bluuebunny/crossref_metadata_2025_split huggingface dataset:
Viroid-Induced Symptoms inNicotiana benthamianaPlants Are Dependent on RDR6 Activity
Authors: Gómez Gustavo , Martínez Germán , Pallás Vicente 
Published: July 2008

AbstractViroids are small self-replicating RNAs that infect plants. How these noncoding pathogenic RNAs interact with hosts to induce disease symptoms is a long-standing unanswered question. Recent experimental data have led to the suggestive proposal of a pathogenic model based on the RNA silencing mechanism. However, evidence of a direct relation between key components of the RNA silencing pathway and symptom expression in infected plants remains elusive. To address this issue, we used a symptomatic transgenic line of Nicotiana benthamiana that expresses and processes dimeric forms of Hop stunt viroid (HSVd). These plants were analyzed under different growing temperature conditions and were used as stocks in grafting assays with the rdr6i-Nb line, in which the RNA-dependent RNA polymerase 6 (RDR6) is constitutively silenced. Here, we show that the symptom expression in N. benthamiana plants is independent of HSVd accumulation levels but dependent on an active state of the viroid-specific RNA silencing pathway. The scion of rdr6i-Nb plants remained asymptomatic when grafted onto symptomatic plants, despite an accumulation of a high level of mature forms of HSVd, indicating the requirement of RDR6 for viroid-induced symptom production. In addition, the RDR6 requirement for symptom expression was also observed in wild-type N. benthamiana plants mechanically infected with HSVd. These results provide biological evidence of the involvement of the viroid-specific RNA silencing pathway in the symptom expression associated with viroid pathogenesis.
Proteome-Wide Characterization of Seed Aging in Arabidopsis: A Comparison between Artificial and Natural Aging Protocols
Authors: Rajjou Loïc , Lovigny Yoann , Groot Steven P.C. , Belghazi Maya , Job Claudette , Job Dominique 
Published: July 2008

AbstractA variety of mechanisms have been proposed to account for the extension of life span in seeds (seed longevity). In this work, we used Arabidopsis (Arabidopsis thaliana) seeds as a model and carried out differential proteomics to investigate this trait, which is of both ecological and agricultural importance. In our system based on a controlled deterioration treatment (CDT), we compared seed samples treated for different periods of time up to 7 d. Germination tests showed a progressive decrease of germination vigor depending on the duration of CDT. Proteomic analyses revealed that this loss in seed vigor can be accounted for by protein changes in the dry seeds and by an inability of the low-vigor seeds to display a normal proteome during germination. Furthermore, CDT strongly increased the extent of protein oxidation (carbonylation), which might induce a loss of functional properties of seed proteins and enzymes and/or enhance their susceptibility toward proteolysis. These results revealed essential mechanisms for seed vigor, such as translational capacity, mobilization of seed storage reserves, and detoxification efficiency. Finally, this work shows that similar molecular events accompany artificial and natural seed aging.
Integration of Carbon and Nitrogen Metabolism with Energy Production Is Crucial to Light Acclimation in the CyanobacteriumSynechocystis
Authors: Singh Abhay K. , Elvitigala Thanura , Bhattacharyya-Pakrasi Maitrayee , Aurora Rajeev , Ghosh Bijoy , Pakrasi Himadri B. 
Published: July 2008

AbstractLight drives the production of chemical energy and reducing equivalents in photosynthetic organisms required for the assimilation of essential nutrients. This process also generates strong oxidants and reductants that can be damaging to the cellular processes, especially during absorption of excess excitation energy. Cyanobacteria, like other oxygenic photosynthetic organisms, respond to increases in the excitation energy, such as during exposure of cells to high light (HL) by the reduction of antenna size and photosystem content. However, the mechanism of how Synechocystis sp. PCC 6803, a cyanobacterium, maintains redox homeostasis and coordinates various metabolic processes under HL stress remains poorly understood. In this study, we have utilized time series transcriptome data to elucidate the global responses of Synechocystis to HL. Identification of differentially regulated genes involved in the regulation, protection, and maintenance of redox homeostasis has offered important insights into the optimized response of Synechocystis to HL. Our results indicate a comprehensive integrated homeostatic interaction between energy production (photosynthesis) and energy consumption (assimilation of carbon and nitrogen). In addition, measurements of physiological parameters under different growth conditions showed that integration between the two processes is not a consequence of limitations in the external carbon and nitrogen levels available to the cells. We have also discovered the existence of a novel glycosylation pathway, to date known as an important nutrient sensor only in eukaryotes. Up-regulation of a gene encoding the rate-limiting enzyme in the hexosamine pathway suggests a regulatory role for protein glycosylation in Synechocystis under HL.
Conifers, Angiosperm Trees, and Lianas: Growth, Whole-Plant Water and Nitrogen Use Efficiency, and Stable Isotope Composition (δ
13C and δ
18O) of Seedlings Grown in a Tropical Environment
Authors: Cernusak Lucas A. , Winter Klaus , Aranda Jorge , Turner Benjamin L. 
Published: July 2008

