bluuebunny/crossref_metadata_2025_split huggingface dataset:
C and O stable isotope variability in recent freshwater carbonates (River Krka, Croatia)
Authors: Lojen S. , Dolenec T. , Vokal B. , Cukrov N. , Mihelčić G. , Papesch W. 
Published: December 2004

AbstractThree types of recent carbonate precipitates from the River Krka, Croatia, were analysed: (1) bulk tufa from four main cascades in a 34 km long section of the river flow through the Krka National Park; (2) a laminar stromatolite‐like incrustation formed in the tunnel of a hydroelectric power plant close to the lowest cascade; and (3) recent precipitates collected on artificial substrates during winter, spring and summer periods. Stable isotope compositions of carbon (δ13C) and oxygen (δ18O) in the carbonate and organic carbon (δ13Corg) were determined and compared with δ18O of water and δ13C of dissolved inorganic carbon (DIC). The source of DIC, which provides C for tufa precipitation, was determined from the slope of the line ([DIC]/[DIC0]−1) vs. (δ13C‐DIC × ([DIC]/[DIC0])) (Sayles & Curry, 1988). The δ13C value of added DIC was −13·6‰, corresponding to the dissolution of CO2 with δ13C between −19·5 and −23·0‰ Vienna Pee Dee Belemnite (VPDB). The observed difference between the measured and calculated equilibrium temperature of precipitation of bulk tufa barriers indicates that the higher the water temperature, the larger the error in the estimated temperature of precipitation. This implies that the climatic signals may be valid only in tufas precipitated at lower and relatively stable temperatures. The laminar crust comprising a continuous record of the last 40 years of precipitation shows a consistent trend of increasing δ13C and decreasing δ18O. The lack of covariation between δ13C and δ18O indicates that precipitation of calcite was not kinetically controlled for either of the elements. δ13C and δ18O of precipitates collected on different artificial substrates show that surface characteristics both of substrates and colonizing biota play an important role in C and O isotope fractionation during carbonate precipitation.
The Pseudomonas syringae type III effector AvrRpt2 functions downstream or independently of SA to promote virulence on Arabidopsis thaliana
Authors: Chen Zhongying , Kloek Andrew P. , Cuzick Alayne , Moeder Wolfgang , Tang Dingzhong , Innes Roger W. , Klessig Daniel F. , McDowell John M. , Kunkel Barbara N. 
Published: December 2004

SummaryAvrRpt2, a Pseudomonas syringae type III effector protein, functions from inside plant cells to promote the virulence of P. syringae pv. tomato strain DC3000 (PstDC3000) on Arabidopsis thaliana plants lacking a functional copy of the corresponding RPS2 resistance gene. In this study, we extended our understanding of AvrRpt2 virulence activity by exploring the hypothesis that AvrRpt2 promotes PstDC3000 virulence by suppressing plant defenses. When delivered by PstDC3000, AvrRpt2 suppresses pathogen‐related (PR) gene expression during infection, suggesting that AvrRpt2 suppresses defenses mediated by salicylic acid (SA). However, AvrRpt2 promotes PstDC3000 growth on transgenic plants expressing the SA‐degrading enzyme NahG, indicating that AvrRpt2 does not promote bacterial virulence by modulating SA levels during infection. AvrRpt2 general virulence activity does not depend on the RPM1 resistance gene, as mutations in RPM1 had no effect on AvrRpt2‐induced phenotypes. Transgenic plants expressing AvrRpt2 displayed enhanced susceptibility to PstDC3000 strains defective in type III secretion, indicating that enhanced susceptibility of these plants is not because of suppression of defense responses elicited by other type III effectors. Additionally, avrRpt2 transgenic plants did not exhibit increased susceptibility to Peronospora parasitica and Erysiphe cichoracearum, suggesting that AvrRpt2 virulence activity is specific to P. syringae.
Forest tent caterpillars (Malacosoma disstria) induce local and systemic diurnal emissions of terpenoid volatiles in hybrid poplar (Populus trichocarpa × deltoides): cDNA cloning, functional characterization, and patterns of gene expression of (−)‐germacrene D synthase, PtdTPS1
Authors: Arimura Gen‐ichiro , Huber Dezene P. W. , Bohlmann Jörg 
Published: December 2004

