; Volcke, Cédric et al

in Chemphyschem : A European Journal of Chemical Physics and Physical Chemistry (2007), 8(7), 1071-1076

Despite the large number of articles and patents dealing with penicillin and other b-lactam antibiotics, there have been no reports about the self-assembly of such substances as monolayers on gold ... [more ▼]

Despite the large number of articles and patents dealing with penicillin and other b-lactam antibiotics, there have been no reports about the self-assembly of such substances as monolayers on gold surfaces. The main reason stems from the high reactivity of the b-lactam ring, which hinders the development of molecules possessing this entity together with a metal-anchoring function. Herein, we present the synthesis of a novel molecule, 6-[(R,S)-5-(1,2-dithiolan-3-yl)pentanoyl-amino]-penicillanic acid, which combines the b-lactam ring and a metal-anchoring group. Using spectroscopic tools, we demonstrate the chemisorption of this compound on gold as self-assembled monolayers without any alteration of the penicillin pharmacophore and document its reactivity towards a penicillin-binding protein, BlaR-CTD. Our work is a preliminary step towards the development of new biosensors and well-ordered protein arrays, both based on the high affinity of penicillin for penicillin-binding proteins. [less ▲]

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See detailMorphological and molecular characterization of planktonic cyanobacteria from Belgium and Luxembourg
Willame, R.; Boutte, C.; Grubisic, Stana ULg et al

in Journal of Phycology (2006), 42(6), 1312-1332

For the first time in Belgium and Luxembourg, the diversity and taxonomy of 95 cyanobacterial strains isolated from freshwater blooms were assessed by the comparison of phenotypes and partial 16S rRNA ... [more ▼]

For the first time in Belgium and Luxembourg, the diversity and taxonomy of 95 cyanobacterial strains isolated from freshwater blooms were assessed by the comparison of phenotypes and partial 16S rRNA gene sequences. The results showed the high diversity of nanoplanktonic, picoplanktonic, and benthic-periphytic cyanobacteria accompanying the main bloom-forming taxa. Indeed, besides 15 morphotypes of bloom-forming taxa, seven non-bloom-forming planktonic morphotypes and 11 morphotypes from benthic-periphytic taxa were isolated in culture from the plankton samples of 35 water bodies. The bloom-forming strains belonged to the genera Microcystis, Woronichinia, Planktothrix, Anabaena, and Aphanizomenon, whereas the other strains isolated from the same samples were assigned to the nanoplanktonic Aphanocapsa, Aphanothece, Snowella, and Pseudanabaena; to the picoplanktonic Cyanobium; and to the benthic periphytic Geitlerinema, Komvophoron, Leptolyngbya, Lyngbya, Phormidium, Calothrix, Nostoc, and Trichormus. The results supported both the polyphyletism of genera such as Aphanocapsa, Aphanothece, Leptolyngbya, Geitlerinema, Anabaena, and Aphanizomenon as well as the validity of genera such as Microcystis, Planktothrix, and Pseudanabaena with gas vesicles and cells constricted at the cross wall. The results obtained showed the close relationship between Snowella and Woronichinia for which very few sequences exist. The first sequence of Komvophoron appeared poorly related to other available cyanobacterial sequences. Although in a few cases a good agreement existed between phenotypic and genotypic features, there was generally a discrepancy. Strains with identical morphotypes show small differences in the 16S rRNA sequences, which might be related to the different chemical properties of their habitats. The results showed the importance of the polyphasic approach in order to improve the taxonomy of cyanobacteria. [less ▲]

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See detailPolyphasic study of Antarctic cyanobacterial strains
Taton, A.; Grubisic, Stana ULg; Ertz, D. et al

in Journal of Phycology (2006), 42(6), 1257-1270

We isolated 59 strains of cyanobacteria from the benthic microbial mats of 23 Antarctic lakes, from five locations in two regions, in order to characterize their morphological and genotypic diversity. On ... [more ▼]