Abstract
Seedlings of several species of gymnosperm trees, angiosperm trees, and angiosperm lianas were grown under tropical field conditions in the Republic of Panama; physiological processes controlling plant C and water fluxes were assessed across this functionally diverse range of species. Relative growth rate, r, was primarily controlled by the ratio of leaf area to plant mass, of which specific leaf area was a key component. Instantaneous photosynthesis, when expressed on a leaf-mass basis, explained 69% of variation in r (P &lt; 0.0001, n = 94). Mean r of angiosperms was significantly higher than that of the gymnosperms; within angiosperms, mean r of lianas was higher than that of trees. Whole-plant nitrogen use efficiency was also significantly higher in angiosperm than in gymnosperm species, and was primarily controlled by the rate of photosynthesis for a given amount of leaf nitrogen. Whole-plant water use efficiency, TEc, varied significantly among species, and was primarily controlled by c i/c a, the ratio of intercellular to ambient CO2 partial pressures during photosynthesis. Instantaneous measurements of c i/c a explained 51% of variation in TEc (P &lt; 0.0001, n = 94). Whole-plant 13C discrimination also varied significantly as a function of c i/c a (R 2 = 0.57, P &lt; 0.0001, n = 94), and was, accordingly, a good predictor of TEc. The 18O enrichment of stem dry matter was primarily controlled by the predicted 18O enrichment of evaporative sites within leaves (R 2 = 0.61, P &lt; 0.0001, n = 94), with some residual variation explained by mean transpiration rate. Measurements of carbon and oxygen stable isotope ratios could provide a useful means of parameterizing physiological models of tropical forest trees.
Mutations in SUPPRESSOR OF VARIEGATION1, a Factor Required for Normal Chloroplast Translation, Suppress var2-Mediated Leaf Variegation in Arabidopsis
Authors: Yu Fei , Liu Xiayan , Alsheikh Muath , Park Sungsoon , Rodermel Steve 
Published: July 2008

Abstract
The Arabidopsis thaliana yellow variegated2 (var2) mutant is variegated due to lack of a chloroplast FtsH-like metalloprotease (FtsH2/VAR2). We have generated suppressors of var2 variegation to gain insight into factors and pathways that interact with VAR2 during chloroplast biogenesis. Here, we describe two such suppressors. Suppression of variegation in the first line, TAG-FN, was caused by disruption of the nuclear gene (SUPPRESSOR OF VARIEGATION1 [SVR1]) for a chloroplast-localized homolog of pseudouridine (Ψ) synthase, which isomerizes uridine to Ψ in noncoding RNAs. svr1 single mutants were epistatic to var2, and they displayed a phenotypic syndrome that included defects in chloroplast rRNA processing, reduced chloroplast translation, reduced chloroplast protein accumulation, and elevated chloroplast mRNA levels. In the second line (TAG-IE), suppression of variegation was caused by a lesion in SVR2, the gene for the ClpR1 subunit of the chloroplast ClpP/R protease. Like svr1, svr2 was epistatic to var2, and clpR1 mutants had a phenotype that resembled svr1. We propose that an impairment of chloroplast translation in TAG-FN and TAG-IE decreased the demand for VAR2 activity during chloroplast biogenesis and that this resulted in the suppression of var2 variegation. Consistent with this hypothesis, var2 variegation was repressed by chemical inhibitors of chloroplast translation. In planta mutagenesis revealed that SVR1 not only played a role in uridine isomerization but that its physical presence was necessary for proper chloroplast rRNA processing. Our data indicate that defects in chloroplast rRNA processing are a common, but not universal, molecular phenotype associated with suppression of var2 variegation.
Badh2, Encoding Betaine Aldehyde Dehydrogenase, Inhibits the Biosynthesis of 2-Acetyl-1-Pyrroline, a Major Component in Rice Fragrance
Authors: Chen Saihua , Yang Yi , Shi Weiwei , Ji Qing , He Fei , Zhang Ziding , Cheng Zhukuan , Liu Xiangnong , Xu Mingliang 
Published: July 2008

