bluuebunny/crossref_metadata_2025 huggingface dataset:
RNA polymerase II elongation factors Spt4p and Spt5p play roles in transcription elongation by RNA polymerase I and rRNA processing
Authors: Schneider D. A. , French S. L. , Osheim Y. N. , Bailey A. O. , Vu L. , Dodd J. , Yates J. R. , Beyer A. L. , Nomura M.
Published: August 2006

Previous investigations into the mechanisms that control RNA Polymerase (Pol) I transcription have primarily focused on the process of transcription initiation, thus little is known regarding postinitiation steps in the transcription cycle. Spt4p and Spt5p are conserved throughout eukaryotes, and they affect elongation by Pol II. We have found that these two proteins copurify with Pol I and associate with the rDNA
in vivo
. Disruption of the gene for Spt4p resulted in a modest decrease in growth and rRNA synthesis rates at the permissive temperature, 30°C. Furthermore, biochemical and EM analyses showed clear defects in rRNA processing. These data suggest that Spt4p, Spt5p, and, potentially, other regulators of Pol I transcription elongation play important roles in coupling rRNA transcription to its processing and ribosome assembly.
Selection and analysis of spontaneous reciprocal mitotic cross-overs in
Saccharomyces cerevisiae
Authors: Barbera Maria A. , Petes Thomas D.
Published: August 2006

We developed a system that allows the selection of the reciprocal products resulting from spontaneous mitotic cross-overs in the yeast
Saccharomyces cerevisiae
. A number of other types of genetic events, including chromosome loss, can be monitored with this system. For a 120-kb chromosome interval on chromosome V (
CEN5-CAN1
), the rate of mitotic cross-overs was 4 × 10
−5
per division, a rate ≈25,000-fold lower than the meiotic rate of cross-overs. We found no suppression of mitotic cross-overs near the centromere of chromosome V, unlike the suppression observed for meiotic exchanges. The rate of reciprocal cross-overs was substantially (38-fold) elevated by treatment of cells with hydroxyurea, a drug that reduces nucleotide pools and slows DNA replication.
Mining frequent stem patterns from unaligned RNA sequences
Authors: Hamada Michiaki , Tsuda Koji , Kudo Taku , Kin Taishin , Asai Kiyoshi
Published: August 2006

Motivation: In detection of non-coding RNAs, it is often necessary to identify the secondary structure motifs from a set of putative RNA sequences. Most of the existing algorithms aim to provide the best motif or few good motifs, but biologists often need to inspect all the possible motifs thoroughly.

Results: Our method RNAmine employs a graph theoretic representation of RNA sequences and detects all the possible motifs exhaustively using a graph mining algorithm. The motif detection problem boils down to finding frequently appearing patterns in a set of directed and labeled graphs. In the tasks of common secondary structure prediction and local motif detection from long sequences, our method performed favorably both in accuracy and in efficiency with the state-of-the-art methods such as CMFinder.

Availability: The software is available upon request.

Contact:  hamada-michiaki@aist.go.jp

Supplementary information: Visit the following URL for Supplementary information, software availability and the information about the web server:
Malignant melanoma: genetics and therapeutics in the genomic era
Authors: Chin Lynda , Garraway Levi A. , Fisher David E.
Published: August 2006

Cell for cell, probably no human cancer is as aggressive as melanoma. It is among a handful of cancers whose dimensions are reported in millimeters. Tumor thickness approaching 4 mm presents a high risk of metastasis, and a diagnosis of metastatic melanoma carries with it an abysmal median survival of 6–9 mo. What features of this malignancy account for such aggressive behavior? Is it the migratory history of its cell of origin or the programmed adaptation of its differentiated progeny to environmental stress, particularly ultraviolet radiation? While the answers to these questions are far from complete, major strides have been made in our understanding of the cellular, molecular, and genetic underpinnings of melanoma. More importantly, these discoveries carry profound implications for the development of therapies focused directly at the molecular engines driving melanoma, suggesting that we may have reached the brink of an unprecedented opportunity to translate basic science into clinical advances. In this review, we attempt to summarize our current understanding of the genetics and biology of this disease, drawing from expanding genomic information and lessons from development and genetically engineered mouse models. In addition, we look forward toward how these new insights will impact on therapeutic options for metastatic melanoma in the near future.
A novel role for Xist RNA in the formation of a repressive nuclear compartment into which genes are recruited when silenced
Authors: Chaumeil Julie , Le Baccon Patricia , Wutz Anton , Heard Edith
Published: August 2006

During early mammalian female development, one of the two X chromosomes becomes inactivated. Although X-chromosome coating by Xist RNA is essential for the initiation of X inactivation, little is known about how this signal is transformed into transcriptional silencing. Here we show that exclusion of RNA Polymerase II and transcription factors from the Xist RNA-coated X chromosome represents the earliest event following Xist RNA accumulation described so far in differentiating embryonic stem (ES) cells. Paradoxically, exclusion of the transcription machinery occurs before gene silencing is complete. However, examination of the three-dimensional organization of X-linked genes reveals that, when transcribed, they are always located at the periphery of, or outside, the Xist RNA domain, in contact with the transcription machinery. Upon silencing, genes shift to a more internal location, within the Xist RNA compartment devoid of transcription factors. Surprisingly, the appearance of this compartment is not dependent on the A-repeats of the Xist transcript, which are essential for gene silencing. However, the A-repeats are required for the relocation of genes into the Xist RNA silent domain. We propose that Xist RNA has multiple functions: A-repeat-independent creation of a transcriptionally silent nuclear compartment; and A-repeat-dependent induction of gene repression, which is associated with their translocation into this silent domain.
Spleen versus pancreas: strict control of organ interrelationship revealed by analyses of Bapx1−/− mice
Authors: Asayesh Amir , Sharpe James , Watson Robert P. , Hecksher-Sørensen Jacob , Hastie Nicholas D. , Hill Robert E. , Ahlgren Ulf
Published: August 2006

