bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cellulose in Cyanobacteria. Origin of Vascular Plant Cellulose Synthase?
Authors: Nobles David R. , Romanovicz Dwight K. , Brown R. Malcolm 
Published: November 2008

Abstract
Although cellulose biosynthesis among the cyanobacteria has been suggested previously, we present the first conclusive evidence, to our knowledge, of the presence of cellulose in these organisms. Based on the results of x-ray diffraction, electron microscopy of microfibrils, and cellobiohydrolase I-gold labeling, we report the occurrence of cellulose biosynthesis in nine species representing three of the five sections of cyanobacteria. Sequence analysis of the genomes of four cyanobacteria revealed the presence of multiple amino acid sequences bearing the DDD35QXXRW motif conserved in all cellulose synthases. Pairwise alignments demonstrated that CesAs from plants were more similar to putative cellulose synthases from Anabaena sp. Pasteur Culture Collection 7120 and Nostoc punctiforme American Type Culture Collection 29133 than any other cellulose synthases in the database. Multiple alignments of putative cellulose synthases from Anabaena sp. Pasteur Culture Collection 7120 and N. punctiforme American Type Culture Collection 29133 with the cellulose synthases of other prokaryotes, Arabidopsis, Gossypium hirsutum, Populus alba × Populus tremula, corn (Zea mays), and Dictyostelium discoideumshowed that cyanobacteria share an insertion between conserved regions U1 and U2 found previously only in eukaryotic sequences. Furthermore, phylogenetic analysis indicates that the cyanobacterial cellulose synthases share a common branch with CesAs of vascular plants in a manner similar to the relationship observed with cyanobacterial and chloroplast 16s rRNAs, implying endosymbiotic transfer of CesA from cyanobacteria to plants and an ancient origin for cellulose synthase in eukaryotes.
Isolation and Characterization of a New Peroxiredoxin from Poplar Sieve Tubes That Uses Either Glutaredoxin or Thioredoxin as a Proton Donor
Authors: Rouhier Nicolas , Gelhaye Eric , Sautiere Pierre-Eric , Brun Annick , Laurent Pascal , Tagu Denis , Gerard Joelle , de Faÿ Elisabeth , Meyer Yves , Jacquot Jean-Pierre 
Published: November 2008

Abstract
A sequence coding for a peroxiredoxin (Prx) was isolated from a xylem/phloem cDNA library from Populus trichocarpaand subsequently inserted into an expression plasmid yielding the construction pET-Prx. The recombinant protein was produced inEscherichia coli cells and purified to homogeneity with a high yield. The poplar Prx is composed of 162 residues, a property that makes it the shortest plant Prx sequence isolated so far. It was shown that the protein is monomeric and possesses two conserved cysteines (Cys). The Prx degrades hydrogen peroxide and alkyl hydroperoxides in the presence of an exogenous proton donor that can be either thioredoxin or glutaredoxin (Grx). Based on this finding, we propose that the poplar protein represents a new type of Prx that differs from the so-called 2-Cys and 1-Cys Prx, a suggestion supported by the existence of natural fusion sequences constituted of a Prx motif coupled to a Grx motif. The protein was shown to be highly expressed in sieve tubes where thioredoxin h and Grx are also major proteins.
Chlorophyll Biosynthesis. Expression of a SecondChl IGene of Magnesium Chelatase in Arabidopsis Supports Only Limited Chlorophyll Synthesis
Authors: Rissler Heather M. , Collakova Eva , DellaPenna Dean , Whelan James , Pogson Barry J. 
Published: November 2008

