Sample records for diel transcriptional response
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Specificity Responses of Grasshoppers in Temperate Grasslands to Diel Asymmetric Warming
Wu, Tingjuan; Hao, Shuguang; Sun, Osbert Jianxin; Kang, Le
2012-01-01
Background Global warming is characterized by not only an increase in the daily mean temperature, but also a diel asymmetric pattern. However, most of the current studies on climate change have only concerned with the mean values of the warming trend. Although many studies have been conducted concerning the responses of insects to climate change, studies that address the issue of diel asymmetric warming under field conditions are not found in the literature. Methodology/Principal Findings We conducted a field climate manipulative experiment and investigated developmental and demographic responses to diel asymmetric warming in three grasshopper species (an early-season species Dasyhippus barbipes, a mid-season species Oedaleus asiaticus, and a late-season species Chorthippus fallax). It was found that warming generally advanced the development of eggs and nymphs, but had no apparent impacts on the hatching rate of eggs, the emergence rate of nymphs and the survival and fecundity of adults in all the three species. Nighttime warming was more effective in advancing egg development than the daytime warming. The emergence time of adults was differentially advanced by warming in the three species; it was advanced by 5.64 days in C. fallax, 3.55 days in O. asiaticus, and 1.96 days in D. barbipes. This phenological advancement was associated with increases in the effective GDDs accumulation. Conclusions/Significance Results in this study indicate that the responses of the three grasshopper species to warming are influenced by several factors, including species traits, developmental stage, and the thermal sensitivity of the species. Moreover, species with diapausing eggs are less responsive to changes in temperature regimes, suggesting that development of diapausing eggs is a protective mechanism in early-season grasshopper for avoiding the risk of pre-winter hatching. Our results highlight the need to consider the complex relationships between climate change and
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Diel biogeochemical processes in terrestrial waters
Nimick, David A.; Gammons, Christopher H.
2011-01-01
Many biogeochemical processes in rivers and lakes respond to the solar photocycle and produce persistent patterns of measureable phenomena that exhibit a day–night, or 24-h, cycle. Despite a large body of recent literature, the mechanisms responsible for these diel fluctuations are widely debated, with a growing consensus that combinations of physical, chemical, and biological processes are involved. These processes include streamflow variation, photosynthesis and respiration, plant assimilation, and reactions involving photochemistry, adsorption and desorption, and mineral precipitation and dissolution. Diel changes in streamflow and water properties such as temperature, pH, and dissolved oxygen concentration have been widely recognized, and recently, diel studies have focused more widely by considering other constituents such as dissolved and particulate trace metals, metalloids, rare earth elements, mercury, organic matter, dissolved inorganic carbon (DIC), and nutrients. The details of many diel processes are being studied using stable isotopes, which also can exhibit diel cycles in response to microbial metabolism, photosynthesis and respiration, or changes in phase, speciation, or redox state. In addition, secondary effects that diel cycles might have, for example, on biota or in the hyporheic zone are beginning to be considered.This special issue is composed primarily of papers presented at the topical session “Diurnal Biogeochemical Processes in Rivers, Lakes, and Shallow Groundwater” held at the annual meeting of the Geological Society of America in October 2009 in Portland, Oregon. This session was organized because many of the growing number of diel studies have addressed just a small part of the full range of diel cycling phenomena found in rivers and lakes. This limited focus is understandable because (1) fundamental aspects of many diel processes are poorly understood and require detailed study, (2) the interests and expertise of individual
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Directory of Open Access Journals (Sweden)
Sarah R Smith
2016-12-01
Full Text Available Environmental fluctuations affect distribution, growth and abundance of diatoms in nature, with iron (Fe availability playing a central role. Studies on the response of diatoms to low Fe have either utilized continuous (24 hr illumination or sampled a single time of day, missing any temporal dynamics. We profiled the physiology, metabolite composition, and global transcripts of the pennate diatom Phaeodactylum tricornutum during steady-state growth at low, intermediate, and high levels of dissolved Fe over light:dark cycles, to better understand fundamental aspects of genetic control of physiological acclimation to growth under Fe-limitation. We greatly expand the catalog of genes involved in the low Fe response, highlighting the importance of intracellular trafficking in Fe-limited diatoms. P. tricornutum exhibited transcriptomic hallmarks of slowed growth leading to prolonged periods of cell division/silica deposition, which could impact biogeochemical carbon sequestration in Fe-limited regions. Light harvesting and ribosome biogenesis transcripts were generally reduced under low Fe while transcript levels for genes putatively involved in the acquisition and recycling of Fe were increased. We also noted shifts in expression towards increased synthesis and catabolism of branched chain amino acids in P. tricornutum grown at low Fe whereas expression of genes involved in central core metabolism were relatively unaffected, indicating that essential cellular function is protected. Beyond the response of P. tricornutum to low Fe, we observed major coordinated shifts in transcript control of primary and intermediate metabolism over light:dark cycles which contribute to a new view of the significance of distinctive diatom pathways, such as mitochondrial glycolysis and the ornithine-urea cycle. This study provides new insight into transcriptional modulation of diatom physiology and metabolism across light:dark cycles in response to Fe availability