During early stages of pancreatic development, the mesenchyme that contributes to the spleen overlies the dorsal pancreatic endoderm. Here, we show that interactions between splenic mesenchyme and pancreas proceed via a highly orchestrated morphogenetic program. Disruption of morphogenesis, as occurs in the Bapx1(Nkx3.2)−/− embryo, results in transformation of these tissues into well-organized, ectopic gut-like structures. Bapx1 plays a crucial organizing role effecting position and separation of the spleen and pancreas to prevent this metaplastic transformation. Similar transformations occur in organ cultures employing wild-type pancreatic endoderm and spleen mesenchyme, revealing the developmental plasticity of the pancreas and that precise spatial and temporal control of tissue interactions are required for development of both organs.
c-Jun/AP-1 controls liver regeneration by repressing p53/p21 and p38 MAPK activity
Authors: Stepniak Ewa , Ricci Romeo , Eferl Robert , Sumara Grzegorz , Sumara Izabela , Rath Martina , Hui Lijian , Wagner Erwin F.
Published: August 2006

The AP-1 transcription factor c-Jun is a key regulator of hepatocyte proliferation. Mice lacking c-Jun in the liver (c-junΔli*) display impaired liver regeneration after partial hepatectomy (PH). This phenotype correlates with increased protein levels of the cdk-inhibitor p21 in the liver. We performed PH experiments in several double-knockout mouse models to genetically identify the signaling events regulated by c-Jun. Inactivation of p53 in c-junΔli* mice abrogated both hepatocyte cell cycle block and increased p21 protein expression. Consistently, liver regeneration was rescued in c-junΔli*p21−/− double-mutant mice. This indicated that c-Jun controls hepatocyte proliferation by a p53/p21-dependent mechanism. Analyses of p21 mRNA and protein expression in livers of c-junΔli* mice after PH revealed that the accumulation of p21 protein is due to a post-transcriptional/post-translational mechanism. We have investigated several candidate pathways implicated in the regulation of p21 expression, and observed increased activity of the stress kinase p38 in regenerating livers of c-junΔli* mice. Importantly, conditional deletion of p38α in livers of c-junΔli* mice fully restored hepatocyte proliferation and attenuated increased p21 protein levels after PH. These data demonstrate that c-Jun/AP-1 regulates liver regeneration through a novel molecular pathway that involves p53, p21, and the stress kinase p38α.
Clarification of Pathway-Specific Inhibition by Fourier Transform Ion Cyclotron Resonance/Mass Spectrometry-Based Metabolic Phenotyping Studies
Authors: Oikawa Akira , Nakamura Yukiko , Ogura Tomonori , Kimura Atsuko , Suzuki Hideyuki , Sakurai Nozomu , Shinbo Yoko , Shibata Daisuke , Kanaya Shigehiko , Ohta Daisaku
Published: August 2006

We have developed a metabolic profiling scheme based on direct-infusion Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR/MS). The scheme consists of: (1) reproducible data collection under optimized FT-ICR/MS analytical conditions; (2) automatic mass-error correction and multivariate analyses for metabolome characterization using a newly developed metabolomics tool (DMASS software); (3) identification of marker metabolite candidates by searching a species-metabolite relationship database, KNApSAcK; and (4) structural analyses by an MS/MS method. The scheme was applied to metabolic phenotyping of Arabidopsis (Arabidopsis thaliana) seedlings treated with different herbicidal chemical classes for pathway-specific inhibitions. Arabidopsis extracts were directly infused into an electrospray ionization source on an FT-ICR/MS system. Acquired metabolomics data were comprised of mass-to-charge ratio values with ion intensity information subjected to principal component analysis, and metabolic phenotypes from the herbicide treatments were clearly differentiated from those of the herbicide-free treatment. From each herbicide treatment, candidate metabolites representing such metabolic phenotypes were found through the KNApSAcK database search. The database search and MS/MS analyses suggested dose-dependent accumulation patterns of specific metabolites including several flavonoid glycosides. The metabolic phenotyping scheme on the basis of FT-ICR/MS coupled with the DMASS program is discussed as a general tool for high throughput metabolic phenotyping studies.
Down-Regulation of the 26S Proteasome Subunit RPN9 Inhibits Viral Systemic Transport and Alters Plant Vascular Development
Authors: Jin Hailing , Li Songtao , Villegas Andy
Published: August 2006