Abstract
In rice (Oryza sativa), the presence of a dominant Badh2 allele encoding betaine aldehyde dehydrogenase (BADH2) inhibits the synthesis of 2-acetyl-1-pyrroline (2AP), a potent flavor component in rice fragrance. By contrast, its two recessive alleles, badh2-E2 and badh2-E7, induce 2AP formation. Badh2 was found to be transcribed in all tissues tested except for roots, and the transcript was detected at higher abundance in young, healthy leaves than in other tissues. Multiple Badh2 transcript lengths were detected, and the complete, full-length Badh2 transcript was much less abundant than partial Badh2 transcripts. 2AP levels were significantly reduced in cauliflower mosaic virus 35S-driven transgenic lines expressing the complete, but not the partial, Badh2 coding sequences. In accordance, the intact, full-length BADH2 protein (503 residues) appeared exclusively in nonfragrant transgenic lines and rice varieties. These results indicate that the full-length BADH2 protein encoded by Badh2 renders rice nonfragrant by inhibiting 2AP biosynthesis. The BADH2 enzyme was predicted to contain three domains: NAD binding, substrate binding, and oligomerization domains. BADH2 was distributed throughout the cytoplasm, where it is predicted to catalyze the oxidization of betaine aldehyde, 4-aminobutyraldehyde (AB-ald), and 3-aminopropionaldehyde. The presence of null badh2 alleles resulted in AB-ald accumulation and enhanced 2AP biosynthesis. In summary, these data support the hypothesis that BADH2 inhibits 2AP biosynthesis by exhausting AB-ald, a presumed 2AP precursor.
Tomato Protein Kinase 1b Mediates Signaling of Plant Responses to Necrotrophic Fungi and Insect Herbivory
Authors: AbuQamar Synan , Chai Mao-Feng , Luo Hongli , Song Fengming , Mengiste Tesfaye 
Published: July 2008

Abstract
The tomato protein kinase 1 (TPK1b) gene encodes a receptor-like cytoplasmic kinase localized to the plasma membrane. Pathogen infection, mechanical wounding, and oxidative stress induce expression of TPK1b, and reducing TPK1b gene expression through RNA interference (RNAi) increases tomato susceptibility to the necrotrophic fungus Botrytis cinerea and to feeding by larvae of tobacco hornworm (Manduca sexta) but not to the bacterial pathogen Pseudomonas syringae. TPK1b RNAi seedlings are also impaired in ethylene (ET) responses. Notably, susceptibility to Botrytis and insect feeding is correlated with reduced expression of the proteinase inhibitor II gene in response to Botrytis and 1-aminocyclopropane-1-carboxylic acid, the natural precursor of ET, but wild-type expression in response to mechanical wounding and methyl-jasmonate. TPK1b functions independent of JA biosynthesis and response genes required for resistance to Botrytis. TPK1b is a functional kinase with autophosphorylation and Myelin Basis Protein phosphorylation activities. Three residues in the activation segment play a critical role in the kinase activity and in vivo signaling function of TPK1b. In sum, our findings establish a signaling role for TPK1b in an ET-mediated shared defense mechanism for resistance to necrotrophic fungi and herbivorous insects.
Haematopoietic lineage‐committed bone marrow cells, but not cloned cultured mesenchymal stem cells, contribute to regeneration of renal tubular epithelium after HgCl2‐induced acute tubular injury
Authors: Fang T.‐C. , Otto W. R. , Rao J. , Jeffery R. , Hunt T. , Alison M. R. , Cook H. T. , Wright N. A. , Poulsom R. 
Published: July 2008