We isolated 59 strains of cyanobacteria from the benthic microbial mats of 23 Antarctic lakes, from five locations in two regions, in order to characterize their morphological and genotypic diversity. On the basis of their morphology, the cyanobacteria were assigned to 12 species that included four Antarctic endemic taxa. Sequences of the ribosomal RNA gene were determined for 56 strains. In general, the strains closely related at the 16S rRNA gene level belonged to the same morphospecies. Nevertheless, divergences were observed concerning the diversity in terms of species richness, novelty, and geographical distribution. For the 56 strains, 21 operational taxonomic units (OTUs, defined as groups of partial 16S rRNA gene sequences with more than 97.5% similarity) were found, including nine novel and three exclusively Antarctic OTUs. Sequences of Petalonema cf. involvens and Chondrocystis sp. were determined for the first time. The internally transcribed spacer (ITS) between the 16S and the 23S rRNA genes was sequenced for 33 strains, and similar groupings were observed with the 16S rRNA gene and the ITS, even when the strains were derived from different lakes and regions. In addition, 48 strains were screened for antimicrobial and cytotoxic activities, and 17 strains were bioactive against the gram-positive Staphylococcus aureus, or the fungi Aspergillus fumigatus and Cryptococcus neoformans. The bioactivities were not in coincidence with the phylogenetic relationships, but rather were specific to certain strains. [less ▲]

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See detailBiogeographical distribution and ecological ranges of benthic cyanobacteria in East Antarctic lakes
Taton, A.; Grubisic, Stana ULg; Balthasart, Pierre ULg et al

in FEMS Microbiology Ecology (2006), 57(2), 272-289

For the first time, the cyanobacterial diversity from microbial mats in lakes of Eastern Antarctica was investigated using microscopic and molecular approaches. The present study assessed the ... [more ▼]

For the first time, the cyanobacterial diversity from microbial mats in lakes of Eastern Antarctica was investigated using microscopic and molecular approaches. The present study assessed the biogeographical distribution of cyanobacteria in Antarctica. Five samples were taken from four lakes spanning a range of different ecological environments in Larsemann Hills, Vestfold Hills and Rauer Islands to evaluate the influence of lake characteristics on the cyanobacterial diversity. Seventeen morphospecies and 28 16S rRNA gene-based operational taxonomic units belonging to the Oscillatoriales, Nostocales and Chroococcales were identified. The internal transcribed spacer was evaluated to complement the 16S rRNA gene data and showed similar but more clear-cut tendencies. The molecular approach suggested that potential Antarctic endemic species, including a previously undiscovered diversity, are more abundant than has been estimated by morphological methods. Moreover, operational taxonomic units, also found outside Antarctica, were more widespread over the continent than potential endemics. The cyanobacterial diversity of the most saline lakes was found to differ from the others, and correlations between the sampling depth and the cyanobacterial communities can also be drawn. Comparison with database sequences illustrated the ubiquity of several cyanobacterial operational taxonomic units and their remarkable range of tolerance to harsh environmental conditions. [less ▲]

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See detailTesting of primers for the study of cyanobacterial molecular diversity by DGGE
Boutte, C.; Grubisic, Stana ULg; Balthasart, Pierre ULg et al

in Journal of Microbiological Methods (2006), 65(3), 542-550

Denaturing Gradient Gel electrophoresis (DGGE) is a PCR-based technique which is widely used in the study of microbial communities. Here, the use of the three specific 16S rRNA cyanobacterial specific ... [more ▼]

Denaturing Gradient Gel electrophoresis (DGGE) is a PCR-based technique which is widely used in the study of microbial communities. Here, the use of the three specific 16S rRNA cyanobacterial specific primers CYA359F, CYA781R(a) and CYA781R(b) on the assessment of the molecular diversity of cyanobacterial communities is examined. Assignments of the reverse primers CYA781R(a) and CYA781R(b) with cyanobacterial strain sequences showed that the former preferentially targets filamentous cyanobacteria whereas the latter targets unicellular cyanobacteria. The influence of the GC clamp position on the forward Or on reverse primer and the use of the two reverse primers separately or in equimolar mixture were investigated. Three environmental samples were subjected to amplification with 6 combinations of primers. The 6 banding patterns as well as the sequences of the bands extracted were analysed and compared. In addition, to assess the effect of the position of the GC clamp, the melting profiles of the sequences of Aphanizomenon flos-aquae PMC9707 and Synechococcus sp. MH305 were determined, with the GC clamp in the 3' or 5' position. Results showed that the use of two separate amplifications allowed a more complete study of the molecular diversity of the cyanobacterial community investigated. Furthermore, similar richness and identical phylogenctic assignments of extracted bands were obtained irrespective of the positioning of the GC clamp. (c) 2005 Elsevier B.V. All rights reserved. [less ▲]

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See detailA polyphasic approach to assess the cyanobacterial diversity of summer samples from Czech reservoirs
Boutte, Christophe; Komarkova, Jarka; Grubisic, Stana ULg et al

in Algological Studies (2005), 117

We used a polyphasic approach combining data from microscopic assessment of fresh biomass and from clone libraries and DGGE fingerprints based on 16S rRNA gene sequences to investigate the cyanobacterial ... [more ▼]