SummaryFeeding forest tent caterpillars (FTCs) induced local and systemic diurnal emissions of (−)‐germacrene D, along with (E)‐β‐ocimene, linalool, (E)‐4,8‐dimethyl‐1,3,7‐nonatriene (DMNT), benzene cyanide, and (E,E)‐α‐farnesene, from leaves of hybrid poplar. FTC feeding induced substantially higher levels of volatiles in local and systemic leaves than did mechanical wounding. A full‐length poplar sesquiterpene synthase cDNA (PtdTPS1) was isolated and functionally identified as (−)‐germacrene D synthase. Expression of PtdTPS1, expression of genes of early, intermediate and late steps in terpenoid biosynthesis, and expression of a lipoxygenase gene (PtdLOX1) were analyzed in local FTC‐infested and systemic leaves. Transcript levels of PtdTPS1 and PtdLOX1 were strongly increased in response to herbivory. PtdTPS1 was also induced by mechanical wounding or by methyl jasmonate (MeJA) treatment. FTC feeding did not affect transcript levels of 3‐hydroxy‐3‐methylglutaryl‐CoA reductase (HMGR), 1‐deoxy‐d‐xylulose 5‐phosphate reductoisomerase (DXR), and isoprene synthase (IPS). Two other TPS genes, PtdTPS2 and PtTPS3, and farnesyl diphosphate synthase were only very transiently induced. These results illustrate differential expression of terpenoid pathway genes in response to insect feeding and a key function of (−)‐germacrene D synthase PtdTPS1 for herbivore‐induced local and systemic volatile emissions in hybrid poplar. FTC‐induced transcripts of PtdTPS1 followed diurnal rhythm. Spatial patterns of FTC‐induced PtdTPS1 transcript accumulation revealed acropetal but not basipetal direction of the systemic response. Implications for tritrophic poplar‐FTC‐predator/parasitoid interactions are discussed.
Glycerol‐insensitive Arabidopsis mutants: gli1 seedlings lack glycerol kinase, accumulate glycerol and are more resistant to abiotic stress
Authors: Eastmond Peter J. 
Published: December 2004

SummaryThe aim of this study was to investigate the process of glycerol catabolism in germinating Arabidopsis seed. A genetic screen was performed to isolate glycerol‐insensitive (gli) mutant seedlings. Three separate mutant loci were identified (gli1, gli2 and gli3). Of these, only gli1 is unable to utilise glycerol. Following germination, gli1 seedlings transiently accumulate glycerol derived from the breakdown of storage oil and are more resistant to hyperosmotic stress, salt stress, oxidative stress, freezing and desiccation. Enzyme assays revealed that gli1 lacks glycerol kinase activity. GLI1 mapped to chromosome 1 near the putative glycerol kinase gene NHO1. Mutations in this gene were identified in three independent gli1 alleles. A cDNA encoding GLI1 was cloned and its function was proven by complementation of an Escherichia coli glycerol kinase (glpK) deletion strain. Quantitative RT‐PCR analysis showed that GLI1 is expressed in all tissues, but is transiently upregulated during early post‐germinative growth and leaf senescence. These data show that glycerol kinase is required for glycerol catabolism in Arabidopsis and that the accumulation of glycerol can enhance resistance to a variety of abiotic stresses associated with dehydration.
GID2, an F‐box subunit of the SCF E3 complex, specifically interacts with phosphorylated SLR1 protein and regulates the gibberellin‐dependent degradation of SLR1 in rice
Authors: Gomi Kenji , Sasaki Akie , Itoh Hironori , Ueguchi‐Tanaka Miyako , Ashikari Motoyuki , Kitano Hidemi , Matsuoka Makoto 
Published: December 2004

SummaryThe phytohormone gibberellin (GA) controls growth and development in plants. Previously, we identified a rice F‐box protein, gibberellin‐insensitive dwarf2 (GID2), which is essential for GA‐mediated DELLA protein degradation. In this study, we analyzed the biological and molecular biological properties of GID2. Expression of GID2 preferentially occurred in rice organs actively synthesizing GA. Domain analysis of GID2 revealed that the C‐terminal regions were essential for the GID2 function, but not the N‐terminal region. Yeast two‐hybrid assay and immunoprecipitation experiments demonstrated that GID2 is a component of the SCF complex through an interaction with a rice ASK1 homolog, OsSkp15. Furthermore, an in vitro pull‐down assay revealed that GID2 specifically interacted with the phosphorylated Slender Rice 1 (SLR1). Taken these results together, we conclude that the phosphorylated SLR1 is caught by the SCFGID2 complex through an interacting affinity between GID2 and phosphorylated SLR1, triggering the ubiquitin‐mediated degradation of SLR1.
Involvement of MEK1 MAPKK, NTF6 MAPK, WRKY/MYB transcription factors, COI1 and CTR1 in N‐mediated resistance to tobacco mosaic virus
Authors: Liu Yule , Schiff Michael , Dinesh‐Kumar S. P. 
Published: December 2004

