bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extracellular Ca2+ Ameliorates NaCl-Induced K+ Loss from Arabidopsis Root and Leaf Cells by Controlling Plasma Membrane K+-Permeable Channels
Authors: Shabala Sergey , Demidchik Vadim , Shabala Lana , Cuin Tracey A. , Smith Susan J. , Miller Anthony J. , Davies Julia M. , Newman Ian A. 
Published: June 2006

Abstract
Calcium can ameliorate Na+ toxicity in plants by decreasing Na+ influx through nonselective cation channels. Here, we show that elevated external [Ca2+] also inhibits Na+-induced K+ efflux through outwardly directed, K+-permeable channels. Noninvasive ion flux measuring and patch-clamp techniques were used to characterize K+ fluxes from Arabidopsis (Arabidopsis thaliana) root mature epidermis and leaf mesophyll under various Ca2+ to Na+ ratios. NaCl-induced K+ efflux was not related to the osmotic component of the salt stress, was inhibited by the K+ channel blocker TEA+, was not mediated by inwardly directed K+ channels (tested in the akt1 mutant), and resulted in a significant decrease in cytosolic K+ content. NaCl-induced K+ efflux was partially inhibited by 1 mm Ca2+ and fully prevented by 10 mm Ca2+. This ameliorative effect was at least partially attributed to a less dramatic NaCl-induced membrane depolarization under high Ca2+ conditions. Patch-clamp experiments (whole-cell mode) have demonstrated that two populations of Ca2+-sensitive K+ efflux channels exist in protoplasts isolated from the mature epidermis of Arabidopsis root and leaf mesophyll cells. The instantaneously activating K+ efflux channels showed weak voltage dependence and insensitivity to external and internal Na+. Another population of K+ efflux channels was slowly activating, steeply rectifying, and highly sensitive to Na+. K+ efflux channels in roots and leaves showed different Ca2+ and Na+ sensitivities, suggesting that these organs may employ different strategies to withstand salinity. Our results suggest an additional mechanism of Ca2+ action on salt toxicity in plants: the amelioration of K+ loss from the cell by regulating (both directly and indirectly) K+ efflux channels.
Natural Variation for Carbohydrate Content in Arabidopsis. Interaction with Complex Traits Dissected by Quantitative Genetics
Authors: Calenge Fanny , Saliba-Colombani Véra , Mahieu Stéphanie , Loudet Olivier , Daniel-Vedele Françoise , Krapp Anne 
Published: June 2006

Abstract
Besides being a metabolic fuel, carbohydrates play important roles in plant growth and development, in stress responses, and as signal molecules. We exploited natural variation in Arabidopsis (Arabidopsis thaliana) to decipher the genetic architecture determining carbohydrate content. A quantitative trait locus (QTL) approach in the Bay-0 × Shahdara progeny grown in two contrasting nitrogen environments led to the identification of 39 QTLs for starch, glucose, fructose, and sucrose contents representing at least 14 distinct polymorphic loci. A major QTL for fructose content (FR3.4) and a QTL for starch content (ST3.4) were confirmed in heterogeneous inbred families. Several genes associated with carbon (C) metabolism colocalize with the identified QTL. QTLs for senescence-related traits, and for flowering time, water status, and nitrogen-related traits, previously detected with the same genetic material, colocalize with C-related QTLs. These colocalizations reflect the complex interactions of C metabolism with other physiological processes. QTL fine-mapping and cloning could thus lead soon to the identification of genes potentially involved in the control of different connected physiological processes.
Synergism between RPBF Dof and RISBZ1 bZIP Activators in the Regulation of Rice Seed Expression Genes
Authors: Yamamoto Masayuki P. , Onodera Yasuyuki , Touno Satoru M. , Takaiwa Fumio 
Published: June 2006