AbstractMagnesium (Mg) chelatase is a heterotrimeric enzyme complex that catalyzes a key regulatory and enzymatic reaction in chlorophyll biosynthesis, the insertion of Mg2+ into protoporphyrin IX. Studies of the enzyme complex reconstituted in vitro have shown that all three of its subunits, CHL I, CHL D, and CHL H, are required for enzymatic activity. However, a new T-DNA knockout mutant of the chlorina locus, ch42-3 (Chl I), in Arabidopsis is still able to accumulate some chlorophyll despite the absence of Chl I mRNA and protein. In barley (Hordeum vulgare), CHL I is encoded by a single gene. We have identified an open reading frame that apparently encodes a second Chl Igene, Chl I2. Chl I1 and Chl I2 mRNA accumulate to similar levels in wild type, yet CHL I2 protein is not detectable in wild type or ch42-3, although the protein is translated and stromally processed as shown by in vivo pulse labeling and in vitro chloroplast imports. It is surprising that CHL D accumulates to wild-type levels in ch42-3, which is in contrast to reports that CHL D is unstable in CHL I-deficient backgrounds of barley. Our results show that limited Mg chelatase activity and CHL D accumulation can occur without detectable CHL I, despite its obligate requirement in vitro and its proposed chaperone-like stabilization and activation of CHL D. Thus, the unusual post-translational regulation of the CHL I2 protein provides an opportunity to study the different steps involved in stabilization and activation of the heterotrimeric Mg chelatase in vivo.
The ram1 Mutant of Arabidopsis Exhibits Severely Decreased β-Amylase Activity
Authors: Laby Ron J. , Kim Donggiun , Gibson Susan I. 
Published: November 2008

Abstract
Despite extensive biochemical analyses, the biological function(s) of plant β-amylases remains unclear. The fact that β-amylases degrade starch in vitro suggests that they may play a role in starch metabolism in vivo. β-Amylases have also been suggested to prevent the accumulation of highly polymerized polysaccharides that might otherwise impede flux through phloem sieve pores. The identification and characterization of a mutant of Arabidopsis var. Columbia with greatly reduced levels of β-amylase activity is reported here. The reduced β-amylase 1 (ram1) mutation lies in the gene encoding the major form of β-amylase in Arabidopsis. Although the Arabidopsis genome contains nine known or putative β-amylase genes, the fact that the ram1 mutation results in almost complete loss of β-amylase activity in rosette leaves and inflorescences (stems) indicates that the gene affected by theram1 mutation is responsible for most of the β-amylase activity present in these tissues. The leaves of ram1plants accumulate wild-type levels of starch, soluble sugars, anthocyanin, and chlorophyll. Plants carrying the ram1mutation also exhibit wild-type rates of phloem exudation and of overall growth. These results suggest that little to no β-amylase activity is required to maintain normal starch levels, rates of phloem exudation, and overall plant growth.
Mutations in Two Independent Genes Lead to Suppression of the Shoot Apical Meristem in Maize
Authors: Pilu Roberto , Consonni Gabriella , Busti Elena , MacCabe Andrew P. , Giulini Anna , Dolfini Silvana , Gavazzi Giuseppe 
Published: November 2008

Abstract
The shoot apical meristem (SAM), initially formed during embryogenesis, gives rise to the aboveground portion of the maize (Zea mays) plant. The shootless phenotype (sml) described here is caused by disruption of SAM formation due to the synergistic interaction of mutations at two genetic loci. Seedlings must be homozygous for both sml (shootmeristemless), and the unlinked dgr (distorted growth) loci for a SAM-less phenotype to occur. Seedlings mutant only for sml are impaired in their morphogenesis to different extents, whereas thedgr mutation alone does not have a recognisable phenotype. Thus, dgr can be envisaged as being a dominant modifier of sml and the 12 (normal):3 (distorted growth):1 (shoot meristemless) segregation observed in the F2 of the double heterozygote is the result of the interaction between the sml and dgrgenes. Other segregation patterns were also observed in the F2, suggesting instability of the dgr gene. Efforts to rescue mutant embryos by growth on media enriched with hormones have been unsuccessful so far. However, mutant roots grow normally on medium supplemented with kinetin at a concentration that suppresses wild-type root elongation, suggesting possible involvement of the mutant in the reception or transduction of the kinetin signal or transport of the hormone. The shootless mutant appears to be a valuable tool with which to investigate the organization of the shoot meristem in monocots as well as a means to assay the origins and relationships between organs such as the scutellum, the coleoptile, and leaves that are initiated during the embryogenic process.
An Aquaglyceroporin Is Abundantly Expressed Early in the Development of the Suspensor and the Embryo Proper of Loblolly Pine
Authors: Ciavatta Vincent T. , Morillon Raphael , Pullman Gerald S. , Chrispeels Maarten J. , Cairney John 
Published: November 2008