Plant viruses utilize the vascular system for systemic movement. The plant vascular network also transports water, photosynthates, and signaling molecules and is essential for plant growth. However, the molecular mechanisms governing vascular development and patterning are still largely unknown. From viral transport suppressor screening using virus-induced gene silencing, we identified a 26S proteasome subunit, RPN9, which is required for broad-spectrum viral systemic transport. Silencing of RPN9 in Nicotiana benthamiana inhibits systemic spread of two taxonomically distinct viruses, Tobacco mosaic virus and Turnip mosaic virus. The 26S proteasome is a highly conserved eukaryotic protease complex controlling many fundamental biochemical processes, but the functions of many 26S proteasome regulatory subunits, especially in plants, are still poorly understood. We demonstrate that the inhibition of viral systemic transport after RPN9 silencing is largely due to alterations in the vascular tissue. RPN9-silenced plants display extra leaf vein formation with increased xylem and decreased phloem. We further illustrate that RPN9 functions at least in part through regulation of auxin transport and brassinosteroid signaling, two processes that are crucial for vascular formation. We propose that RPN9 regulates vascular formation by targeting a subset of regulatory proteins for degradation. The brassinosteroid-signaling protein BZR1 is one of the targets.
Arabidopsis Carboxyl-Terminal Domain Phosphatase-Like Isoforms Share Common Catalytic and Interaction Domains But Have Distinct in Planta Functions
Authors: Bang Wooyoung , Kim Sewon , Ueda Akihiro , Vikram Meenu , Yun Daejin , Bressan Ray A. , Hasegawa Paul M. , Bahk Jeongdong , Koiwa Hisashi
Published: August 2006

An Arabidopsis (Arabidopsis thaliana) multigene family (predicted to be more than 20 members) encodes plant C-terminal domain (CTD) phosphatases that dephosphorylate Ser residues in tandem heptad repeat sequences of the RNA polymerase II C terminus. CTD phosphatase-like (CPL) isoforms 1 and 3 are regulators of osmotic stress and abscisic acid (ABA) signaling. Evidence presented herein indicates that CPL3 and CPL4 are homologs of a prototype CTD phosphatase, FCP1 (TFIIF-interacting CTD-phosphatase). CPL3 and CPL4 contain catalytic FCP1 homology and breast cancer 1 C terminus (BRCT) domains. Recombinant CPL3 and CPL4 interact with AtRAP74, an Arabidopsis ortholog of a FCP1-interacting TFIIF subunit. A CPL3 or CPL4 C-terminal fragment that contains the BRCT domain mediates molecular interaction with AtRAP74. Consistent with their predicted roles in transcriptional regulation, green fluorescent protein fusion proteins of CPL3, CPL4, and RAP74 all localize to the nucleus. cpl3 mutations that eliminate the BRCT or FCP1 homology domain cause ABA hyperactivation of the stress-inducible RD29a promoter, whereas RNAi suppression of CPL4 results in dwarfism and reduced seedling growth. These results indicate CPL3 and CPL4 are a paralogous pair of general transcription regulators with similar biochemical properties, but are required for the distinct developmental and environmental responses. CPL4 is necessary for normal plant growth and thus most orthologous to fungal and metazoan FCP1, whereas CPL3 is an isoform that specifically facilitates ABA signaling.
A Transgenic Approach to Understanding the Influence of Carbonic Anhydrase on C18OO Discrimination during C4 Photosynthesis
Authors: Cousins Asaph B. , Badger Murray R. , von Caemmerer Susanne
Published: August 2006

The oxygen isotope composition of atmospheric CO2 is an important signal that helps distinguish between ecosystem photosynthetic and respiratory processes. In C4 plants the carbonic anhydrase (CA)-catalyzed interconversion of CO2 and bicarbonate (HCO3  −) is an essential first reaction for C4 photosynthesis but also plays an important role in the CO2-H2O exchange of oxygen as it enhances the rate of isotopic equilibrium between CO2 and water. The C4 dicot Flaveria bidentis containing genetically reduced levels of leaf CA (CAleaf) has been used to test whether changing leaf CA activity influences online measurements of C18OO discrimination (Δ18O) and the proportion of CO2 in isotopic equilibrium with leaf water at the site of oxygen exchange (θ). The Δ18O in wild-type F. bidentis, which contains high levels of CA relative to the rates of net CO2 assimilation, was less than predicted by models of Δ18O. Additionally, Δ18O was sensitive to small decreases in CAleaf. However, reduced CA activity in F. bidentis had little effect on net CO2 assimilation, transpiration rates (E), and stomatal conductance (g  s) until CA levels were less than 20% of wild type. The values of θ determined from measurements of Δ18O and the 18O isotopic composition of leaf water at the site of evaporation (δ  e) were low in the wild-type F. bidentis and decreased in transgenic plants with reduced levels of CA activity. Measured values of θ were always significantly lower than the values of θ predicted from in vitro CA activity and gas exchange. The data presented here indicates that CA content in a C4 leaf may not represent the CA activity associated with the CO2-H2O oxygen exchange and therefore may not be a good predictor of θ during C4 photosynthesis. Furthermore, uncertainties in the isotopic composition of water at the site of exchange may also limit the ability to accurately predict θ in C4 plants.
Effects of Zinc Deficiency on Rice Growth and Genetic Factors Contributing to Tolerance
Authors: Wissuwa Matthias , Ismail Abdelbagi M. , Yanagihara Seiji
Published: August 2006