Abstract
The Dof (DNA binding with one finger) transcriptional activator rice (Oryza sativa) prolamin box binding factor (RPBF), which is involved in gene regulation of rice seed storage proteins, has been isolated from rice cDNA expressed sequence tag clones containing the conserved Dof. RPBF is found as a single gene per haploid genome. Comparison of RPBF genomic and cDNA sequences revealed that the genomic copy is interrupted by one long intron of 1,892 bp in the 5′ noncoding region. We demonstrated by transient expression in rice callus protoplasts that the isolated RPBF trans-activated several storage protein genes via an AAAG target sequence located within their promoters, and with methylation interference experiments the additional AAAG-like sequences in promoters of genes expressed in maturing seeds were recognized by the RPBF protein. Binding was sequence specific, since mutation of the AAAG motif or its derivatives decreased both binding and trans-activation by RPBF. Synergism between RPBF and RISBZ1 recognizing the GCN4 motif [TGA(G/C)TCA] was observed in the expression of many storage protein genes. Overexpression of both transcription factors gave rise to much higher levels of expression than the sum of individual activities elicited by either RPBF or RISBZ1 alone. Furthermore, mutation of recognition sites suppressed reciprocal trans-activation ability, indicating that there are mutual interactions between RISBZ1 and RPBF. The RPBF gene is predominantly expressed in maturing endosperm and coordinately expressed with seed storage protein genes, and is involved in the quantitative regulation of genes expressed in the endosperm in cooperation with RISBZ1.
RCN1-Regulated Phosphatase Activity and EIN2 Modulate Hypocotyl Gravitropism by a Mechanism That Does Not Require Ethylene Signaling
Authors: Muday Gloria K. , Brady Shari R. , Argueso Cristiana , Deruère Jean , Kieber Joseph J. , DeLong Alison 
Published: June 2006

Abstract
The roots curl in naphthylphthalamic acid1 (rcn1) mutant of Arabidopsis (Arabidopsis thaliana) has altered auxin transport, gravitropism, and ethylene response, providing an opportunity to analyze the interplay between ethylene and auxin in control of seedling growth. Roots of rcn1 seedlings were previously shown to have altered auxin transport, growth, and gravitropism, while rcn1 hypocotyl elongation exhibited enhanced ethylene response. We have characterized auxin transport and gravitropism phenotypes of rcn1 hypocotyls and have explored the roles of auxin and ethylene in controlling these phenotypes. As in roots, auxin transport is increased in etiolated rcn1 hypocotyls. Hypocotyl gravity response is accelerated, although overall elongation is reduced, in etiolated rcn1 hypocotyls. Etiolated, but not light grown, rcn1 seedlings also overproduce ethylene, and mutations conferring ethylene insensitivity restore normal hypocotyl elongation to rcn1. Auxin transport is unaffected by treatment with the ethylene precursor 1-aminocyclopropane carboxylic acid in etiolated hypocotyls of wild-type and rcn1 seedlings. Surprisingly, the ethylene insensitive2-1 (ein2-1) and ein2-5 mutations dramatically reduce gravitropic bending in hypocotyls. However, the ethylene resistant1-3 (etr1-3) mutation does not significantly affect hypocotyl gravity response. Furthermore, neither the etr1 nor the ein2 mutation abrogates the accelerated gravitropism observed in rcn1 hypocotyls, indicating that both wild-type gravity response and enhanced gravity response in rcn1 do not require an intact ethylene-signaling pathway. We therefore conclude that the RCN1 protein affects overall hypocotyl elongation via negative regulation of ethylene synthesis in etiolated seedlings, and that RCN1 and EIN2 modulate hypocotyl gravitropism and ethylene responses through independent pathways.
Endocytosis Is Essential for Pathogenic Development in the Corn Smut Fungus Ustilago maydis
Authors: Fuchs Uta , Hause Gerd , Schuchardt Isabel , Steinberg Gero 
Published: June 2006

Abstract
It is well established that polarized exocytosis is essential for fungal virulence. By contrast, the contribution of endocytosis is unknown. We made use of a temperature-sensitive mutant in the endosomal target soluble N-ethylmaleimide–sensitive factor attachment protein receptor Yup1 and demonstrate that endocytosis in Ustilago maydis is essential for the initial steps of pathogenic development, including pheromone perception and cell–cell fusion. Furthermore, spore formation and germination were drastically reduced, whereas colonization of the plant was only slightly inhibited. The function of endocytosis in the recognition of mating pheromone through the G protein–coupled pheromone receptor Pra1 was analyzed in greater detail. Biologically active Pra1–green fluorescent protein localizes to the plasma membrane and is constitutively endocytosed. Yup1ts mutants that are blocked in the fusion of endocytic transport vesicles with early endosomes are impaired in pheromone perception and conjugation hyphae formation. This is attributable to an accumulation of Pra1-carrying endocytic vesicles in the cytoplasm and the depletion of the receptor from the membrane. Consistently, strong Pra1 expression rescues the signaling defects in endocytosis mutants, but subsequent cell fusion is still impaired. Thus, we conclude that endocytosis is essential for recognition of the partner at the beginning of the pathogenic program but has additional roles in mating as well as spore formation and germination.
AGL80Is Required for Central Cell and Endosperm Development inArabidopsis
Authors: Portereiko Michael F. , Lloyd Alan , Steffen Joshua G. , Punwani Jayson A. , Otsuga Denichiro , Drews Gary N. 
Published: June 2006