SummaryThe tobacco N gene, a member of the Toll‐interleukin 1 homology region/nucleotide binding site/leucine‐rich repeat (TIR–NBS–LRR) class of resistance (R) genes, confers resistance to tobacco mosaic virus (TMV). We used a candidate gene approach to identify known defense genes that were also involved in N signaling. The requirement for these genes was determined by downregulating their expression using the well‐established tobacco rattle virus (TRV)‐based virus‐induced gene silencing (VIGS). Silencing of genes encoding a mitogen‐activated protein kinase (MAPK) NTF6/NRK1, or an MAPK kinase (MAPKK) MEK1/NQK1, attenuated N‐mediated resistance to TMV. We also found that N resistance is compromised in plants in which expression of WRKY1–WRKY3 and MYB1 transcription factors were downregulated. In addition, suppression of jasmonic acid (JA) signaling component COI1 ortholog affected N function. However, downregulation of expression of CTR1 ortholog leads to more rapid hypersensitive response (HR). The involvement of these genes in N‐ and other R‐gene‐mediated defense provides further evidence for the convergence of downstream signaling pathways of different R genes.
Phenotypic characterization of a photomorphogenic mutant
Authors: Fankhauser Christian , Casal Jorge J. 
Published: December 2004

SummaryLight is arguably the most important abiotic factor controlling plant growth and development throughout their life cycle. Plants have evolved sophisticated light‐sensing mechanisms to monitor fluctuations in light quality, intensity, direction and periodicity (day length). InArabidopsis, three families of photoreceptors have been identified by molecular genetic studies. The UV‐A/blue light receptors cryptochromes and the red/far‐red receptors phytochromes control an overlapping set of responses including photoperiodic flowering induction and de‐etiolation. Phototropins are the primary photoreceptors for a set of specific responses to UV‐A/blue light such as phototropism, chloroplast movement and stomatal opening. Mutants affecting a photoreceptor have a characteristic phenotype. It is therefore possible to determine the specific developmental responses and the photoreceptor pathway(s) affected in a mutant by performing an appropriate set of photobiological and genetic experiments. In this paper, we outline the principal and easiest experiments that can be performed to obtain a first indication about the nature of the photobiological defect in a given mutant.
Establishing gene function by mutagenesis in Arabidopsis thaliana
Authors: Østergaard Lars , Yanofsky Martin F. 
Published: December 2004

SummaryThe nuclear genome of Arabidopsis thaliana was sequenced to near completion a few years ago, and ahead lies the challenge of understanding its meaning and discerning its potential. How many genes are there? What are they? What do they do? Computer algorithms combined with genome array technologies have proven efficient in addressing the first two questions as shown in a recent report (Yamada et al., 2003). However, assessing the function of every gene in every cell will require years of careful analyses of the phenotypes caused by mutations in each gene. Current progress in generating large numbers of molecular markers and near‐saturation insertion mutant collections has immensely facilitated functional genomics studies in Arabidopsis. In this review, we focus on how gene function can be revealed through the analysis of mutants by either forward or reverse genetics. These mutants generally fall into two distinct classes. The first class typically includes point mutations or small deletions derived from chemical or fast neutron mutagenesis whereas the second class includes insertions of transferred‐DNA or transposon elements. We describe the current methods that are used to identify the gene corresponding to these mutations, which can then be used as a probe to further dissect its function.
Applications and advantages of virus‐induced gene silencing for gene function studies in plants
Authors: Burch‐Smith Tessa M. , Anderson Jeffrey C. , Martin Gregory B. , Dinesh‐Kumar S. P. 
Published: December 2004

