bluuebunny/crossref_metadata_2025_split huggingface dataset:
Species recognition in the truffle genus Tuber– the synonyms Tuber aestivum and Tuber uncinatum
Authors: Wedén Christina , Danell Eric , Tibell Leif 
Published: September 2005

SummaryThe two morphologically similar truffles Tuber aestivum and T. uncinatum have caused confusion because T. uncinatum is regarded by different authors, as either a distinct species, variety, subspecies, or synonym of T. aestivum. A clarification of the relationship between the two truffles would help both conservation biology and cultivation. We aimed both to test the reliability of the only quantitative morphological character used to distinguish the two taxa, i.e. the height of the spore reticulum, and to compare sequences of the ribosomal DNA (rDNA) internal transcribed spacer (ITS) region. Our study included 117 fruit bodies of T. aestivum and T. uncinatum, originating from eight European countries. The results showed that the spore reticulum height is not diagnostic. The phylogenetic analysis of ITS sequences from 81 fruit bodies and an additional 32 sequences from GenBank showed that T. aestivum and T. uncinatum were intermingled in one highly supported (100% bootstrap) monophyletic clade, separate from its sister species Tuber mesentericum. We conclude that T. aestivum and T. uncinatum are synonyms and the species should be named T. aestivum, as the oldest name has priority. For traders, T. aestivum syn. T. uncinatum should be used until conformity has been reached.
Methanogen communities and Bacteria along an ecohydrological gradient in a northern raised bog complex
Authors: Juottonen Heli , Galand Pierre E. , Tuittila Eeva‐Stiina , Laine Jukka , Fritze Hannu , Yrjälä Kim 
Published: September 2005

SummaryMires forming an ecohydrological gradient from nutrient‐rich, groundwater‐fed mesotrophic and oligotrophic fens to a nutrient‐poor ombrotrophic bog were studied by comparing potential methane (CH4) production and methanogenic microbial communities. Methane production was measured from different depths of anoxic peat and methanogen communities were detected by detailed restriction fragment length polymorphism (RFLP) analysis of clone libraries, sequencing and phylogenetic analysis. Potential CH4 production changed along the ecohydrological gradient with the fens displaying much higher production than the ombrotrophic bog. Methanogen diversity also decreased along the gradient. The two fens had very similar diversity of methanogenic methyl‐coenzyme M reductase gene (mcrA), but in the upper layer of the bog the methanogen diversity was strikingly lower, and only one type of mcrA sequence was retrieved. It was related to the Fen cluster, a group of novel methanogenic sequences found earlier in Finnish mires. Bacterial 16S rDNA sequences from the fens fell into at least nine phyla, but only four phyla were retrieved from the bog. The most common bacterial groups were Deltaproteobacteria, Verrucomicrobia and Acidobacteria.
Global physiological analysis of carbon‐ and energy‐limited growing Escherichia coli confirms a high degree of catabolic flexibility and preparedness for mixed substrate utilization
Authors: Ihssen Julian , Egli Thomas 
Published: September 2005

SummaryGrowth conditions for heterotrophic bacteria in the environment are characterized by low concentrations of carbon and energy sources and complex substrate mixtures. While mechanisms of starvation‐survival in the absence of carbon substrates have been studied in considerable detail, information on the physiology of slow growth under oligotrophic conditions is limited. We intended to elucidate general strategies by which Escherichia coli adapts to low concentrations of a mixed carbon and energy source pool. A new screening method based on BIOLOG AN MicroPlatesTM, which allowed us to distinguish repressed and induced catabolic functions in E. coli, was combined with the analysis of periplasmic high‐affinity binding proteins. Extending previous findings for E. coli and other microbial species, we found that numerous alternative catabolic functions and high‐affinity binding proteins are derepressed under either glucose‐ or arabinose‐limited growth conditions, in spite of the absence of the respective inducers. Escherichia coli cells growing in carbon‐limited complex medium chemostat cultures exhibited an even higher degree of catabolic flexibility and were able to oxidize 43 substrates. The BIOLOG respiration pattern indicated simultaneous dissimilation of diverse sugars, amino acids and dipeptides (mixed substrate growth). The observed physiological adaptations of E. coli to low concentrations of carbon and energy substrates presumably are advantageous in many natural growth situations and also offer an explanation why many heterotrophic bacteria have and maintain such a broad carbon substrate range.
Methane fluxes in permafrost habitats of the Lena Delta: effects of microbial community structure and organic matter quality
Authors: Wagner Dirk , Lipski André , Embacher Arndt , Gattinger Andreas 
Published: September 2005