AbstractDuring plant reproduction, the central cell of the female gametophyte becomes fertilized to produce the endosperm, a storage tissue that nourishes the developing embryo within the seed. The molecular mechanisms controlling the specification and differentiation of the central cell are poorly understood. We identified a female gametophyte mutant in Arabidopsis thaliana, fem111, that is affected in central cell development. In fem111 female gametophytes, the central cell's nucleolus and vacuole fail to mature properly. In addition, endosperm development is not initiated after fertilization of fem111 female gametophytes. fem111 contains a T-DNA insertion in AGAMOUS-LIKE80 (AGL80). FEM111/AGL80 is a member of the MADS box family of genes that likely encode transcription factors. An AGL80–green fluorescent protein fusion protein is localized to the nucleus. Within the ovule and seed, FEM111/AGL80 is expressed exclusively in the central cell and uncellularized endosperm. FEM111/AGL80 expression is also detected in roots, leaves, floral stems, anthers, and young flowers by real-time RT-PCR. FEM111/AGL80 is required for the expression of two central cell–expressed genes, DEMETER and DD46, but not for a third central cell–expressed gene, FERTILIZATION-INDEPENDENT SEED2. Together, these data suggest that FEM111/AGL80 functions as a transcription factor within the central cell gene regulatory network and controls the expression of downstream genes required for central cell development and function.
Proteomic Analysis of the Eyespot ofChlamydomonas reinhardtiiProvides Novel Insights into Its Components and Tactic Movements
Authors: Schmidt Melanie , Geßner Gunther , Luff Matthias , Heiland Ines , Wagner Volker , Kaminski Marc , Geimer Stefan , Eitzinger Nicole , Reißenweber Tobias , Voytsekh Olga , Fiedler Monika , Mittag Maria , Kreimer Georg 
Published: June 2006

AbstractFlagellate green algae have developed a visual system, the eyespot apparatus, which allows the cell to phototax. To further understand the molecular organization of the eyespot apparatus and the phototactic movement that is controlled by light and the circadian clock, a detailed understanding of all components of the eyespot apparatus is needed. We developed a procedure to purify the eyespot apparatus from the green model alga Chlamydomonas reinhardtii. Its proteomic analysis resulted in the identification of 202 different proteins with at least two different peptides (984 in total). These data provide new insights into structural components of the eyespot apparatus, photoreceptors, retina(l)-related proteins, members of putative signaling pathways for phototaxis and chemotaxis, and metabolic pathways within an algal visual system. In addition, we have performed a functional analysis of one of the identified putative components of the phototactic signaling pathway, casein kinase 1 (CK1). CK1 is also present in the flagella and thus is a promising candidate for controlling behavioral responses to light. We demonstrate that silencing CK1 by RNA interference reduces its level in both flagella and eyespot. In addition, we show that silencing of CK1 results in severe disturbances in hatching, flagellum formation, and circadian control of phototaxis.
KNAT6: AnArabidopsisHomeobox Gene Involved in Meristem Activity and Organ Separation
Authors: Belles-Boix Enric , Hamant Olivier , Witiak Sarah Melissa , Morin Halima , Traas Jan , Pautot Véronique 
Published: June 2006