Zinc (Zn) deficiency is the most widespread micronutrient disorder in rice (Oryza sativa), but efforts to develop cultivars with improved tolerance have been hampered by insufficient understanding of genetic factors contributing to tolerance. The objective of this paper was to examine alternative evaluation methods and to identify the most informative traits that would provide realistic information for rice breeders and to map quantitative trait loci (QTLs) associated with tolerance. Screening experiments in low-Zn nutrient solution and in a Zn-deficient field did not produce similar tolerance rankings in a set of segregating lines, which suggested that rhizosphere effects were of greater importance for lowland rice than internal Zn efficiency. The most severe symptom in the field was high plant mortality. The occurrence of leaf bronzing, usually regarded as indicative of susceptibility, did not necessarily concur with high plant mortality, which implied that both were under independent genetic control. The QTL mapping experiment conducted in the field with a population derived from a cross of IR74 (intolerant) with Jalmagna (tolerant) largely confirmed this. Four QTLs associated with plant mortality were detected, and only one of those colocalized with one of the four QTLs detected for leaf bronzing. The two most influential QTLs for plant mortality were detected on chromosomes 2 and 12. They explained 16.6% and 24.2% of the variation, and alleles of the tolerant donor parent Jalmagna reduced mortality by 16.6% and 14.8%, respectively. QTLs for plant mortality acted in a purely additive manner, whereas digenic epistatic interactions were important for leaf bronzing.
Whole-Plant Growth Stage Ontology for Angiosperms and Its Application in Plant Biology
Authors: Pujar Anuradha , Jaiswal Pankaj , Kellogg Elizabeth A. , Ilic Katica , Vincent Leszek , Avraham Shulamit , Stevens Peter , Zapata Felipe , Reiser Leonore , Rhee Seung Y. , Sachs Martin M. , Schaeffer Mary , Stein Lincoln , Ware Doreen , McCouch Susan
Published: August 2006

Plant growth stages are identified as distinct morphological landmarks in a continuous developmental process. The terms describing these developmental stages record the morphological appearance of the plant at a specific point in its life cycle. The widely differing morphology of plant species consequently gave rise to heterogeneous vocabularies describing growth and development. Each species or family specific community developed distinct terminologies for describing whole-plant growth stages. This semantic heterogeneity made it impossible to use growth stage description contained within plant biology databases to make meaningful computational comparisons. The Plant Ontology Consortium (http://www.plantontology.org) was founded to develop standard ontologies describing plant anatomical as well as growth and developmental stages that can be used for annotation of gene expression patterns and phenotypes of all flowering plants. In this article, we describe the development of a generic whole-plant growth stage ontology that describes the spatiotemporal stages of plant growth as a set of landmark events that progress from germination to senescence. This ontology represents a synthesis and integration of terms and concepts from a variety of species-specific vocabularies previously used for describing phenotypes and genomic information. It provides a common platform for annotating gene function and gene expression in relation to the developmental trajectory of a plant described at the organismal level. As proof of concept the Plant Ontology Consortium used the plant ontology growth stage ontology to annotate genes and phenotypes in plants with initial emphasis on those represented in The Arabidopsis Information Resource, Gramene database, and MaizeGDB.
Quantification of Plasmodesmatal Endoplasmic Reticulum Coupling between Sieve Elements and Companion Cells Using Fluorescence Redistribution after Photobleaching
Authors: Martens Helle J. , Roberts Alison G. , Oparka Karl J. , Schulz Alexander
Published: August 2006

Transgenic tobacco (Nicotiana tabacum) was studied to localize the activity of phloem loading during development and to establish whether the endoplasmic reticulum (ER) of the companion cell (CC) and the sieve element (SE) reticulum is continuous by using a SUC2 promoter-green fluorescent protein (GFP) construct targeted to the CC-ER. Expression of GFP marked the collection phloem in source leaves and cotyledons as expected, but also the transport phloem in stems, petioles, midveins of sink leaves, nonphotosynthetic flower parts, roots, and newly germinated seedlings, suggesting that sucrose retrieval along the pathway is an integral component of phloem function. GFP fluorescence was limited to CCs where it was visualized as a well-developed ER network in close proximity to the plasma membrane. ER coupling between CC and SEs was tested in wild-type tobacco using an ER-specific fluorochrome and fluorescence redistribution after photobleaching (FRAP), and showed that the ER is continuous via pore-plasmodesma units. ER coupling between CC and SE was quantified by determining the mobile fraction and half-life of fluorescence redistribution and compared with that of other cell types. In all tissues, fluorescence recovered slowly when it was rate limited by plasmodesmata, contrasting with fast intracellular FRAP. FRAP was unaffected by treatment with cytochalasin D. The highest degree of ER coupling was measured between CC and SE. Intimate ER coupling is consistent with a possible role for ER in membrane protein and signal exchange between CC and SE. However, a complete lack of GFP transfer between CC and SE indicated that the intraluminal pore-plasmodesma contact has a size exclusion limit below 27 kD.
Dual Temporal Role of Plastid Sigma Factor 6 in Arabidopsis Development
Authors: Loschelder Heike , Schweer Jennifer , Link Brigitte , Link Gerhard
Published: August 2006

