bluuebunny/crossref_metadata_2025_split huggingface dataset:
Elucidating the Germination Transcriptional Program Using Small Molecules
Authors: Bassel George W. , Fung Pauline , Chow Tsz-fung Freeman , Foong Justin A. , Provart Nicholas J. , Cutler Sean R. 
Published: March 2008

AbstractThe transition from seed to seedling is mediated by germination, a complex process that starts with imbibition and completes with radicle emergence. To gain insight into the transcriptional program mediating germination, previous studies have compared the transcript profiles of dry, dormant, and germinating after-ripened Arabidopsis (Arabidopsis thaliana) seeds. While informative, these approaches did not distinguish the transcriptional responses due to imbibition, shifts in metabolism, or breaking of dormancy from those triggered by the initiation of germination. In this study, three mechanistically distinct small molecules that inhibit Arabidopsis seed germination (methotrexate, 2, 4-dinitrophenol, and cycloheximide) were identified using a small-molecule screen and used to probe the germination transcriptome. Germination-responsive transcripts were defined as those with significantly altered transcript abundance across all inhibitory treatments with respect to control germinating seeds, using data from ATH1 microarrays. This analysis identified numerous germination regulators as germination responsive, including the DELLA proteins GAI, RGA, and RGL3, the abscisic acid-insensitive proteins ABI4, ABI5, ABI8, and FRY1, and the gibberellin receptor GID1A. To help visualize these and other publicly available seed microarray data, we designed a seed mRNA expression browser using the electronic Fluorescent Pictograph platform. An overall decrease in gene expression and a 5-fold greater number of transcripts identified as statistically down-regulated in drug-inhibited seeds point to a role for mRNA degradation or turnover during seed germination. The genes identified in our study as responsive to germination define potential uncharacterized regulators of this process and provide a refined transcriptional signature for germinating Arabidopsis seeds.
The Ionic Environment Controls the Contribution of the Barley HvHAK1 Transporter to Potassium Acquisition
Authors: Fulgenzi Fabiana R. , Peralta María Luisa , Mangano Silvina , Danna Cristian H. , Vallejo Augusto J. , Puigdomenech Pere , Santa-María Guillermo E. 
Published: March 2008

Abstract
The control of potassium (K+) acquisition is a critical requirement for plant growth. Although HAK1 (high affinity K+ 1) transporters provide a pathway for K+ acquisition, the effect exerted by the ionic environment on their contribution to K+ capture remains essentially unknown. Here, the influence of the ionic environment on the accumulation of transcripts coding for the barley (Hordeum vulgare) HvHAK1 transporter as well as on HvHAK1-mediated K+ capture has been examined. In situ mRNA hybridization studies show that HvHAK1 expression occurs in most root cells, being augmented at the outermost cell layers. Accumulation of HvHAK1 transcripts is enhanced by K+ deprivation and transiently by exposure to high salt concentrations. In addition, studies on the accumulation of transcripts coding for HvHAK1 and its close homolog HvHAK1b revealed the presence of two K+-responsive pathways, one repressed and the other insensitive to ammonium. Experiments with Arabidopsis (Arabidopsis thaliana) HvHAK1-expressing transgenic plants showed that K+ deprivation enhances the capture of K+ mediated by HvHAK1. A detailed study with HvHAK1-expressing Saccharomyces cerevisiae cells also revealed an increase of K+ uptake after K+ starvation. This increase did not occur in cells grown at high Na+ concentrations but took place for cells grown in the presence of NH4 +. 3,3′-Dihexyloxacarbocyanine iodide accumulation measurements indicate that the increased capture of K+ in HvHAK1-expressing yeast cells cannot be explained only by changes in the membrane potential. It is shown that the yeast protein phosphatase PPZ1 as well as the halotolerance HAL4/HAL5 kinases negatively regulate the HvHAK1-mediated K+ transport.
Genotype, Age, Tissue, and Environment Regulate the Structural Outcome of Glucosinolate Activation
Authors: Wentzell Adam M. , Kliebenstein Daniel J. 
Published: March 2008