AbstractThe homeobox gene family plays a crucial role during the development of multicellular organisms. The KNOTTED-like genes from Arabidopsis thaliana (KNAT6 and KNAT2) are close relatives of the meristematic genes SHOOT MERISTEMLESS (STM) and BREVIPEDICELLUS, but their function is not currently known. To investigate their role, we identified null alleles of KNAT6 and KNAT2. We demonstrate that KNAT6 contributes redundantly with STM to the maintenance of the shoot apical meristem (SAM) and organ separation. Consistent with this role, the expression domain of KNAT6 in the SAM marks the boundaries between the SAM and cotyledons. The lack of meristematic activity in the knat6 stm-2 double mutant and the fusion of cotyledons were linked to the modulation of CUP-SHAPED COTYLEDON (CUC) activity. During embryogenesis, KNAT6 is expressed later than STM and CUC. In agreement with this fact, CUC1 and CUC2 were redundantly required for KNAT6 expression. These data provide the basis for a model in which KNAT6 contributes to SAM maintenance and boundary establishment in the embryo via the STM/CUC pathway. KNAT2, although the closest related member of the family to KNAT6, did not have such a function.
MicroRNA-Targeted and Small Interfering RNA–Mediated mRNA Degradation Is Regulated by Argonaute, Dicer, and RNA-Dependent RNA Polymerase inArabidopsis
Authors: Ronemus Michael , Vaughn Matthew W. , Martienssen Robert A. 
Published: June 2006

AbstractARGONAUTE1 (AGO1) of Arabidopsis thaliana mediates the cleavage of microRNA (miRNA)-targeted mRNAs, and it has also been implicated in the posttranscriptional silencing of transgenes and the maintenance of chromatin structure. Mutations in AGO1 severely disrupt plant development, indicating that miRNA function and possibly other aspects of RNA interference are essential for maintaining normal patterns of gene expression. Using microarrays, we found that 1 to 6% of genes display significant expression changes in several alleles of ago1 at multiple developmental stages, with the majority showing higher levels. Several classes of known miRNA targets increased markedly in ago1, whereas others showed little or no change. Cleavage of mRNAs within miRNA-homologous sites was reduced but not abolished in an ago1 -null background, indicating that redundant slicer activity exists in Arabidopsis. Small interfering RNAs and larger 30- to 60-nucleotide RNA fragments corresponding to highly upregulated miRNA target genes accumulated in wild-type plants but not in ago1, the RNA-dependent RNA polymerase mutants rdr2 and rdr6, or the Dicer-like mutants dcl1 and dcl3. Both sense and antisense RNAs corresponding to these miRNA targets accumulated in the ago1 and dcl1 backgrounds. These results indicate that a subset of endogenous mRNA targets of RNA interference may be regulated through a mechanism of second-strand RNA synthesis and degradation initiated by or in addition to miRNA-mediated cleavage.
A Genome-Wide Survey ofRGene Polymorphisms inArabidopsis
Authors: Bakker Erica G. , Toomajian Christopher , Kreitman Martin , Bergelson Joy 
Published: June 2006

AbstractWe used polymorphism analysis to study the evolutionary dynamics of 27 disease resistance (R) genes by resequencing the leucine-rich repeat (LRR) region in 96 Arabidopsis thaliana accessions. We compared single nucleotide polymorphisms (SNPs) in these R genes to an empirical distribution of SNP in the same sample based on 876 fragments selected to sample the entire genome. LRR regions are highly polymorphic for protein variants but not for synonymous changes, suggesting that they generate many alleles maintained for short time periods. Recombination is also relatively common and important for generating protein variants. Although none of the genes is nearly as polymorphic as RPP13, a locus previously shown to have strong signatures of balancing selection, seven genes show weaker indications of balancing selection. Five R genes are relatively invariant, indicating young alleles, but all contain segregating protein variants. Polymorphism analysis in neighboring fragments yielded inconclusive evidence for recent selective sweeps at these loci. In addition, few alleles are candidates for rapid increases in frequency expected under directional selection. Haplotype sharing analysis revealed significant underrepresentation of R gene alleles with extended haplotypes compared with 1102 random genomic fragments. Lack of convincing evidence for directional selection or selective sweeps argues against an arms race driving R gene evolution. Instead, the data support transient or frequency-dependent selection maintaining protein variants at a locus for variable time periods.
State‐of‐the‐art management models for lakes and reservoirs
Authors: Jørgensen S. E. 
Published: June 2006