AbstractIn contrast to angiosperms, pines and other gymnosperms form well-developed suspensors in somatic embryogenic cultures. This creates a useful system to study suspensor biology. In a study of gene expression during the early stages of conifer embryogenesis, we identified a transcript, PtNIP1;1, that is abundant in immature loblolly pine (Pinus taeda) zygotic and somatic embryos, but is undetectable in later-stage embryos, megagametophytes, and roots, stems, and needles from 1 year-old seedlings. Analysis ofPtNIP1;1 transcript in embryo proper and suspensor tissues by reverse transcription-polymerase chain reaction suggests preferential expression in the suspensor. Based on comparisons of derived amino acid sequences, PtNIP1;1 belongs to the nodulin-like members of the major intrinsic protein superfamily branch of the aquaporin (major intrinsic protein) superfamily. Through heterologous expression in Xenopus laevis oocytes and the yeast (Saccharomyces cerevisiae)fps1 − mutant, PtNIP1;1 has been shown to be an active aquaglyceroporin.
Resistance against Herbicide Isoxaben and Cellulose Deficiency Caused by Distinct Mutations in Same Cellulose Synthase Isoform CESA6
Authors: Desprez Thierry , Vernhettes Samantha , Fagard Mathilde , Refrégier Guislaine , Desnos Thierry , Aletti Estelle , Py Nicolas , Pelletier Sandra , Höfte Herman 
Published: November 2008

Abstract
Isoxaben is a pre-emergence herbicide that inhibits cellulose biosynthesis in higher plants. Two loci identified by isoxaben-resistant mutants (ixr1-1,ixr1-2, and ixr2-1) in Arabidopsis have been reported previously. IXR1 was recently shown to encode the cellulose synthase catalytic subunit CESA3 (W.-R. Scheible, R. Eshed, T. Richmond, D. Delmer, and C. Somerville [2001] Proc Natl Acad Sci USA 98: 10079–10084). Here, we report on the cloning of IXR2, and show that it encodes another cellulose synthase isoform, CESA6. ixr2-1 carries a mutation substituting an amino acid close to the C terminus of CESA6 that is highly conserved among CESA family members. Transformation of wild-type plants with the mutated gene and not with the wild-type gene conferred increased resistance against the herbicide. The simplest interpretation for the existence of these two isoxaben-resistant loci is that CESA3 and CESA6 have redundant functions. However, loss of functionprocuste1 alleles of CESA6 were previously shown to have a strong growth defect and reduced cellulose content in roots and dark-grown hypocotyls. This indicates that in these mutants, the presence of CESA3 does not compensate for the absence of CESA6 in roots and dark-grown hypocotyls, which argues against redundant functions for CESA3 and CESA6. Together, these observations are compatible with a model in which CESA6 and CESA3 are active as a protein complex.
Dasatinib sensitizes primary chronic lymphocytic leukaemia lymphocytes to chlorambucil and fludarabine in vitro
Authors: Amrein Lilian , Hernandez Tiffany A. , Ferrario Cristiano , Johnston James , Gibson Spencer B. , Panasci Lawrence , Aloyz Raquel 
Published: November 2008

SummaryThe dual c‐abl/Src kinase inhibitor, dasatinib, utilized to treat chronic myeloid leukaemia (CML) when used at clinically attainable sublethal concentrations, synergistically sensitized primary chronic lymphocytic leukaemia (CLL) lymphocytes to chlorambucil and fludarabine. In contrast, dasatinib alone demonstrated toxicity to CLL lymphocytes at concentrations that are generally not clinically attainable. Dasatinib resistance and poorer dasatinib‐mediated sensitization to chlorambucil and fludarabine was associated with higher expression of c‐abl protein levels. In contrast, chlorambucil and fludarabine resistance correlated with basal p53 protein levels. Moreover, Western blot analysis after in vitro treatment of primary CLL lymphocytes with dasatinib, chlorambucil and/or fludarabine, showed that dasatinib: (i) inhibited c‐abl function (e.g. downregulation of c‐abl protein levels and decreased the phosphorylation of a c‐abl downstream target, Dok2), (ii) decreased chlorambucil/fludarabine induced accumulation of p53 protein levels, (iii) altered the response to chlorambucil/fludarabine induced DNA‐damage as evidenced by an increase in chlorambucil/fludarabine‐induced H2AX phosphorylation, and (iv) accentuated the c‐abl downregulation induced by chlorambucil/fludarabine. Our results suggest that dasatinib in combination with chlorambucil or fludarabine may improve the therapy of CLL.
Proton interactions with soil organic matter: the importance of aggregation and the weak acids of humin
Authors: Cooke J. D. , Tipping E. , Hamilton‐Taylor J. 
Published: November 2008