Plants contain nuclear-coded sigma factors for initiation of chloroplast transcription. The in vivo function of individual members of the sigma gene family has become increasingly accessible by knockout and complementation strategies. Here we have investigated plastid gene expression in an Arabidopsis (Arabidopsis thaliana) mutant with a defective gene for sigma factor 6. RNA gel-blot hybridization and real-time reverse transcription polymerase chain reaction together indicate that this factor has a dual developmental role, with both early and persistent (long-term) activities. The early role is evident from the sharp decrease of certain plastid transcripts only in young mutant seedlings. The second (persistent) role is reflected by the up- and down-regulation of other transcripts at the time of primary leaf formation and subsequent vegetative development. We conclude that sigma 6 does not represent a general factor, but seems to have specialized roles in developmental stage- and gene-specific plastid transcription. The possibility that plastid DNA copy number might be responsible for the altered transcript patterns in mutant versus wild type was excluded by the results of DNA gel-blot hybridization. Retransformation of the knockout line with the full-length sigma 6 cDNA further established a causal relationship between the functional sigma gene and the resulting phenotype.
The Cytoskeleton Maintains Organelle Partitioning Required for Single-Cell C4 Photosynthesis in Chenopodiaceae Species
Authors: Chuong Simon D.X. , Franceschi Vincent R. , Edwards Gerald E.
Published: August 2006

Recently, three Chenopodiaceae species, Bienertia cycloptera, Bienertia sinuspersici, and Suaeda aralocaspica, were shown to possess novel C4 photosynthesis mechanisms through the compartmentalization of organelles and photosynthetic enzymes into two distinct regions within a single chlorenchyma cell. Bienertia has peripheral and central compartments, whereas S. aralocaspica has distal and proximal compartments. This compartmentalization achieves the equivalent of spatial separation of Kranz anatomy, including dimorphic chloroplasts, but within a single cell. To characterize the mechanisms of organelle compartmentalization, the distribution of the major organelles relative to the cytoskeleton was examined. Examination of the distribution of the cytoskeleton using immunofluorescence studies and transient expression of green fluorescent protein–tagged cytoskeleton markers revealed a highly organized network of actin filaments and microtubules associating with the chloroplasts and showed that the two compartments in each cell had different cytoskeletal arrangements. Experiments using cytoskeleton-disrupting drugs showed in Bienertia and S. aralocaspica that microtubules are critical for the polarized positioning of chloroplasts and other organelles. Compartmentalization of the organelles in these species represents a unique system in higher plants and illustrates the degree of control the plant cell has over the organization and integration of multiorganellar processes within its cytoplasm.
ArabidopsisEPSIN1 Plays an Important Role in Vacuolar Trafficking of Soluble Cargo Proteins in Plant Cells via Interactions with Clathrin, AP-1, VTI11, and VSR1
Authors: Song Jinhee , Lee Myoung Hui , Lee Gil-Je , Yoo Cheol Min , Hwang Inhwan
Published: August 2006

Epsin and related proteins play important roles in various steps of protein trafficking in animal and yeast cells. Many epsin homologs have been identified in plant cells from analysis of genome sequences. However, their roles have not been elucidated. Here, we investigate the expression, localization, and biological role in protein trafficking of an epsin homolog, Arabidopsis thaliana EPSIN1, which is expressed in most tissues we examined. In the cell, one pool of EPSIN1 is associated with actin filaments, producing a network pattern, and a second pool localizes primarily to the Golgi complex with a minor portion to the prevacuolar compartment, producing a punctate staining pattern. Protein pull-down and coimmunoprecipitation experiments reveal that Arabidopsis EPSIN1 interacts with clathrin, VTI11, γ-adaptin-related protein (γ-ADR), and vacuolar sorting receptor1 (VSR1). In addition, EPSIN1 colocalizes with clathrin and VTI11. The epsin1 mutant, which has a T-DNA insertion in EPSIN1, displays a defect in the vacuolar trafficking of sporamin:green fluorescent protein (GFP), but not in the secretion of invertase:GFP into the medium. Stably expressed HA:EPSIN1 complements this trafficking defect. Based on these data, we propose that EPSIN1 plays an important role in the vacuolar trafficking of soluble proteins at the trans-Golgi network via its interaction with γ-ADR, VTI11, VSR1, and clathrin.
Tobacco WLIM1 Is a Novel F-Actin Binding Protein Involved in Actin Cytoskeleton Remodeling
Authors: Thomas Clément , Hoffmann Céline , Dieterle Monika , Van Troys Marleen , Ampe Christophe , Steinmetz André
Published: August 2006

We used confocal microscopy and in vitro analyses to show that Nicotiana tabacum WLIM1, a LIM domain protein related to animal Cys-rich proteins, is a novel actin binding protein in plants. Green fluorescent protein (GFP)–tagged WLIM1 protein accumulated in the nucleus and cytoplasm of tobacco BY2 cells. It associated predominantly with actin cytoskeleton, as demonstrated by colabeling and treatment with actin-depolymerizing latrunculin B. High-speed cosedimentation assays revealed the ability of WLIM1 to bind directly to actin filaments with high affinity. Fluorescence recovery after photobleaching and fluorescence loss in photobleaching showed a highly dynamic in vivo interaction of WLIM1-GFP with actin filaments. Expression of WLIM1-GFP in BY2 cells significantly delayed depolymerization of the actin cytoskeleton induced by latrunculin B treatment. WLIM1 also stabilized actin filaments in vitro. Importantly, expression of WLIM1-GFP in Nicotiana benthamiana leaves induces significant changes in actin cytoskeleton organization, specifically, fewer and thicker actin bundles than in control cells, suggesting that WLIM1 functions as an actin bundling protein. This hypothesis was confirmed by low-speed cosedimentation assays and direct observation of F-actin bundles that formed in vitro in the presence of WLIM1. Taken together, these data identify WLIM1 as a novel actin binding protein that increases actin cytoskeleton stability by promoting bundling of actin filaments.
Biz1, a Zinc Finger Protein Required for Plant Invasion byUstilago maydis, Regulates the Levels of a Mitotic Cyclin
Authors: Flor-Parra Ignacio , Vranes Miroslav , Kämper Jörg , Pérez-Martín José
Published: August 2006