Abstract.  Objective: Our previous studies have demonstrated that endogenous bone marrow cells (BMCs) contribute to renal tubular regeneration after acute tubular injury. The aim of this study was to examine which fraction of BMCs, haematopoietic lineage marrow cells (HLMCs) or mesenchymal stem cells (MSCs), are effective. Materials and methods: Six‐week‐old female mice were lethally irradiated and were transplanted with female enhanced green fluorescent protein‐positive (GFP+), plastic non‐adherent marrow cells (as a source of HLMCs) plus cloned cultured male GFP− MSCs. Four weeks later, they were assigned into two groups: control mice with vehicle treatment and mice treated with HgCl2. Tritiated thymidine was given 1 h before animal killing which occurred at intervals over 2 weeks. Kidney sections were stained for a tubular epithelial marker, cell origin indicated by GFP immunohistochemistry or Y chromosome in situ hybridization; periodic acid‐Schiff staining was performed, and samples were subjected to autoradiography. One thousand consecutive renal tubular epithelial cells per mouse, in S phase, were scored as either female (indigenous) GFP+ (HLMC‐derived) or male (MSC‐derived). Results: Haematopoietic lineage marrow cells and MSCs stably engrafted into bone marrow and spleen, but only HLMC‐derived cells, not MSCs, were found in the renal tubules and were able to undergo DNA synthesis after acute renal injury. A few MSCs were detected in the renal interstitium, but their importance needs to be further explored. Conclusion: Haematopoietic lineage marrow cells, but not cloned cultured MSCs, can play a role not only in normal wear‐and‐tear turnover of renal tubular cells, but also in repair after tubular injury.
Using soil knowledge for the evaluation of mid‐infrared diffuse reflectance spectroscopy for predicting soil physical and mechanical properties
Authors: Minasny B. , McBratney A. B. , Tranter G. , Murphy B. W. 
Published: July 2008

SummaryMid‐infrared diffuse reflectance spectroscopy can provide rapid, cheap and relatively accurate predictions for a number of soil properties. Most studies have found that it is possible to estimate chemical properties that are related to surface and solid material composition. This paper focuses on prediction of physical and mechanical properties, with emphasis on the elucidation of possible mechanisms of prediction. Soil physical properties that are based on pore‐space relationships such as bulk density, water retention and hydraulic conductivity cannot be predicted well using MIR spectroscopy. Hydraulic conductivity was measured using a tension‐disc permeameter, excluding the macropore effect, but MIR spectroscopy did not give a good prediction. Properties based on the soil solid composition and surfaces such as clay content and shrink‐swell potential can be predicted reasonably well. Macro‐aggregate stability in water can be predicted reasonably as it has a strong correlation with carbon content in the soil. We found that most of the physical and mechanical properties can be related back to the fundamental soil properties such as clay content, carbon content, cation exchange capacity and bulk density. These connections have been explored previously in pedotransfer functions studies. The concept of a spectral soil inference system is reiterated: linking the spectra to basic soil properties and connecting basic soil properties to other functional soil properties via pedotransfer functions.
Distribution and community structure of ichthyoplankton from the northern and central California Current in May 2004–06
Authors: AUTH TOBY D. 
Published: July 2008

AbstractThe distributions, concentrations, and community structure of pelagic larval fishes collected from the central and northern California Current in the northeast Pacific Ocean during May 2004, 2005, and 2006 were analyzed to investigate inter‐annual, latitudinal, cross‐shelf, and depth‐stratified variability. The inter‐annual climate‐induced variability during the sampling period provided a unique opportunity to observe how larval fish communities adjust to rapidly changing environmental conditions. The 170 depth‐stratified samples collected from three cruises yielded 14 819 fish larvae from 56 taxa representing 23 families. Dominant larval taxa were Engraulis mordax, Citharichthys spp., Sebastes spp., and Stenobrachius leucopsarus. Larval concentrations decreased significantly in 2006 from 2004 and 2005 levels following the anomalous oceanic conditions observed in 2005 and decreased water temperature in 2006. Larvae were generally found in higher concentrations at northern (>43°N) versus southern (<43°N) stations, with larval E. mordax and Citharichthys spp. found almost exclusively in the north during all sampled years. Inter‐annual variability related to dynamic upwelling intensity was observed in cross‐shelf larval distributions, although concentrations of S. leucopsarus larvae consistently increased in the offshore direction, while larval Sebastes spp. were generally found in highest concentrations at intermediate stations along the shelf. Multivariate analyses revealed that latitude, station depth, and sea‐surface temperature were the most important factors explaining variability in larval concentrations. The present study shows that the ichthyoplankton community of the central and northern California Current changed dramatically in response to the variable environmental conditions of 2004–06.
Scale dependence in the species‐discharge relationship for fishes of the southeastern U.S.A.
Authors: MCGARVEY DANIEL J. , WARD G. MILTON 
Published: July 2008