SummarySamples of three organic‐rich soils (ombrotrophic peat, podzol H‐horizon, humic ranker) were extensively washed with dilute nitric acid, dialysed against deionised water, and then subjected to acid‐base titrations over the pH range 3–10, in 0.3–300 mm NaNO3, and with soil concentrations in the range 2–150 g l−1. The results for the three soils were quantitatively similar. Comparison of the titration data with previously published results for humic acids isolated from the same soils showed the soil organic matter to have a greater ionic strength dependency of proton binding and to possess relatively greater buffering capacity at high pH, attributable to weak acid groups (c. 2–5 mmol g–1) in the humin fraction of the soils. To describe the soil titration data quantitatively, we modified Humic Ion‐Binding Model VI‐FD, which utilizes a fixed Donnan volume to describe counterion accumulation, by increasing the content of weak acid groups. When artefacts in pH measurement caused by the suspension effect were taken into account, the resulting Model VI‐FD2 provided good or fair simulations of all the titration data. The results suggest that soil structure, specifically aggregation, plays a significant role in cation binding by organic soils in situ. The lack of dependence of the titration results on soil suspension concentration suggests that the findings can be applied to soils in situ.
Distribution patterns of groundwater communities across aquifer types in south‐western Germany
Authors: HAHN HANS JÜRGEN , FUCHS ANDREAS 
Published: November 2008

Summary1. Classification of groundwater habitats and communities at different spatial scales is emphasised as a basic requirement for the implementation of groundwater ecology into legislation. Such a classification would also facilitate prediction of groundwater biodiversity, abundance and community structure, but is not currently available.2. To identify the factors influencing the distribution of stygofauna at the landscape scale, the groundwater fauna of Baden–Württemberg in South‐western Germany was sampled from November 2001 to December 2002. A total of 304 boreholes were sampled twice with a phreatic net. Boreholes were originally selected to represent the full range of geographic, geological and hydrographic variation within the sampling area. However, bores in porous aquifers were overrepresented because the monitoring networks that could be used in this study were originally designed for hydrogeological purposes.3. In total, 105 taxa (including 60 stygobionts) were found. Most of the stygobionts were rare, with 52% of them occurring in less than 1% of the boreholes. Stygobiotic taxonomic richness in a region or so‐called geological unit was directly correlated with the number of bores sampled. Species richness accumulation curves indicated that the real taxonomic richness of Baden–Württemberg is considerably higher than the recorded number of 60 stygobiotic taxa. This finding is in accordance with studies from other regions and suggests that groundwater biodiversity generally is strongly underestimated, probably resulting mainly from huge heterogeneity of groundwater systems and reliance on broad‐scale hydrological monitoring networks.4. To identify regional distribution patterns, the sampling area was separated into regional geological units, each comprising all aquifers of identical geology in a particular region (size: hundred to several thousand square kilometres). Distribution patterns of the aquatic subterranean fauna (including non‐stygobionts) were found to be influenced to some degree by the geographical position of the bores, and to a large extent by hydrogeological aquifer type rather than by affiliation of aquifers to a given geological unit. Four types of aquifers could be distinguished: Compact aquifers (aquitards) with reduced pore spaces, and porous, fractured and karstic aquifers.5. Communities of porous and karstic aquifers were found to be more similar to each other than the communities of compact and fractured aquifers. Therefore, for the purpose of recording groundwater biodiversity and defining undisturbed groundwater habitats, we suggest focusing more strongly than in the past on aquifer hydraulic conductivity and, in particular, on compact and fractured aquifers.
Impact of intentionally injected carbon dioxide hydrate on deep‐sea benthic foraminiferal survival
Authors: BERNHARD JOAN M. , BARRY JAMES P. , BUCK KURT R. , STARCZAK VICTORIA R. 
Published: November 2008