SummaryFor the understanding and assessment of recent and future carbon dynamics of arctic permafrost soils the processes of CH4 production and oxidation, the community structure and the quality of dissolved organic matter (DOM) were studied in two soils of a polygonal tundra. Activities of methanogens and methanotrophs differed significantly in their rates and distribution patterns among the two investigated profiles. Community structure analysis showed similarities between both soils for ester‐linked phospholipid fatty acids (PLFAs) and differences in the fraction of unsaponifiable PLFAs and phospholipid ether lipids. Furthermore, a shift of the overall composition of the microbiota with depth at both sites was indicated by an increasing portion of iso‐ and anteiso‐branched fatty acids related to the amount of straight‐chain fatty acids. Although permafrost soils represent a large carbon pool, it was shown that the reduced quality of organic matter leads to a substrate limitation of the microbial metabolism. It can be concluded from our and previous findings first that microbial communities in the active layer of an Arctic polygon tundra are composed by members of all three domains of life, with a total biomass comparable to temperate soil ecosystems, and second that these microorganisms are well adapted to the extreme temperature gradient of their environment.
Grazing resistance of Pseudomonas aeruginosa biofilms depends on type of protective mechanism, developmental stage and protozoan feeding mode
Authors: Weitere Markus , Bergfeld Tanja , Rice Scott A. , Matz Carsten , Kjelleberg Staffan 
Published: September 2005

SummaryIn a previous study we identified microcolony formation and inhibitor production as the major protective mechanisms of Pseudomonas aeruginosa biofilms against flagellate grazing [Matz, C., Bergfeld, T., Rice, S.A., and Kjelleberg, S. (2004) Microcolonies, quorum sensing and cytotoxicity determine the survival of Pseudomonas aeruginosa biofilms exposed the protozoan grazing. Environ Microbiol 6: 218–226]. Here we compared the efficacy of these two key protective mechanisms by exposing biofilms of the non‐toxic alginate overproducing strain PDO300 and the wild‐type toxic strain PAO1 to a range of feeding types commonly found in the succession of protozoans associated with natural biofilms. Alginate‐mediated microcolony formation conferred effective protection for strain PDO300 against the suspension feeding flagellate Bodo saltans and, as reported earlier, the surface feeding flagellate Rhynchomonas nasuta, both of which are considered as early biofilm colonizers. However, microcolonies of mature PDO300 biofilms were highly susceptible to late biofilm colonizers, the surface‐feeding amoeba Acanthamoeba polyphaga and the planktonic ciliate Tetrahymena sp., resulting in a significant reduction of biofilm biomass. Mature biofilms of strain PAO1 inhibited growth of flagellates and A. polyphaga while the grazing activity of Tetrahymena sp. remained unaffected. Our findings suggest that inhibitor production of mature P. aeruginosa biofilms is effective against a wider range of biofilm‐feeding predators while microcolony‐mediated protection is only beneficial in the early stages of biofilm formation.
A green light‐absorbing phycoerythrin is present in the high‐light‐adapted marine cyanobacterium Prochlorococcus sp. MED4
Authors: Steglich Claudia , Frankenberg‐Dinkel Nicole , Penno Sigrid , Hess Wolfgang R. 
Published: September 2005