SummaryVirus‐induced gene silencing (VIGS) is a recently developed gene transcript suppression technique for characterizing the function of plant genes. The approach involves cloning a short sequence of a targeted plant gene into a viral delivery vector. The vector is used to infect a young plant, and in a few weeks natural defense mechanisms of the plant directed at suppressing virus replication also result in specific degradation of mRNAs from the endogenous plant gene that is targeted for silencing. VIGS is rapid (3–4 weeks from infection to silencing), does not require development of stable transformants, allows characterization of phenotypes that might be lethal in stable lines, and offers the potential to silence either individual or multiple members of a gene family. Here we briefly review the discoveries that led to the development of VIGS and what is known about the experimental requirements for effective silencing. We describe the methodology of VIGS and how it can be optimized and used for both forward and reverse genetics studies. Advantages and disadvantages of VIGS compared with other loss‐of‐function approaches available for plants are discussed, along with how the limitations of VIGS might be overcome. Examples are reviewed where VIGS has been used to provide important new insights into the roles of specific genes in plant development and plant defense responses. Finally, we examine the future prospects for VIGS as a powerful tool for assessing and characterizing the function of plant genes.
Two Arabidopsis srfr (suppressor of rps4‐RLD) mutants exhibit avrRps4‐specific disease resistance independent of RPS4
Authors: Kwon Soon Il , Koczan Jessica M. , Gassmann Walter 
Published: December 2004

Summary RPS4 specifies the Arabidopsis disease resistance response to Pseudomonas syringae pv. tomato expressing avrRps4 and was cloned based on the identification of RLD as a naturally occurring susceptible accession. To dissect the molecular and genetic basis of disease resistance, we used a genetic approach to identify suppressor mutations that reactivate the avrRps4‐triggered defense response in RLD. In this report, we describe two non‐allelic srfr (suppressor of rps4‐RLD) mutants, srfr1 and srfr3, that were susceptible to virulent P. syringae pv. tomato strain DC3000, but resistant to DC3000 expressing avrRps4. In quantitative bacterial growth assays, growth of DC3000 was similar in wild‐type control and both mutant lines, indicating that basal resistance was not enhanced in srfr1 and srfr3. Growth of DC3000 (avrRps4) was approximately 30‐fold lower in srfr1 and srfr3 than in RLD, but intermediate compared with fully resistant Col‐0 and transgenic RLD containing RPS4‐Col. The srfr1 and srfr3 mutants did not develop spontaneous lesions prior to inoculation or constitutively express the pathogenesis‐related gene PR‐1. Therefore, srfr1 and srfr3 constitute novel avr‐specific mutants that differ from previously described Arabidopsis mutants with elevated disease resistance. The srfr1 and srfr3 mutations were recessive, and both mapped to the bottom of chromosome IV. Genetic analysis indicated that resistance in srfr1 and srfr3 was independent of the rps4‐RLD allele, but dependent on a second gene in RLD. We propose that SRFR1 and SRFR3 are negative regulators of avrRps4‐triggered gene‐for‐gene disease resistance.
A single amino acid substitution in the Arabidopsis FIERY1/HOS2 protein confers cold signaling specificity and lithium tolerance
Authors: Xiong Liming , Lee Hojoung , Huang Rongfeng , Zhu Jian‐Kang 
Published: December 2004

SummaryLow temperature induces the expression of many plant genes through undefined signaling pathways. To gain insight into cold signal transduction mechanisms, we isolated Arabidopsis mutants that exhibited altered regulation of low temperature‐induced gene expression. One such mutant, hos2, was shown previously to have an enhanced induction of stress‐responsive genes by cold, whereas the expression of these genes under osmotic stress or the phytohormone absciscic acid (ABA) treatments was not affected. Here we further define the targets of HOS2 by examining the regulation of upstream cold‐specific CBF transcription factor genes. It was found that the transcript levels of CBF2 and CBF3 were significantly higher in hos2 mutant plants than in the wild type under cold treatments, suggesting that HOS2 may act upstream of CBFs. The HOS2 gene was cloned using a map‐based strategy. Surprisingly, HOS2 is identical to the FIERY1 gene that we had described previously. FIERY1 is a general negative regulator that controls cold, osmotic stress, and ABA signal transduction and possesses inositol polyphosphate 1‐phosphatase activity. The hos2 mutation rendered the HOS2/FIERY1 recombinant protein completely inactive in the cold but did not substantially affect its activity at warm temperatures. Interestingly, the hos2 mutant protein is extremely tolerant to Li+. This study provides a unique example of a single amino acid substitution in a critical regulator that can lead to conditional changes in protein functions and distinct plant phenotypes. The results reinforce the notion that phosphoinositols are important second messengers in cold signal transduction, and shed light on how the diversity of plant tolerance to cold and other abiotic stresses may evolve due to variations in a common molecular switch.
Sequence composition, organization, and evolution of the core Triticeae genome
Authors: Li Wanlong , Zhang Peng , Fellers John P. , Friebe Bernd , Gill Bikram S. 
Published: December 2004