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Facile approach to prepare pH and redox-responsive nanogels via Diels-Alder click reaction
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C. M. Q. Le
2018-08-01
Full Text Available A novel pH and redox responsive system of sub-100 nm nanogels was prepared by arm-first approach via Diels-Alder click reaction. First, well-defined poly(ethylene glycol-block-poly(styrene-alt-maleic anhydride (PEG-b-PSM was synthesized and subsequently functionalized with furfuryl amine, leading to the formation of the dual-functional block copolymer of PEG-b-PSMf. The furfuryl groups in the PSMf block were employed to incorporate a redox-responsive linkage and the carboxylic acid moieties generated through functionalization acted as a pH-responsive part. The Diels-Alder click reaction between a bismaleimide crosslinker and PEG-b-PSMf was conducted at 60 °C, affording star-like nanogel structures. Doxorubicin, a model anticancer drug, was loaded into to the core of the nanogels primarily by the ionic interaction with carboxylates of core blocks and a highest drug loading capacity of 38.1% was obtained. Furthermore, the in vitro profile showed a low release percentage (11.2% of DOX at PBS pH 7.4, whereas a burst release (62% at pH 5.0 in the presence of 10 mM glutathione, indicating the effective pH and redox responsive characteristic of the PEG-b-PSMf nanogels.
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Kadye, Wilbert T; Booth, Anthony J
2014-01-01
Animals exhibit diel periodicity in their activity in part to meet energy requirements whilst evading predation. A competing hypothesis suggests that partitioning of diel activities is less important because animals capitalise on opportunity. To test these hypotheses we examined the diel activity patterns for two cyprinid minnows, chubbyhead barb Barbus anoplus and the Eastern Cape redfin minnow Pseudobarbus afer that both occur within headwater streams in the Eastern Cape, South Africa. Chubbyhead barbs exhibited consistent nocturnal activity based on both field and laboratory observations. Due to the absence of fish predators within its habitat, its nocturnal behaviour suggests a response to the cost associated with diurnal activity, such as predation risk by diving and wading birds. In contrast, redfin minnows showed high diurnal activity and a shoaling behaviour in the wild, whereas, in the laboratory, they showed high refuge use during the diel cycle. Despite their preference for refuge in the laboratory, they were diurnally active, a behaviour that was consistent with observations in the wild. The diurnal activity of this species suggests a response to the cost associated with nocturnal activity. Such a cost could be inferred from the presence of the longfin eel, a native predator that was active at night, whereas the daytime shoaling behaviour suggests an anti-predator mechanism to diurnal visual predators. The implications of these findings relate to the impacts associated with the potential invasions by non-native piscivores that occur in the mainstem sections. Diurnal activity patterns for redfin minnows, that are IUCN-listed as endangered, may, in part, explain their susceptibility to high predation by visual non-native piscivores, such as bass and trout. In contrast, the nocturnal habits of chubbyhead barbs suggest a probable pre-adaptation to visual predation. The likelihood of invasion by nocturnally-active sharptooth catfish Clarias gariepinus
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Directory of Open Access Journals (Sweden)
Wilbert T Kadye
Full Text Available Animals exhibit diel periodicity in their activity in part to meet energy requirements whilst evading predation. A competing hypothesis suggests that partitioning of diel activities is less important because animals capitalise on opportunity. To test these hypotheses we examined the diel activity patterns for two cyprinid minnows, chubbyhead barb Barbus anoplus and the Eastern Cape redfin minnow Pseudobarbus afer that both occur within headwater streams in the Eastern Cape, South Africa. Chubbyhead barbs exhibited consistent nocturnal activity based on both field and laboratory observations. Due to the absence of fish predators within its habitat, its nocturnal behaviour suggests a response to the cost associated with diurnal activity, such as predation risk by diving and wading birds. In contrast, redfin minnows showed high diurnal activity and a shoaling behaviour in the wild, whereas, in the laboratory, they showed high refuge use during the diel cycle. Despite their preference for refuge in the laboratory, they were diurnally active, a behaviour that was consistent with observations in the wild. The diurnal activity of this species suggests a response to the cost associated with nocturnal activity. Such a cost could be inferred from the presence of the longfin eel, a native predator that was active at night, whereas the daytime shoaling behaviour suggests an anti-predator mechanism to diurnal visual predators. The implications of these findings relate to the impacts associated with the potential invasions by non-native piscivores that occur in the mainstem sections. Diurnal activity patterns for redfin minnows, that are IUCN-listed as endangered, may, in part, explain their susceptibility to high predation by visual non-native piscivores, such as bass and trout. In contrast, the nocturnal habits of chubbyhead barbs suggest a probable pre-adaptation to visual predation. The likelihood of invasion by nocturnally-active sharptooth catfish