SummaryIn the high‐light‐adapted unicellular marine cyanobacterium Prochlorococcus sp. MED4 the cpeB gene is the only gene coding for a structural phycobiliprotein. The absence of any other phycoerythrin gene in the fully sequenced genome of this organism, the previous inability to detect a gene product, and the mutation of two out of four cysteine residues, normally involved in binding chromophores, suggested that MED4‐cpeB might not code for a functional protein. Here, transcription of MED4‐cpeB at a low level was detected and the transcriptional start site was mapped. Enrichment of the protein identified phycoerythrobilin as its sole chromophore in vivo, which was confirmed by chromophorylation assays in vitro using the recombinant protein. Phycourobilin is the major chromophore in low‐light‐adapted Prochlorococcus ecotypes such as strain SS120. Therefore, spectrally tuned phycoerythrins are a characteristic feature of distinct Prochlorococcus ecotypes. Further in vitro mutagenesis experiments replacing one or both cysteines C61R/C82S by arginine or serine, respectively, revealed that only Cys82 is required for chromophore binding. Thus, an unusual green light‐absorbing phycoerythrin evolved in the high‐light‐adapted ecotypes of Prochlorococcus, which potentially serves as a photoreceptor.
Bacterial communities associated with benthic organic matter in headwater stream microhabitats
Authors: Fazi Stefano , Amalfitano Stefano , Pernthaler Jakob , Puddu Alberto 
Published: September 2005

SummaryBacterial communities associated with a variety of benthic detritus types were studied in three streams in the context of the chemical characteristics of the sediment material and the stream water. A cell purification assay was developed for a quantitative microscopic evaluation of bacterial community structure in detritus samples by fluorescence in situ hybridization (FISH). The efficiency of FISH with fluorescently monolabelled probes was compared with FISH with signal amplification by catalysed reporter deposition (CARD‐FISH). In detritus types poor in organic carbon and nitrogen, the numbers of prokaryotes were related to the chemical characteristics of the stream water column, whereas no such relationship was found for detritus types rich in organic carbon and nitrogen. These results might help to provide criteria for the selection of detritus types for river ecosystem assessment and monitoring. The percentage of bacteria detected by FISH with monolabelled probes was correlated with the detritus total organic matter (OM). This is likely attributed to a higher ribosome content of microbial cells on substrates rich in OM. Cell detection by CARD‐FISH did not show any correlation with OM content, indicating that this technique renders the results more independent from the activity state of cells. Fluorescence in situ hybridization with four group‐specific probes suggested a relationship between substrate quality and the composition of the microbial assemblages on the various types of detritus. The improved protocol for cell purification and CARD‐FISH may facilitate future investigations on the relationship between the riverine benthic detritus quality and microbial community composition.
Contrasting microcystin production and cyanobacterial population dynamics in two Planktothrix‐dominated freshwater lakes
Authors: Janse Ingmar , Kardinaal W. Edwin A. , Agterveld Miranda Kamst‐van , Meima Marion , Visser Petra M. , Zwart Gabriel 
Published: September 2005

SummaryMicrocystin concentrations in two Dutch lakes with an important Planktothrix component were related to the dynamics of cyanobacterial genotypes and biovolumes. Genotype composition was analysed by using denaturing gradient gel electrophoresis (DGGE) profiling of the intergenic transcribed spacer region of the rrn operon (rRNA‐ITS), and biovolumes were measured by using microscopy. In Lake Tjeukemeer, microcystins were present throughout summer (maximum concentration 30 µg l−1) while cyanobacterial diversity was low and very constant. The dominant phototroph was Planktothrix agardhii. In contrast, Lake Klinckenberg showed a high microcystin peak (up to 140 µg l−1) of short duration. In this lake, cyanobacterial diversity was higher and very dynamic with apparent genotype successions. Several genotypes derived from DGGE field profiles matched with genotypes from cultures isolated from field samples. The microcystin peak measured in Lake Klinckenberg could be confidently linked to a bloom of Planktothrix rubescens, as microscopic and genotypic analysis showed identity of bloom samples and a toxin‐producing P. rubescens culture. Toxin‐producing genotypes were detected in the microbial community before they reached densities at which they were detected by using microscopy. Cyanobacterial biovolumes provided additional insights in bloom dynamics. In both lakes, the microcystin content per cell was highest at the onset of the blooms. Our results suggest that while genotypic characterization of a lake can be valuable for detection of toxic organisms, for some lakes a monitoring of algal biomass has sufficient predictive value for an assessment of toxin production.
Phylogenetic resolution and habitat specificity of members of the Photobacterium phosphoreum species group
Authors: Ast Jennifer C. , Dunlap Paul V. 
Published: September 2005