Summary1. Species‐discharge relationships (SDR) are aquatic analogues of species‐area relationships, and are increasingly used in both basic research and conservation planning. SDR studies are often limited, however, by two shortcomings. First, they do not determine whether reported SDRs, which normally use complete drainage basins as sampling units, are scale dependent. Second, they do not account for the effects of habitat diversity within or among samples.2. We addressed both problems by using discrete fish zones as sampling units in a SDR analysis. To do so, we first tested for longitudinal zonation in three rivers in the southeastern U.S.A. In each river, we detected successive ‘lower’, ‘middle’, and ‘upper’ fish zones, which were characterized by distinct fish assemblages with predictable habitat requirements. Because our analyses combined fish data from multiple sources, we also used rarefaction and Monte Carlo simulation to ensure that our zonation results were robust to spurious sampling effects.3. Next, we estimated the average discharge within each zone, and plotted these estimates against the respective species richness within each zone (log10 data). This revealed a significant, linear SDR (r2 = 0.83; P < 0.01). Notably, this zonal SDR fit the empirical data better than a comparable SDR that did not discriminate among longitudinal zones. We therefore conclude that the southeastern fish SDR is scale dependent, and that accounting for within‐basin habitat diversity is an important step in explaining the high diversity of southeastern fishes.4. We then discuss how our zonal SDR can be used to improve conservation planning. Specifically, we show how the slope of the SDR can be used to forecast potential extinction rates, and how the zonal data can be used to identify species of greatest concern.
Inferring long‐distance dispersal and topographic barriers during post‐glacial colonization from the genetic structure of red maple (Acer rubrum L.) in New England
Authors: Gugger Paul F. , McLachlan Jason S. , Manos Paul S. , Clark James S. 
Published: July 2008

AbstractAim  This study aims to assess the role of long‐distance seed dispersal and topographic barriers in the post‐glacial colonization of red maple (Acer rubrum L.) using chloroplast DNA (cpDNA) variation, and to understand whether this explains the relatively higher northern diversity found in eastern North American tree species compared with that in Europe.Location  North‐eastern United States.Methods  The distribution of intraspecific cpDNA variation in temperate tree populations has been used to identify aspects of post‐glacial population spread, including topographic barriers to population expansion and spread by long‐distance seed dispersal. We sequenced c. 370 cpDNA base pairs from 221 individuals in 100 populations throughout the north‐eastern United States, and analysed spatial patterns of diversity and differentiation.Results  Red maple has high genetic diversity near its northern range limit, but this diversity is not partitioned by topographic barriers, suggesting that the northern Appalachian Mountains were not a barrier to the colonization of red maple. We also found no evidence of the patchy genetic structure that has been associated with spread by rare long‐distance seed dispersal in previous studies.Main conclusions  Constraints on post‐glacial colonization in eastern North America seem to have been less stringent than those in northern Europe, where bottlenecks arising from long‐distance colonization and topographic barriers appear to have strongly reduced genetic diversity. In eastern North America, high northern genetic diversity may have been maintained by a combination of frequent long‐distance dispersal, minor topographic obstacles and diffuse northern refugia near the ice sheet.
Characterization of CetA and CetB, a bipartite energy taxis system in Campylobacter jejuni
Authors: Elliott Kathryn T. , DiRita Victor J. 
Published: July 2008

SummaryThe energy taxis receptor Aer, in Escherichia coli, senses changes in the redox state of the electron transport system via an flavin adenine dinucleotide cofactor bound to a PAS domain. The PAS domain (a sensory domain named after three proteins Per, ARNT and Sim, where it was first identified) is thought to interact directly with the Aer HAMP domain to transmit this signal to the highly conserved domain (HCD) found in chemotaxis receptors. An apparent energy taxis system in Campylobacter jejuni is composed of two proteins, CetA and CetB, that have the domains of Aer divided between them. CetB has a PAS domain, while CetA has a predicted transmembrane region, HAMP domain and the HCD. In this study, we examined the expression of cetA and cetB and the biochemical properties of the proteins they encode. cetA and cetB are co‐transcribed independently of the flagellar regulon. CetA has two transmembrane helices in a helical hairpin while CetB is a peripheral membrane protein tightly associated with the membrane. CetB levels are CetA dependent. Additionally, we demonstrated that both CetA and CetB participate in complexes, including a likely CetB dimer and a complex that may include both CetA and CetB. This study provides a foundation for further characterization of signal transduction mechanisms within CetA/CetB.