Abstract
Glucosinolates are the inert storage form of a two-part phytochemical defense system in which the enzyme myrosinase generates an unstable intermediate that rapidly rearranges into the biologically active product. This rearrangement step generates simple nitriles, epithionitriles, or isothiocyanates, depending on the structure of the parent glucosinolate and the presence of proteins that promote specific structural outcomes. Glucosinolate accumulation and myrosinase activity differ by plant age and tissue type and respond to environmental stimuli such as planting density and herbivory; however, the influence of these factors on the structural outcome of the rearrangement step remains unknown. We show that the structural outcome of glucosinolate activation is controlled by interactions among plant age, planting density, and natural genetic variation in Arabidopsis (Arabidopsis thaliana) rosette leaves using six well-studied accessions. We identified a similarly complex interaction between tissue type and the natural genetic variation present within these accessions. This raises questions about the relative importance of these novel levels of regulation in the evolution of plant defense. Using mutants in the structural specifier and glucosinolate activation genes identified previously in Arabidopsis rosette leaves, we demonstrate the requirement for additional myrosinases and structural specifiers controlling these processes in the roots and seedlings. Finally, we present evidence for a novel EPITHIOSPECIFIER PROTEIN-independent, simple nitrile-specifying activity that promotes the formation of simple nitriles but not epithionitriles from all glucosinolates tested.
Low-Temperature and Daylength Cues Are Integrated to Regulate FLOWERING LOCUS T in Barley
Authors: Hemming Megan N. , Peacock W. James , Dennis Elizabeth S. , Trevaskis Ben 
Published: March 2008

Abstract
Interactions between flowering time genes were examined in a doubled haploid barley (Hordeum vulgare) population segregating for H. vulgare VERNALIZATION1 (HvVRN1), HvVRN2, and PHOTOPERIOD1 (PPD-H1). A deletion allele of HvVRN2 was associated with rapid inflorescence initiation and early flowering, but only in lines with an active allele of PPD-H1. In these lines, the floral promoter FLOWERING LOCUS T (HvFT1) was expressed at high levels without vernalization, and this preceded induction of HvVRN1. Lines with the deletion allele of HvVRN2 and the inactive ppd-H1 allele did not undergo rapid inflorescence initiation and were late flowering. These data suggest that HvVRN2 counteracts PPD-H1 to prevent flowering prior to vernalization. An allele of HvVRN1 that is expressed at high basal levels (HvVRN1-1) was associated with rapid inflorescence initiation regardless of HvVRN2 or PPD-H1 genotype. HvFT1 was expressed without vernalization in lines with the HvVRN1-1 allele and HvFT1 transcript levels were highest in lines with the active PPD-H1 allele; this correlated with rapid apex development postinflorescence initiation. Thus, expression of HvVRN1 promotes inflorescence initiation and up-regulates HvFT1. Analysis of HvVRN1 expression in different genetic backgrounds postvernalization showed that HvVRN2, HvFT1, and PPD-H1 are unlikely to play a role in low-temperature induction of HvVRN1. In a vernalization responsive barley, HvFT1 is not induced by low temperatures alone, but can be induced by long days following prolonged low-temperature treatment. We conclude that low-temperature and daylength flowering-response pathways are integrated to control expression of HvFT1 in barley, and that this might occur through regulation of HvVRN2 activity.
Mild Reductions in Mitochondrial Citrate Synthase Activity Result in a Compromised Nitrate Assimilation and Reduced Leaf Pigmentation But Have No Effect on Photosynthetic Performance or Growth
Authors: Sienkiewicz-Porzucek Agata , Nunes-Nesi Adriano , Sulpice Ronan , Lisec Jan , Centeno Danilo C. , Carillo Petronia , Leisse Andrea , Urbanczyk-Wochniak Ewa , Fernie Alisdair R. 
Published: March 2008

Abstract
Transgenic tomato (Solanum lycopersicum) plants, expressing a fragment of the mitochondrial citrate synthase gene in the antisense orientation and exhibiting mild reductions in the total cellular activity of this enzyme, displayed essentially no visible phenotypic alteration from the wild type. A more detailed physiological characterization, however, revealed that although these plants were characterized by relatively few changes in photosynthetic parameters they displayed a decreased relative flux through the tricarboxylic acid cycle and an increased rate of respiration. Furthermore, biochemical analyses revealed that the transformants exhibited considerably altered metabolism, being characterized by slight decreases in the levels of organic acids of the tricarboxylic acid cycle, photosynthetic pigments, and in a single line in protein content but increases in the levels of nitrate, several amino acids, and starch. We additionally determined the maximal catalytic activities of a wide range of enzymes of primary metabolism, performed targeted quantitative PCR analysis on all three isoforms of citrate synthase, and conducted a broader transcript profiling using the TOM1 microarray. Results from these studies confirmed that if the lines were somewhat impaired in nitrate assimilation, they were not severely affected by this, suggesting the presence of strategies by which metabolism is reprogrammed to compensate for this deficiency. The results are discussed in the context of carbon-nitrogen interaction and interorganellar coordination of metabolism.
Genotype‐specific IL8RA gene expression in bovine neutrophils in response to Escherichia coli lipopolysaccharide challenge
Authors: Leyva‐Baca I. , Pighetti G. , Karrow N. A. 
Published: March 2008