SummarySubstantial ambiguity exists regarding the phylogenetic status of facultatively psychrophilic luminous bacteria identified as Photobacterium phosphoreum, a species thought to be widely distributed in the world's oceans and believed to be the specific bioluminescent light‐organ symbiont of several deep‐sea fishes. Members of the P. phosphoreum species group include luminous and non‐luminous strains identified phenotypically from a variety of different habitats as well as phylogenetically defined lineages that appear to be evolutionarily distinct. To resolve this ambiguity and to begin developing a meaningful knowledge of the geographic distributions, habitats and symbiotic relationships of bacteria in the P. phosphoreum species group, we carried out a multilocus, fine‐scale phylogenetic analysis based on sequences  of  the  16S  rRNA,  gyrB and  luxABFE  genes of many newly isolated luminous strains from symbiotic and saprophytic habitats, together with previously isolated luminous and non‐luminous strains identified as P. phosphoreum from these and other habitats. Parsimony analysis unambiguously resolved three evolutionarily distinct clades, phosphoreum, iliopiscarium and kishitanii. The tight phylogenetic clustering within these clades and the distinct separation between them indicates they are different species, P. phosphoreum, Photobacterium iliopiscarium and the newly recognized ‘Photobacterium kishitanii’. Previously reported non‐luminous strains, which had been identified phenotypically as P. phosphoreum, resolved unambiguously as P. iliopiscarium, and all examined deep‐sea fishes (specimens of families Chlorophthalmidae, Macrouridae, Moridae, Trachichthyidae and Acropomatidae) were found to harbour ‘P. kishitanii’, not P. phosphoreum, in their light organs. This resolution revealed also that ‘P. kishitanii’ is cosmopolitan in its geographic distribution. Furthermore, the lack of phylogenetic variation within ‘P. kishitanii’ indicates that this facultatively symbiotic bacterium is not cospeciating with its phylogenetically divergent host fishes. The results of this fine‐scale phylogenetic analysis support the emerging view that bacterial species names should designate singular historical entities, i.e. discrete lineages diagnosed by a significant divergence of shared derived nucleotide characters.
Regulation of Arabidopsis thaliana 4‐coumarate:coenzyme‐A ligase‐1 expression by artificial zinc finger chimeras
Authors: Sánchez Juan Pablo , Ullman Christopher , Moore Michael , Choo Yen , Chua Nam‐Hai 
Published: September 2005

SummaryThe use of artificial zinc finger chimeras to manipulate the expression of a gene of interest is a promising approach because zinc finger proteins can be engineered to bind any given DNA sequence in the genome. We have previously shown that a zinc finger chimera with a VP16 activation domain can activate a reporter gene in transgenic Arabidopsis thaliana (Sánchez, J.P., Ullman, C., Moore, M., Choo, Y. and Chua, N.H. (2002) Regulation of gene expression in Arabidopsis thaliana by artificial zinc finger chimeras. Plant Cell Physiol. 43, 1465–1472). Here, we report the use of artificial zinc finger chimeras to specifically regulate the 4‐coumarate:coenzyme‐A ligase‐1 (At4CL1) gene in A. thaliana. At4CL1 is a key enzyme in lignin biosynthesis and the down‐regulation of At4CL1 can lead to a decrease in lignin content, which has a significant commercial value for the paper industry. To this end, we designed zinc finger chimeras containing either an activation or a repression domain, which bind specifically to the At4CL1 promoter region. Transgenic lines expressing a zinc finger chimera with the VP16 activation domain showed an increase in At4CL1 expression and enzyme activity. In contrast, transgenic lines expressing a chimera with the KOX (KRAB) repression domain displayed repression of At4CL1 expression and enzyme activity. The activation of At4CL1 expression produced an increase in lignin content, and transgenic plant stems showed ectopic lignin distribution. Repression of the At4CL1 gene resulted in reduced lignin content, and lignin distribution in transgenic stems was severely diminished. Our results confirm and extend previous studies of gene regulation using various artificial zinc finger chimeras in animal and plant systems, and show that this system can be used to up‐ and down‐regulate the expression of an endogenous plant gene such as At4CL1.
Conservative Alliance Building and African American Support of Vouchers: The End of Brown's Promise or a New Beginning?
Authors: Apple Michael W. , Pedroni Thomas C. 
Published: September 2005