AbstractThis paper reviews current models that can be used in lake management, mainly for eutrophication and wetland areas. The latter type of model, in particular, has developed rapidly during the past decade due to the increasing importance of wetlands as traps for nutrients originating from non‐point sources. The experience gained in lake modelling since the mid‐1980s can be summarized as follows: (i) 3‐D hydrodynamic models are available today but are not necessarily the right answer to a given modelling problem (dependent on data availability); (ii) models with a wide spectrum of complexities are available which make it possible to select a type of model appropriate to available data; and (iii) several models with general applicability are available, yet it is necessary to tailor a model for each individual case (generally based on experience from previous model studies). The experience gained by the use of the so‐called Glumsø model on 25 case studies led to the same conclusion: modifications are needed in the original model for each new case study to allow for the specific characteristics of the lake modelled. Lake management models have been developed for eutrophication, oxygen depletion, various specific pollution problems, thermocline formation, acidification, and the use of wetlands to cope with non‐point pollution, particularly for removal of nitrogen by denitrification. An overview of available models, including their shortcomings, is given in the text. We have experience in using models for many different environmental problems of lakes, but it is necessary to improve these models by including more ecological components. These improvements are discussed in relation to the most recent experiences in the use of models with dynamic structures.
Relative contribution of bacteria, algae and ciliates to the microplankton biomass in an eutrophic lake
Authors: Aleya L. , Hartmann H. J. 
Published: June 2006

AbstractBiomass in size‐fractionated plankton (0.2–1.2 μm; 1.2–12/μm; 12–45 μm and 45–160 μm), together with that of ciliated protozoans (size fraction 1–160 μm), were assessed during stratification, in an eutrophic lake (Lake Aydat, Massif Central, France). Samples (51) were gathered from depths of 2, 7 and 14 m during 17 weekly samplings in the centre of the lake. Three biomass estimations were performed: cell‐counts, chlorophyll a and ATP assays. Ciliates were counted live.Five species groups dominated the ciliate community: Loxodes striatus, Frontonia spp., Spirostomum ambiguum, Strombidium spp. and Dexiotrica plagia. Frontonia always had the highest cell concentration (54–64% of total cell counts), while the bulk of biomass was divided between Loxodes (42–70% of total) and Frontonia (29–53% of total).In terms of carbon, both the bacteria and ciliate contributions to the total microplanktonic biomass (size fraction 1–160 μm, i.e. bacteria + phytoplankton + ciliates) depends on the choice of the phytoplankton biomass estimation technique used. Thus, the contributions increase respectively from 16% and 19%, when phytoplankton biomass is estimated from chlorophyll α concentrations, to 24% and 27%, when phytoplankton biomass is based on biovolume.Relationships between bacteria, phytoplankton and ciliated protozoans reveal that ATP data are greatly overestimated by bacteria and ciliate interferences, especially in the metalimnion and hypolimnion. In the epilimnion, this interference is less. Interpretations of phytoplankton dynamics and metabolic activity from ATP assays should be made with extreme care, especially in eutrophic environments.
The management of lakes and the role of industry
Authors: Willurns Jan‐Olaf 
Published: June 2006

AbstractThis paper reviews the role of industry in responding to global environmental issues, looking specifically at the environmental management of lakes and rivers. The link between industry and lake conservation and the importance of industry in these links are evaluated. The challenges facing industry in this respect are divided into three tasks; minimizing effluent pollution, reducing water consumption, and encouraging active conservation of lakes, wetlands and rivers. Two case studies show how corporations have met the challenges of reducing water pollution and managing freshwater resources. The author suggests that the new management principle of‘eco‐efficient leadership’may be a useful way for industry to contribute towards reducing the environmental impact on lakes and rivers, and outlines the conditions required for eco‐efficiency. Finally, the author stresses the need for a better and more systematic approach to environmental training and education in engineering and business schools.
Physico‐chemical characteristics and seasonal changes of plankton communities in a river reservoir
Authors: Toman M. J. 
Published: June 2006

AbstractLimnological investigations of the river reservoir Mavčiče (the Sava River, Slovenia) were carried out between May and October at regular three‐week intervals. The scope of our investigation was to determine physico‐chemical parameters, species composition, abundance and changes in the plankton community during summer stratification. The dominant taxa of phytoplankton were Chlorophyceae and Dinophyceae, and less so Cyanophyceae and Bacillariophyceae, while Rotatoria and less so Ciliata, Heliozoa and Cladocera were common zooplankton taxa. Eutrophication is in progress and primarily results from the high input of municipal and industrial wastewater from the nearest town. The concentration of total phosphorus and nitrates regulates the extent of primary production in the reservoir. The result is oxygen depletion in the hypolimnetic layer and anoxic conditions in the sediments.