SummaryAssociations between the AC150887.4:c.‐1768T>A SNP (rs41255711), which is located in the 5′ upstream region of the IL8RA gene (also known as CXCR1), and the estimated breeding values for somatic cell score in the first (P = 0.019) and second (P = 0.035) lactations were previously reported in a population of Canadian Holstein bulls. In the present study, we evaluated the impact of this SNP on the expression of IL8RA by qRT‐PCR. Neutrophils were isolated from whole blood samples from a group of cows with genotypes c.‐1768AA (n = 4), c.‐1768AT (n = 5) and c.‐1768TT (n = 5) after the cows had been challenged in vitro with lipopolysaccharide (LPS). This study demonstrated that LPS‐induced expression of IL8RA in cows with the c.‐1768AA genotype was significantly greater when compared with the c.‐1768AT and c.‐1768TT genotypes (P < 0.05) before as well as after in vitro LPS challenge.
Bortezomib, doxorubicin and dexamethasone (PAD) front‐line treatment of multiple myeloma: updated results after long‐term follow‐up
Authors: Popat Rakesh , Oakervee Heather E. , Hallam Simon , Curry Nicola , Odeh Liz , Foot Nicola , Esseltine Dixie‐Lee , Drake Mary , Morris Curly , Cavenagh Jamie D. 
Published: March 2008

SummaryBortezomib, doxorubicin and dexamethasone (PAD) was evaluated as induction before stem cell transplantation in newly diagnosed multiple myeloma (MM) patients, using bortezomib 1·3 mg/m2 (PAD1, N = 21) or 1·0 mg/m2 (PAD2, N = 20). Complete/very good partial response rates with PAD1/PAD2 were 62%/42% postinduction and 81%/53% post‐transplant. Progression‐free survival (29 vs. 24 months), time to re‐treatment (36 vs. 29 months) and overall survival (1 year: 100% vs. 95%; 2 years: 95% vs. 73%) were statistically similar but favoured PAD1 versus PAD2. Toxicity was lower in PAD2; bortezomib dose reduction may help manage toxicities while retaining efficacy. PAD is highly active as front‐line induction in MM.
Albacore (Thunnus alalunga) fishing ground in relation to oceanographic conditions in the western North Pacific Ocean using remotely sensed satellite data
Authors: ZAINUDDIN MUKTI , SAITOH KATSUYA , SAITOH SEI‐ICHI 
Published: March 2008

AbstractSatellite‐based oceanographic data of sea surface temperature (SST), sea surface chlorophyll‐a concentration (SSC), and sea surface height anomaly (SSHA) together with catch data were used to investigate the relationship between albacore fishing ground and oceanographic conditions and also to predict potential habitats for albacore in the western North Pacific Ocean. Empirical cumulative distribution function and high catch data analyses were used to calculate preferred ranges of the three oceanographic conditions. Results indicate that highest catch per unit efforts (CPUEs) corresponded with areas of SST 18.5–21.5°C, SSC 0.2–0.4 mg m−3, and SSHA −5.0 to 32.2 cm during the winter in the period 1998–2000. We used these ranges to generate a simple prediction map for detecting potential fishing grounds. Statistically, to predict spatial patterns of potential albacore habitats, we applied a combined generalized additive model (GAM) / generalized linear model (GLM). To build our model, we first constructed a GAM as an exploratory tool to identify the functional relationships between the environmental variables and CPUE; we then made parameters out of these relationships using the GLM to generate a robust prediction tool. The areas of highest CPUEs predicted by the models were consistent with the potential habitats on the simple prediction map and observation data, suggesting that the dynamics of ocean eddies (November 1998 and 2000) and fronts (November 1999) may account for the spatial patterns of highest albacore catch rates predicted in the study area. The results also suggest that multispectrum satellite data can provide useful information to characterize and predict potential tuna habitats.
Climatic conditions, diapause and migration in a troglophile caddisfly
Authors: SALAVERT V. , ZAMORA‐MUÑOZ C. , RUIZ‐RODRÍGUEZ M. , FERNÁNDEZ‐CORTÉS A. , SOLER J. J. 
Published: March 2008