We used a polyphasic approach combining data from microscopic assessment of fresh biomass and from clone libraries and DGGE fingerprints based on 16S rRNA gene sequences to investigate the cyanobacterial diversity of Czech reservoirs during the summer in 2001 and 2002. In total, 15 genera were identified using the microscopic analysis in 38 samples analysed. They were Aphanizomenon, Anabaena, Anabaenopsis, Aphanocapsa, Aphanothece, Pseudanabaena, Planktothrix, Planktolyngbya, Limnothrix, Woronichinia, Snowella, Romeria, Microcystis, Merismopedia, and Coelomoron. We recovered 113 DGGE band sequences from the same samples. In addition, 128 partial 16S rRNA sequences were obtained from two clone libraries of reservoirs Pilská and Orlík. The phylogenetic comparison with the currently available rRNA sequences in databases showed that our sequences belonged to 8 clusters: Woronichinia, Microcystis, Synechococcus, Snowella, Planktothrix, Anabaena/Aphanizomenon, Limnothrix and a plastid related to Chrysochromulina polylepis. The microscopic enumeration and the molecular results were generally congruent concerning the major populations determined in these samples (for 32 samples among 38). Anabaena/Aphanizomenon, Microcystis and Woronichinia were the major genera in the Czech reservoirs during summer, and were present in most of the samples. This study showed some discrepancies between the genera retrieved by the traditional method and the molecular analyses. Differences concerned the presence of minor populations belonging to Aphanothece, Romeria, Merismopedia, Synechococcus, Snowella and Pseudanabena. These differences could be explained by biases specific to each method (competitive amplification, difficulty to obtain sequences from DGGE bands, not precise microscopic observation of the small-sized genera). [less ▲]

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See detail(WO/2004/104211) METHOD FOR DETECTING TOXIC AND NON-TOXIC CYANOBACTERIA
SIVONEN, Kaarina; RANTALA, Anne; Rouhianen, Leo et al

Patent (2004)

This invention is related to a method for detecting toxic and non-toxic cyanobacteria. The method comprises that nucleic acid from a biological sample is brought into contact with an oligonucleotide ... [more ▼]

This invention is related to a method for detecting toxic and non-toxic cyanobacteria. The method comprises that nucleic acid from a biological sample is brought into contact with an oligonucleotide designed to be specific for particular regions of the mcyE gene, the mcyE in combination with mcyD, and with an oligonucleotide designed to be specific for 16SrDNA, and the presence or absence of toxic cyanobacteria is detected by a suitable molecular biology method. The invention is related also to oligonucleotides used in the method. [less ▲]

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See detailDevelopment of a universal microarray based on the ligation detection reaction and 16S rRNA gene polymorphism to target diversity of cyanobacteria
Castiglioni, Bianca; Rizzi, Ermann; Frosini, Andrea et al

in Applied and Environmental Microbiology (2004), 70(12), 7161-7172

The cyanobacteria are photosynthetic prokaryotes of significant ecological and biotechnological interest, since they strongly contribute to primary production and are a rich source of bioactive compounds ... [more ▼]

The cyanobacteria are photosynthetic prokaryotes of significant ecological and biotechnological interest, since they strongly contribute to primary production and are a rich source of bioactive compounds. In eutrophic fresh and brackish waters, their mass occurrences (water blooms) are often toxic and constitute a high potential risk for human health. Therefore, rapid and reliable identification of cyanobacterial species in complex environmental samples is important. Here we describe the development and validation of a microarray for the identification of cyanobacteria in aquatic environments. Our approach is based on the use of a ligation detection reaction coupled to a universal array. Probes were designed for detecting 19 cyanobacterial groups including Anabaena/Aphanizomenon, Calothrix, Cylindrospermopsis, Cylindrospermum, Gloeothece, halotolerants, Leptolyngbya, Palau Lyngbya, Microcystis, Nodularia, Nostoc, Planktothrix, Antarctic Phormidium, Prochlorococcus, Spirulina, Synechococcus, Synechocystis, Trichodesmium, and Woronichinia. These groups were identified based on an alignment of over 300 cyanobacterial 16S rRNA sequences. For validation of the microarrays, 95 samples (24 axenic strains from culture collections, 27 isolated strains, and 44 cloned fragments recovered from environmental samples) were tested. The results demonstrated a high discriminative power and sensitivity to 1 fmol of the PCR-amplified 16S rRNA gene. Accurate identification of target strains was also achieved with unbalanced mixes of PCR amplicons from different cyanobacteria and an environmental sample. Our universal array method shows great potential for rapid and reliable identification of cyanobacteria. It can be easily adapted to future development and could thus be applied both in research and environmental monitoring. [less ▲]