Plant invasion by pathogenic fungi involves regulated growth and highly organized fungal morphological changes. For instance, when the smut fungus Ustilago maydis infects maize (Zea mays), its dikaryotic infective filament is cell cycle arrested, and appressoria are differentiated prior to plant penetration. Once the filament enters the plant, the cell cycle block is released and fungal cells begin proliferation, suggesting a tight interaction between plant invasion and the cell cycle and morphogenesis control systems. We describe a novel factor, Biz1 (b-dependent zinc finger protein), which has two Cys2His2 zinc finger domains and nuclear localization, suggesting a transcriptional regulatory function. The deletion of biz1 shows no detectable phenotypic alterations during axenic growth. However, mutant cells show a severe reduction in appressoria formation and plant penetration, and those hyphae that invade the plant arrest their pathogenic development directly after plant penetration. biz1 is induced via the b-mating–type locus, the key control instance for pathogenic development. The gene is expressed at high levels throughout pathogenic development, which induces a G2 cell cycle arrest that is a direct consequence of the downregulation of the mitotic cyclin Clb1. Our data support a model in which Biz1 is involved in cell cycle arrest preceding plant penetration as well as in the induction of appressoria.
Visualizing Plant Development and Gene Expression in Three Dimensions Using Optical Projection Tomography
Authors: Lee Karen , Avondo Jerome , Morrison Harris , Blot Lilian , Stark Margaret , Sharpe James , Bangham Andrew , Coen Enrico
Published: August 2006

A deeper understanding of the mechanisms that underlie plant growth and development requires quantitative data on three-dimensional (3D) morphology and gene activity at a variety of stages and scales. To address this, we have explored the use of optical projection tomography (OPT) as a method for capturing 3D data from plant specimens. We show that OPT can be conveniently applied to a wide variety of plant material at a range of scales, including seedlings, leaves, flowers, roots, seeds, embryos, and meristems. At the highest resolution, large individual cells can be seen in the context of the surrounding plant structure. For naturally semitransparent structures, such as roots, live 3D imaging using OPT is also possible. 3D domains of gene expression can be visualized using either marker genes, such as β-glucuronidase, or more directly by whole-mount in situ hybridization. We also describe tools and software that allow the 3D data to be readily quantified and visualized interactively in different ways.
The Synechocystis sp PCC 6803 Oxa1 Homolog Is Essential for Membrane Integration of Reaction Center Precursor Protein pD1
Authors: Ossenbühl Friedrich , Inaba-Sulpice Masami , Meurer Jörg , Soll Jürgen , Eichacker Lutz A.
Published: August 2006

Synechocystis sp PCC 6803 Slr1471p, an Oxa1p/Alb3/YidC homolog, is an essential protein for cell viability for which functions in thylakoid membrane biogenesis and cell division have been proposed. Using a fusion of green fluorescent protein to the C terminus of Slr1471p, we found that the mutant slr1471-gfp is photochemically inhibited when light intensities increase to 80 μmol·m−2·s−1. We show that photoinhibition correlates with an increased redox potential of the reaction center quinone QA  − and a decreased redox potential of QB  −. Analysis reveals that membrane integration of the D1 precursor protein is affected, leading to the accumulation of pD1 in the membrane phase. We show that Slr1471p interacts directly with the D1 protein and discuss why the accumulation of pD1 in two reaction center assembly intermediates is dependent on Slr1471p.
Hemophilia joint health score reliability study
Authors: HILLIARD P. , FUNK S. , ZOURIKIAN N. , BERGSTROM B.‐M. , BRADLEY C. S. , MCLIMONT M. , MANCO‐JOHNSON M. , PETRINI P. , VAN DEN BERG M. , FELDMAN B. M.
Published: August 2006

Summary.  Measurement of joint health is critically important when assessing children with haemophilia. Few measures exist; they lack sensitivity to small changes, don't account for normal development and were never formally validated. To address these concerns, the Hemophilia Joint Health Score (HJHS) was developed by modifying existing scores. Objective: To test the inter‐observer and test–retest reliability of the HJHS. Methods: Using a fully factorial design, four physiotherapists (from Canada, the United States and Sweden) examined eight boys with severe haemophilia A on two consecutive days using the HJHS. The boys ranged in age from 4–12 years and presented with variable joint damage. Six index joints (elbows, knees and ankles) were assessed on 11 impairment items including swelling, flexion and extension loss and gait. Concordance was measured by the intra‐class correlation co‐efficient. Results: Reliability of the HJHS was excellent with an inter‐observer co‐efficient of 0.83 and a test–retest of 0.89. Conclusion: This study is the first in a series to assess the psychometric properties of the HJHS, a promising new measure of joint health in boys with haemophilia.
Retrospective comparative examination of the long term effects of venous access devices on upper extremity limb measurement in children with haemophilia: pilot observations from a single haemophilia treatment centre
Authors: CHRISTIE B. A. , BAUMANN K. , KURTH M. H.
Published: August 2006