Summary1. Factors explaining the end of diapause include environmental conditions such as daily photoperiod, temperature and humidity. However, because all these factors are almost constant inside deep caves, they would hardly affect diapause termination in many animal taxa that use such habitats in which to aestivate or hibernate (such as bats and some insects, snakes or frogs).2. An innate biological signal, based on body reserves (mass), could determine the end of diapause in cave‐dwelling animals. Another possibility is that the diapausing animals may use as a stimulus convective air circulation, produced by a fall in temperature outside the cave to a value below that inside (i.e. temperature inversions). Here, we explored these two non‐exclusive hypotheses explaining the end of diapause and the start of migration in the caddisMesophylax aspersus. This species aestivates as an adult in caves, as a physiological adaptation to seasonal drought and stream drying.3. The variation in body mass of individuals entering and leaving the cave was similar, suggesting no role for the ‘reserve level’ hypothesis in breaking diapause. However, the onset of a temperature inversion in autumn coincided with the breaking of diapause followed after a few days by the migration of the caddisflies.4. We conclude that the seasonal air currents, produced by thermal inversions, could be the migration stimulus for caddisflies and many other animals that spend a period of diapause in caves.
Warming and elevated CO2 affect the relationship between seed mass, germinability and seedling growth in Austrodanthonia caespitosa, a dominant Australian grass
Authors: HOVENDEN MARK J. , WILLS KAREN E. , CHAPLIN REBECCA E. , VANDER SCHOOR JACQUELINE K. , WILLIAMS AMITY L. , OSANAI YUI , NEWTON PAUL C. D. 
Published: March 2008

AbstractWhile the influence of elevated CO2 on the production, mass and quality of plant seeds has been well studied, the effect of warming on these characters is largely unknown; and there is practically no information on possible interactions between warming and elevated CO2, despite the importance of these characters in population maintenance and recovery. Here, we present the impacts of elevated CO2 and warming, both in isolation and combination, on seed production, mass, quality, germination success and subsequent seedling growth of Austrodanthonia caespitosa, a dominant temperate C3 grass from Australia, using seeds collected from the TasFACE experiment. Mean seed production and mass were not significantly affected by either elevated CO2 or warming, but elevated CO2 more than doubled the proportion of very light, inviable seeds (P < 0.05) and halved mean seed N concentration (P < 0.04) and N content (P < 0.03). The dependence of seed germination success on seed mass was affected by an elevated CO2× warming interaction (P < 0.004), such that maternal exposure to elevated CO2 or warming reduced germination if applied in isolation, but not when applied in combination. Maternal effects were retained when seedlings were grown in a common environment for 6 weeks, with seedlings descended from warmed plants 20% smaller (P < 0.008) with a higher root : shoot ratio (P < 0.001) than those from unwarmed plants. Given that both elevated CO2 and warming reduced seed mass, quality, germinability or seedling growth, it is likely that global change will reduce population growth or distribution of this dominant species.
Interannual variability in carbon dioxide fluxes and flux–climate relationships on grazed and ungrazed northern mixed‐grass prairie
Authors: WAYNE POLLEY H. , FRANK ALBERT B. , SANABRIA JOAQUIN , PHILLIPS REBECCA L. 
Published: March 2008