AbstractSequestration of carbon dioxide (CO2) in the ocean is being considered as a feasible mechanism to mitigate the alarming rate in its atmospheric rise. Little is known, however, about how the resulting hypercapnia and ocean acidification may affect marine fauna. In an effort to understand better the protistan reaction to such an environmental perturbation, the survivorship of benthic foraminifera, which is a prevalent group of protists, was studied in response to deep‐sea CO2 release. The survival response of calcareous, agglutinated, and thecate foraminifera was determined in two experiments at ∼3.1 and 3.3 km water depth in Monterey Bay (California, USA). Approximately 5 weeks after initial seafloor CO2 release, in situ incubations of the live–dead indicator CellTracker Green were executed within seafloor‐emplaced pushcores. Experimental treatments included direct exposure to CO2 hydrate, two levels of lesser exposure adjacent to CO2 hydrate, and controls, which were far removed from the CO2 hydrate release. Results indicate that survivorship rates of agglutinated and thecate foraminifera were not significantly impacted by direct exposure but the survivorship of calcareous foraminifera was significantly lower in direct exposure treatments compared with controls. Observations suggest that, if large scale CO2 sequestration is enacted on the deep‐sea floor, survival of two major groups of this prevalent protistan taxon will likely not be severely impacted, while calcareous foraminifera will face considerable challenges to maintain their benthic populations in areas directly exposed to CO2 hydrate.
The Fusobacterium nucleatum outer membrane protein RadD is an arginine‐inhibitable adhesin required for inter‐species adherence and the structured architecture of multispecies biofilm
Authors: Kaplan Christopher W. , Lux Renate , Haake Susan Kinder , Shi Wenyuan 
Published: November 2008

SummaryA defining characteristic of the suspected periodontal pathogen Fusobacterium nucleatum is its ability to adhere to a plethora of oral bacteria. This distinguishing feature is suggested to play an important role in oral biofilm formation and pathogenesis, with fusobacteria proposed to serve as central ‘bridging organisms’ in the architecture of the oral biofilm bringing together species which would not interact otherwise. Previous studies indicate that these bacterial interactions are mediated by galactose‐ or arginine‐inhibitable adhesins although genetic evidence for the role and nature of these proposed adhesins remains elusive. To characterize these adhesins at the molecular level, the genetically transformable F. nucleatum strain ATCC 23726 was screened for adherence properties, and arginine‐inhibitable adhesion was evident, while galactose‐inhibitable adhesion was not detected. Six potential arginine‐binding proteins were isolated from the membrane fraction of F. nucleatum ATCC 23726 and identified via mass spectroscopy as members of the outer membrane family of proteins in F. nucleatum. Inactivation of the genes encoding these six candidates for arginine‐inhibitable adhesion and two additional homologues revealed that only a mutant derivative carrying an insertion in Fn1526 (now designated as radD) demonstrated significantly decreased co‐aggregation with representatives of the Gram‐positive ‘early oral colonizers’. Lack of the 350 kDa outer membrane protein encoded by radD resulted in the failure to form the extensive structured biofilm observed with the parent strain when grown in the presence of Streptococcus sanguinis ATCC 10556. These findings indicate that radD is responsible for arginine‐inhibitable adherence of F. nucleatum and provides definitive molecular evidence that F. nucleatum adhesins play a vital role in inter‐species adherence and multispecies biofilm formation.
Investigations concerning the role of Chalara fraxinea in declining Fraxinus excelsior
Authors: Bakys R. , Vasaitis R. , Barklund P. , Ihrmark K. , Stenlid J. 
Published: November 2008

A study was carried out to clarify the role of the fungus Chalara fraxinea in decline of Fraxinus excelsior, which is observed on a large scale in central and northern Europe with high incidence of tree mortality. The aims of this work were: (i) to check for the presence of C. fraxinea in various tissues of declining F. excelsior by agar culture isolations and by direct analysis of plant tissues using molecular techniques (DNA extraction, ITS‐PCR, cloning, ITS sequencing and T‐RFLP); (ii) to study fungal communities inhabiting tissues with symptoms; and (iii) to test the pathogenicity of C. fraxinea to F. excelsior. Chalara fraxinea was isolated from 93% of stem cankers, 91% of necrotic leaf stalks, 27–28% of bark wounds and 30% of visually healthy leaf stalks. Molecular analyses of necrotic leaves, leaf stalks and bark revealed the presence of 25 different fungal taxa, 14 of which were detected in all three types of tissue sample. Chalara fraxinea was the second most common species (61% of samples), and only Cryptococcus foliicola occurred more often (70%). All eight of the tested C. fraxinea isolates induced necroses in bark and cambium on each of 86 inoculated trees, and all controls remained healthy. Average length of necroses caused by different C. fraxinea strains varied from 4·2 to 8·9 cm, but the differences were statistically insignificant. Instead, differences in resistance of individual trees to C. fraxinea were observed.