Summary.  Background: Venous access devices (VADs) have been used in some individuals with haemophilia to facilitate infusions of factor concentrates. Studies have reported complications of infection and thrombosis with VADs but there have been no studies looking at the potential effect that VADs may have on growth of the upper extremities in children with haemophilia. We hypothesize that there could be potential growth discrepancies in upper extremities in children with VADs related to changes in blood flow to the extremity caused by the VADs. Methods: This study was a cohort descriptive comparative study to determine if VAD use correlated to discrepancies in upper extremity limb measurement data. A multivariate analysis compared limb measurements with VAD use, bleeding, clotting, infections, surgeries, chest wall collateral patterns and magnetic resonance venogram results. Results: A total of 59 children with haemophilia participated (36 subjects with VADs, 23 subjects without). Overall, in subjects with VADs the non‐VAD side was found to be shorter and measured less in girth than the VAD side. These differences did not reach statistical significance except bicep/tricep girth in the 11–15 age group. There was no correlation found between duration of VAD placement and subject age vs. length and girth measurements. When comparing subjects with VADs to those without VADs, no differences in measurements were seen. Differences in girth were measured between dominant hand and non‐dominant hand in all subjects indicating that the dominant hand arm was larger. Reproducibility of this data may be hampered by limitations of sample size, subject homogeneity and variability in bleeding history between subject groups.
Why do raptors take domestic prey? The case of Bonelli's eagles and pigeons
Authors: PALMA LUIS , BEJA PEDRO , PAIS MIGUEL , CANCELA DA FONSECA LUIS
Published: August 2006

Predator conservation management requires detailed understanding of the ecological circumstances associated with predation, especially that on economically valuable prey. We examined the mechanisms behind Bonelli's eagle Hieraaetus fasciatus predation on prey of domestic origin, using dietary data from 22 pairs breeding in south‐west Portugal (1992–2001) together with information on landscape composition and prey availability.

Numerically, 42·7% (37·7% in biomass) of eagle prey comprised domestic species, about 70% of which were rural pigeons Columba livia and the remainder were racing pigeons Columba livia and domestic fowl Gallus gallus. Rabbits Oryctolagus cuniculus, red‐legged partridges Alectoris rufa and jays Garrulus glandarius were the most frequent wild prey (43·1%; 50·8% in biomass). This dietary pattern was remarkably stable over a decade, but within each year the intake of pigeons almost halved over the course of the breeding season.

Landscape composition significantly affected the dietary proportion of wild and domestic prey items. This was particularly evident in territories dominated by eucalyptus Eucalyptus globulus plantations, where there was reduced consumption of rural pigeons and partridges, an increased intake of minor avian prey items and greater diversity in the diet overall.

Bonelli's eagles showed type II functional responses while preying on the most important wild (rabbit) and domestic (rural pigeon) prey, although the former was much stronger. Eagle predation on rabbits declined with increasing abundance of pigeons, and vice versa, but there was no switching in the traditional sense, as selection between these two species was inversely frequency dependent.

Synthesis and applications. Predation by Bonelli's eagle on domestic pigeons results from a combination of high vulnerability of the pigeons to eagles and a shortage of key wild prey such as rabbits and partridges, especially during the early breeding season. Given the relatively low economic value of rural pigeons and their importance in the diet of Bonelli's eagles, they could probably be used as a conservation tool to enhance food resources in breeding territories and to deflect predation from more valuable prey such as partridges and racing pigeons.
Invasive pneumococcal disease in children <5 years of age in rural Mozambique
Authors: Roca A. , Sigaúque B. , Quintó Ll. , Mandomando I. , Vallès X. , Espasa M. , Abacassamo F. , Sacarlal J. , Macete E. , Nhacolo A. , Levine M. , Alonso P.
Published: August 2006

Objectives  To estimate the incidence and epidemiological characteristics of invasive pneumococcal disease (IPD) in children <5 years of age living in a rural area of southern Mozambique.

Methods  As part of the clinical management of children admitted to Manhiça District Hospital, prospective surveillance for invasive bacterial disease was conducted from June 2001 to May 2003. The level of antibiotic resistance of the isolates was also analysed.

Results  Pneumococcus was the most commonly isolated bacterium, accounting for 212 episodes. The estimated crude incidence rate of IPD in the study area among children <5 years of age was 416/100 000 per child‐year at risk. The youngest age group (<3 months) had the highest incidence (779/100 000). Cases were detected during both rainy and dry seasons. The most common clinical diagnosis was pneumonia, made in 146/212 (69%) of the episodes of IPD. The overall case fatality rate was 10%, being highest among children with pneumococcal meningitis (5/9 = 56%). Pneumococcal isolates were highly susceptible to penicillin (86% susceptible and 14% with intermediate resistance) and chloramphenicol (98% susceptible). In contrast, up to 37% of the isolates tested were non‐susceptible to cotrimoxazole.