AbstractThe annual carbon (C) budget of grasslands is highly dynamic, dependent on grazing history and on effects of interannual variability (IAV) in climate on carbon dioxide (CO2) fluxes. Variability in climatic drivers may directly affect fluxes, but also may indirectly affect fluxes by altering the response of the biota to the environment, an effect termed ‘functional change’. We measured net ecosystem exchange of CO2 (NEE) and its diurnal components, daytime ecosystem CO2 exchange (PD) and night‐time respiration (RE), on grazed and ungrazed mixed‐grass prairie in North Dakota, USA, for five growing seasons. Our primary objective was to determine how climatic anomalies influence variability in CO2 exchange. We used regression analysis to distinguish direct effects of IAV in climate on fluxes from functional change. Functional change was quantified as the improvement in regression on fitting a model in which slopes of flux–climate relationships vary among years rather than remain invariant. Functional change and direct effects of climatic variation together explained about 20% of variance in weekly means of NEE, PD, and RE. Functional change accounted for more than twice the variance in fluxes of direct effects of climatic variability. Grazing did not consistently influence the contribution of functional change to flux variability, but altered which environmental variable best explained year‐to‐year differences in flux–climate slopes, reduced IAV in seasonal means of fluxes, lessened the strength of flux–climate correlations, and increased NEE by reducing RE relatively more than PD. Most of these trends are consistent with the interpretation that grazing reduced the influence of plants on ecosystem fluxes. Because relationships between weekly values of fluxes and climatic regulators changed annually, year‐to‐year differences in the C balance of these ecosystems cannot be predicted from knowledge of IAV in climate alone.
Addressing the influence of instrument surface heat exchange on the measurements of CO2 flux from open‐path gas analyzers
Authors: BURBA GEORGE G. , McDERMITT DAYLE K. , GRELLE ACHIM , ANDERSON DANIEL J. , XU LIUKANG 
Published: March 2008

AbstractThere is a growing concern in the flux community that using the eddy covariance method with open‐path CO2 analyzers often leads to measurements of an apparent ecosystem CO2 uptake during off‐season periods, especially in cold climates. Such uptake has not been observed when measurements were made with closed‐path analyzers, chambers, or profile methods, suggesting it is an artifact due in some way to the use of open‐path analyzers. In this study, a series of laboratory tests and field experiments were conducted to determine the magnitude of the instrument surface heat exchange in the open path and its relationship with the measured CO2 flux. Results showed that (1) the surface of an open‐path instrument became substantially warmer than ambient due to electronics and radiation load during daytime, while at night, radiative cooling moderated temperature increases in the path; (2) high‐frequency temperature measurements inside the path were correlated with vertical wind speed producing sensible heat flux inside the instrument path exceeding the ambient heat flux by up to 14%; (3) enclosing the open‐path instrument eliminated the sensible heat flux in the path, and caused measured CO2 flux to match a closed‐path reference; (4) using sensible heat flux measured directly inside the open path in the WPL term instead of the ambient sensible heat flux also led to a match in CO2 flux between open‐path instrument and closed‐path reference; and (5) correcting previously collected open‐path CO2 flux data was possible by estimating the instrument heating effect with a semi‐empirical model using standard weather variables. Results showed that all proposed techniques led to a significant reduction in apparent CO2 uptake during off‐season periods and to a reduction of the underestimation of CO2 release in other periods. Close agreement between the open‐path measurements and closed‐path references was achieved in all cases.
Calcitonin receptor immunoreactivity associated with specific cell types in diseased radial and internal mammary arteries
Authors: Wookey P J , Zulli A , Buxton B F , Hare D L 
Published: March 2008

Aims:  To determine and quantify calcitonin receptor (CTR) immunoreactivity associated with specific cell types within, and associated with, the endothelial layers, neo‐intima, media and vasa vasorum of diseased radial and internal mammary arteries.Methods and results:  Immunohistochemistry and anti‐CTR antibodies were used to identify positive cells within remnants of diseased human radial (n = 3) and internal mammary arteries (n = 4) that remained after bypass surgery. Three cell types expressed CTR, including endothelial cells, fibroblast‐like cells within the neo‐intima, and cellular structures aligned with the smooth muscle cells of the media. Other smaller cells within the surrounding parenchyma of the vasa vasorum of diseased vessels and blood‐borne cells were also immunoreactive. Immunoquantification of CTR expression (Intensity × Proportional Area) in the endothelium (P < 0.05), neo‐intima (P < 0.02) and media (P < 0.03) established a significant statistical correlation (Students’ two‐tailed t‐test) with the ratio of intimal/media thickness.Conclusions:  Increased immunoreactivity developed using anti‐CTR antibodies was associated with specific cell types in the endothelial layers, neo‐intima, media and vasa vasorum of diseased regions of radial and internal mammary arteries, in which there was an increased intimal/media ratio. Furthermore, CTR+, blood‐borne cells present in the vessels of diseased regions suggest recruitment into these surrounding tissues.