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See detailCyanobacterial diversity in natural and artificial microbial mats of Lake Fryxell (McMurdo dry valleys, Antarctica): A morphological and molecular approach
Taton, A.; Grubisic, Stana ULg; Brambilla, E. et al

in Applied and Environmental Microbiology (2003), 69(9), 5157-5169

Currently, there is no consensus concerning the geographic distribution and extent of endemism in Antarctic cyanobacteria. In this paper we describe the phenotypic and genotypic diversity of cyanobacteria ... [more ▼]

Currently, there is no consensus concerning the geographic distribution and extent of endemism in Antarctic cyanobacteria. In this paper we describe the phenotypic and genotypic diversity of cyanobacteria in a field microbial mat sample from Lake Fryxell and in an artificial cold-adapted sample cultured in a benthic gradient chamber (BGC) by using an inoculum from the same mat. Light microscopy and molecular tools, including 16S rRNA gene clone libraries, denaturing gradient gel electrophoresis, and sequencing, were used. For the first time in the study of cyanobacterial diversity of environmental samples, internal transcribed spacer (ITS) sequences were retrieved and analyzed to complement the information obtained from the 16S rRNA gene. Microscopy allowed eight morphotypes to be identified, only one of which is likely to be an Antarctic endemic morphotype. Molecular analysis, however, revealed an entirely different pattern. A much higher number of phylotypes (15 phylotypes) was found, but no sequences from Nodularia and Hydrocoryne, as observed by microscopy, were retrieved. The 16S rRNA gene sequences determined in this study were distributed in 11 phylogenetic lineages, 3 of which were exclusively Antarctic and 2 of which were novel. Collectively, these Antarctic sequences together with all the other polar sequences were distributed in 22 lineages, 9 of which were exclusively Antarctic, including the 2 novel lineages observed in this study. The cultured BGC mat had lower diversity than the field mat. However, the two samples shared three morphotypes and three phylotypes. Moreover, the BGC mat allowed enrichment of one additional phylotype. ITS sequence analysis revealed a complex signal that was difficult to interpret. Finally, this study provided evidence of molecular diversity of cyanobacteria in Antarctica that is much greater than the diversity currently known based on traditional microscopic analysis. Furthermore, Antarctic endemic species were more abundant than was estimated on the basis of morphological features. Decisive arguments concerning the global geographic distribution of cyanobacteria should therefore incorporate data obtained with the molecular tools described here. [less ▲]

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See detailRemarkable conservation of internally transcribed spacer sequences of Arthrospira ("Spirulina") (Cyanophyceae, Cyanobacteria) strains from four continents and of recent and 30-year-old dried samples from Africa
Baurain, Denis ULg; Renquin, Laurent; Grubisic, Stana ULg et al

in Journal of Phycology (2002), 38(2), 384-393

The internally transcribed spacer (ITS) sequences of 21 Arthrospira clonal strains from four continents and assigned to four different species (A. platensis, A. maxima, A. fusiformis, A. indica) in the ... [more ▼]

The internally transcribed spacer (ITS) sequences of 21 Arthrospira clonal strains from four continents and assigned to four different species (A. platensis, A. maxima, A. fusiformis, A. indica) in the culture collections were determined. Two main clusters, I and H, were differentiated by 49 positions out of 475 nt or 477 nt, respectively. Each cluster was further subdivided into two subclusters. Subclusters LA and I.B were separated by two substitutions, whereas subclusters II.A, and II.B were distinguished by four substitutions. After direct sequencing of the PCR products, three dried samples from Chad aged between 3 months and 35 years yielded a sequence belonging to subcluster I.A, as did a recent commercial product. The strains grown in production plants belonged to the same (sub)clusters as strains from culture collections, mainly LA and II. PCR primers specific for each cluster and subcluster were designed and tested with crude cell lysates of Arthrospira strains. One dried sample ("dihe' 1) and a herbarium sample from Lake Sonachi (Kenya) only contained I.A sequences, whereas the commercial product was a mixture of the four genotypes and the other two dried samples contained minor polymorphisms characteristic of different clusters. Five clonal Arthrospira strains, thought to be duplicates, showed the simultaneous presence of the two :Forms of the four diagnostic positions that distinguish subclusters genotype H.A and genotype II.B. This is likely to be caused by multiple copies of the rDNA operon, in a intermediate stage of homogenization between subcluster II.A and subcluster II.B. The high conservation of ITS sequences is in contrast with the assignment to four different species, the great morphological variability of the strains, and their wide geographic distribution. [less ▲]

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