Conclusions  Incidence rates of IPD and associated mortality shown in this study highlight the need for pneumococcal vaccines in rural Africa, which must be effective in infants and young children.
Microbiological performance of a water treatment unit designed for household use in developing countries
Authors: Clasen Thomas , Nadakatti Suresh , Menon Shashikala
Published: August 2006

Interventions to improve water quality, particularly when deployed at the household level, are an effective means of preventing endemic diarrhoeal disease, a leading cause of mortality and morbidity. Following a national survey indicating widespread faecal contamination of drinking water in Indian cities, a point‐of‐use water treatment unit was developed, which combines filtration and disinfection, does not require power or water pressure and has an operating cost of Rs. 0.25 (US$0.0057) per litre. We assessed the microbiological performance of the unit in the laboratory over the full 1500 l design life of the unit's consumable components. Geometric mean reductions for the units were more than 6 logs (99.9999%) for bacteria, more than 7 logs (99.99999%) for viruses and more than 3 logs (99.9%) for the test surrogate for protozoan cysts. Geometric mean reductions exceeded levels established for microbial water purifiers. The product water was free of detectable chlorine. If these results are validated in field trials, the deployment of the unit on a wide scale among vulnerable populations may make an important contribution to public health efforts to control intractable waterborne diseases.
Filling in the gaps: modelling native species richness and invasions using spatially incomplete data
Authors: Jarnevich Catherine S. , Stohlgren Thomas J. , Barnett David , Kartesz John
Published: August 2006

Detailed knowledge of patterns of native species richness, an important component of biodiversity, and non‐native species invasions is often lacking even though this knowledge is essential to conservation efforts. However, we cannot afford to wait for complete information on the distribution and abundance of native and harmful invasive species. Using information from counties well surveyed for plants across the USA, we developed models to fill data gaps in poorly surveyed areas by estimating the density (number of species km−2) of native and non‐native plant species. Here, we show that native plant species density is non‐random, predictable, and is the best predictor of non‐native plant species density. We found that eastern agricultural sites and coastal areas are among the most invaded in terms of non‐native plant species densities, and that the central USA appears to have the greatest ratio of non‐native to native species. These large‐scale models could also be applied to smaller spatial scales or other taxa to set priorities for conservation and invasion mitigation, prevention, and control efforts.
Diversity, ecological structure, and conservation of the landbird community of Dadia reserve, Greece
Authors: Kati Vassiliki I. , Sekercioglu Cagan H.
Published: August 2006

Birds are integral to many environmental monitoring schemes. However, there has been little research on the ecological basis of utilizing bird species as indicators of their respective communities and habitats. We used point counts to survey 72 landbird species, 16 of conservation concern, in the Dadia Nature Reserve, Greece, in order to understand the ecology of bird diversity patterns, analyse community composition, identify species characteristic of major vegetation types, and improve long‐term management and monitoring protocols. We sampled 36 sites representing 21 vegetation types. Highly heterogeneous sites were the most species rich and rural mosaics (small fields and pastures of low intensity land use, separated by thick hedgerows and tree lines) were twice as rich as intensified crop monocultures. Using multivariate analysis, we found that vegetation cover and height affected the composition of the avifauna. Twenty‐one predefined vegetation categories clustered into eight distinct bird habitat types: field crops, rural mosaics, mosaic sites, poplar trees, broadleaved woods, pinewoods, shrubs, and heaths. Ten bird species were highly characteristic of the main bird habitat types in the study area. Our results emphasize the importance of conserving rural mosaics, hedgerows, and openings within forests for landbird conservation in the Mediterranean countryside. We also provide evidence in support of maintaining horizontal heterogeneity at a local scale. Finally, we suggest that monitoring populations of certain indicator bird species can be a cost‐effective and efficient way to monitor the state and habitat quality of the entire landbird community, thereby integrating the knowledge of community structure into conservation decision‐making.
A Redescription of the Cestodes Proteocephalus filicollis (Rudolphi) from Gasterosteus aculeatus L., and P. ambiguus (Dujardin) from Pungitius pungitius (L.)
Authors: RØDLAND J. TORE
Published: August 2006

Based on material from two stickleback species living in the same biotope, Proteocephalus filicollis (Rudolphi, 1802) and Proteocephalus ambiguus (Dujardin, 1845) are regarded as two distinct species. The most useful character for their discrimination is the presence and absence of an apical scolex of P. filicollis and P. ambiguus, respectively. Furthermore, transverse sections revealed that the longitudinal muscles consist of approximately 5 layers of muscle fibres in P. filicollis, as opposed to a single layer in P. ambiguus. The two species differ also in total length, width, number of segments and in the state (progress) of maturation of the proglottids along the strobila.
Phylogeny of Paragnathorhynchus Meixner and Aculeorhynchus Schilke (Turbellaria, Kalyptorhynchia)
Authors: KARLING TOR G.
Published: August 2006

Paragnathorhynchus subterraneus Meixner is redescribed and identified with Prognathorhynchus stilofer Schilke. The paired tubular extracapsular secretory sacs in the proboscis apparatus of Aculeorhynchus glandulis Schilke are interpreted as evolutionary derivatives of intracapsular secretory vesicles in the proboscis of some Gnathorhynchidae. Aculeorhynchus Schilke is interpreted as an apomorph sister taxon of a group of taxa in the Gnathorhynchidae.
Systematics of the Genus Eubothrium Nybelin (Cestoda, Pseudophyllidea), with Partial Re‐description of the Species
Authors: ANDERSEN KARIN I. , KENNEDY CLIVE R.
Published: August 2006

Material from as many species of the cestode genus Eubothrium as could be obtained (six out of nine existing species), from a range of hosts and from both marine and freshwater habitats, were examined both by light and scanning electron microscopy. The scolex shape as seen with SEM turned out to be a very valuable specific character. Particular attention was also paid to the possibility that intra‐specific races, distinguishable on biological criteria, might in addition exhibit characteristic morphological differences.