SummaryWe investigated the composition and the basis of genome expansion in the core Triticeae genome using Aegilops tauschii, the D‐genome donor of bread wheat. We sequenced an unfiltered genomic shotgun (trs) and a methylation–filtration (tmf) library of A. tauschii, and analyzed wheat expressed sequence tags (ESTs) to estimate the expression of genes and transposable elements (TEs). The sampled D‐genome sequences consisted of 91.6% repetitive elements, 2.5% known genes, and 5.9% low‐copy sequences of unknown function. TEs constituted 68.2% of the D‐genome compared with 50% in maize and 14% in rice. The DNA transposons constituted 13% of the D‐genome compared with 2% in maize. TEs were methylated unevenly within and among elements and families, and most were transcribed which contributed to genome expansion in the core Triticeae genome. The copy number of a majority of repeat families increased gradually following polyploidization. Certain TE families occupied discrete chromosome territories. Nested insertions and illegitimate recombination occurred extensively between the TE families, and a majority of the TEs contained internal deletions. The GC content varied significantly among the three sequence sets examined ranging from 42% in tmf to 46% in trs and 52% in the EST. Based on enrichment of genic sequences, methylation–filtration offers one option, although not as efficient as in maize, for isolating gene‐rich regions from the large genome of wheat.
The NAC domain mediates functional specificity of CUP‐SHAPED COTYLEDON proteins
Authors: Taoka Ken‐ichiro , Yanagimoto Yoshiko , Daimon Yasufumi , Hibara Ken‐ichiro , Aida Mitsuhiro , Tasaka Masao 
Published: December 2004

SummaryIn higher plants, although several genes involved in shoot apical meristem (SAM) formation and organ separation have been isolated, the molecular mechanisms by which they function are largely unknown. CUP‐SHAPED COTYLEDON (CUC) 1 and CUC2 are examples of two such genes that encode the NAC domain proteins. This study investigated the molecular basis for their activities. Nuclear localization assays indicated that green fluorescent protein (GFP)‐CUC proteins accumulate in the nucleus. Yeast one‐hybrid and transient expression assays demonstrated that the C‐terminal domain (CTD) of the CUC has transactivation activity. Domain‐swapping experiments revealed that the functional specificity of the CUC for promoting adventitious shoot formation resides in the highly conserved NAC domain, not in the CTD in which motifs specific to the CUC subfamily are located. Taken together, these observations suggest that CUC proteins transactivate the target genes involved in SAM formation and organ separation through a specific interaction between the NAC domain and the promoter region of the target genes.
Out of hospital treatment of patients with melioidosis using ceftazidime in 24 h elastomeric infusors, via peripherally inserted central catheters
Authors: Huffam Sarah , Jacups Susan P. , Kittler Paulene , Currie Bart J. 
Published: December 2004

SummaryBackground  In the tropical north of the Northern Territory, Australia, 25–50 patients are admitted to Royal Darwin Hospital (RDH) each year with Burkholderia pseudomallei infection, or melioidosis. Treatment consists of initial intensive therapy with 2–4 weeks of intravenous antibiotics. Clinical improvement may occur early and patients often prefer to be managed out of hospital in the Hospital in the Home (HITH).Objectives  To evaluate safety and efficacy of HITH management of patients with melioidosis.Methods  A prospective observational study of our standard management which consists of 24 h infusions of ceftazidime infused through a peripherally inserted central catheter (PICC) line, plus oral sulphamethoxazole trimethoprim. Treatment is administered in the home, which may be in Darwin, regional areas or remote communities, or in a self‐care unit located in the hospital grounds.Results  From February 1998 to December 2001 150 patients were admitted to RDH with culture confirmed B. pseudomallei infection. Of these, 73 patients were treated with 24 h infusions of ceftazidime, of which 70 patients were managed by HITH. Complications of treatment include a PICC line complication rate of 10.6/1000 days in situ. Nine patients had relapse or recrudescence of disease, nearly all as a result of poor adherence to subsequent oral eradication therapy, these patients were all re‐treated successfully. One patient remains infected with B. pseudomallei.Conclusion  This clinical outcome study suggests that out of hospital management of melioidosis with 24 h infusions of ceftazidime via a PICC line is safe and effective.