A new kind of conservatism has evolved and has taken center stage in many nations, one that is best seen as “conservative modernization.” Although parts of these conservative positions may have originated within the New Right, they are now not limited to what has traditionally been called the Right. They have been taken up by a much larger segment of government and policy makers and have also even been appropriated by groups that one might least expect to do so, such as African American activists in cities like Milwaukee. In this article, we examine a growing phenomenon: the growth of seemingly conservative sentiments among some of the least powerful groups in this society. Perhaps the most significant organization to emerge has been the Black Alliance for Educational Options (BAEO). It has mobilized around voucher advocacy for urban working-class communities of color. BAEO has attracted significant attention not just for its iconoclastic alignment with conservative educational reform, but also for accepting funding from far-Right foundations. This article analyzes the complexity of the discursive and sociopolitical space that BAEO occupies. The organization's awareness of its critics, allies, and the limited range of educational options within which low-income African American families must act belies the notion, put forward by some, that BAEO is simply a front organization for the educational Right. Nevertheless, BAEO's importance to the larger rightist project in education cannot be overstated. At the core of our analysis is a concern about what is at stake for all of us if a rightist educational agenda succeeds in redefining what and whose knowledge is of most worth and what our social and educational policies are meant to do. Yet, no matter what one's position is on the wisdom of BAEO's strategic actions, this case provides a crucial example of the politics of how social movements and alliances are formed and reformed out of the material and ideological conditions of daily life. A critical but sympathetic understanding of groups such as BAEO may enable us to avoid the essentialism and reductionism that enters into critical sociological work on the nature of ongoing struggles over educational reform. It can provide a more nuanced sense of social actors and the possibilities and limits of strategic alliances in a time of major conflicts over educational reform during a period of conservative modernization.
Plant self‐incompatibility systems: a molecular evolutionary perspective
Authors: Charlesworth Deborah , Vekemans Xavier , Castric Vincent , Glémin Sylvain 
Published: September 2005

SummaryIncompatibility recognition systems preventing self‐fertilization have evolved several times in independent lineages of Angiosperm plants, and three main model systems are well characterized at the molecular level [the gametophytic self‐incompatibility (SI) systems of Solanaceae, Rosaceae and Anthirrhinum, the very different system of poppy, and the system in Brassicaceae with sporophytic control of pollen SI reactions]. In two of these systems, the genes encoding both components of pollen‐pistil recognition are now known, showing clearly that these two proteins are distinct, that is, SI is a lock‐and‐key mechanism. Here, we review recent findings in the three well‐studied systems in the light of these results and analyse their implications for understanding polymorphism and coevolution of the two SI genes, in the context of a tightly linked genome region.
Epigenetics and plant evolution
Authors: Rapp Ryan A. , Wendel Jonathan F. 
Published: September 2005

SummaryA fundamental precept of evolutionary biology is that natural selection acts on phenotypes determined by DNA sequence variation within natural populations. Recent advances in our understanding of gene regulation, however, have elucidated a spectrum of epigenetic molecular phenomena capable of altering the temporal, spatial, and abundance patterns of gene expression. These modifications may have morphological, physiological, and ecological consequences, and are heritable across generations, suggesting they are important in evolution. A corollary is that genetic variation per se is not always a prerequisite to evolutionary change. Here, we provide an introduction to epigenetic mechanisms in plants, and highlight some of the empirical studies illustrative of the possible connections between evolution and epigenetically mediated alterations in gene expression and morphology.