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Directory of Open Access Journals (Sweden)
Millie T. Olsen
2015-06-01
Full Text Available Genomes were obtained for three closely related strains of Synechococcus that are representative of putative ecotypes that predominate at different depths in the 1 mm-thick, upper-green layer in the 60°C mat of Mushroom Spring, Yellowstone National Park, and exhibit different light adaptation and acclimation responses. The genomes were compared to the published genome of a previously obtained, closely related strain from a neighboring spring, and differences in both gene content and orthologous gene alleles between high-light-adapted and low-light-adapted strains were identified. Evidence of genetic differences that relate to adaptation to light intensity and/or quality, CO2 uptake, nitrogen metabolism, organic carbon metabolism, and uptake of other nutrients were found between strains of the different putative ecotypes. In situ diel transcription patterns of genes, including genes unique to either low-light-adapted or high-light-adapted strains and different alleles of an orthologous photosystem gene, revealed that expression is fine-tuned to the different light environments experienced by ecotypes prevalent at various depths in the mat. This study suggests that strains of closely related putative ecotypes have different genomic adaptations that enable them to inhabit distinct ecological niches while living in close proximity within a microbial community.
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Rhythmic diel pattern of gene expression in juvenile maize leaf.
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Maciej Jończyk
Full Text Available BACKGROUND: Numerous biochemical and physiological parameters of living organisms follow a circadian rhythm. Although such rhythmic behavior is particularly pronounced in plants, which are strictly dependent on the daily photoperiod, data on the molecular aspects of the diurnal cycle in plants is scarce and mostly concerns the model species Arabidopsis thaliana. Here we studied the leaf transcriptome in seedlings of maize, an important C4 crop only distantly related to A. thaliana, throughout a cycle of 10 h darkness and 14 h light to look for rhythmic patterns of gene expression. RESULTS: Using DNA microarrays comprising ca. 43,000 maize-specific probes we found that ca. 12% of all genes showed clear-cut diel rhythms of expression. Cluster analysis identified 35 groups containing from four to ca. 1,000 genes, each comprising genes of similar expression patterns. Perhaps unexpectedly, the most pronounced and most common (concerning the highest number of genes expression maxima were observed towards and during the dark phase. Using Gene Ontology classification several meaningful functional associations were found among genes showing similar diel expression patterns, including massive induction of expression of genes related to gene expression, translation, protein modification and folding at dusk and night. Additionally, we found a clear-cut tendency among genes belonging to individual clusters to share defined transcription factor-binding sequences. CONCLUSIONS: Co-expressed genes belonging to individual clusters are likely to be regulated by common mechanisms. The nocturnal phase of the diurnal cycle involves gross induction of fundamental biochemical processes and should be studied more thoroughly than was appreciated in most earlier physiological studies. Although some general mechanisms responsible for the diel regulation of gene expression might be shared among plants, details of the diurnal regulation of gene expression seem to differ
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Directory of Open Access Journals (Sweden)
Han Zheng
Full Text Available Evapotranspiration (ET is an important component of the water cycle in terrestrial ecosystems. Understanding the ways in which ET changes with meteorological factors is central to a better understanding of ecological and hydrological processes. In this study, we used eddy covariance measurements of ET from a typical alpine shrubland meadow ecosystem in China to investigate the hysteresis response of ET to environmental variables including air temperature (Ta, vapor pressure deficit (VPD and net radiation (Rn at a diel timescale. Meanwhile, the simulated ET by Priestly-Taylor equation was used to interpret the measured ET under well-watered conditions. Pronounced hysteresis was observed in both Ta and VPD response curves of ET. At a similar Ta and VPD, ET was always significantly depressed in the afternoon compared with the morning. But the hysteresis response of ET to Rn was not evident. Similar hysteresis patterns were also observed in the Ta/VPD response curves of simulated ET. The magnitudes of the measured and simulated hysteresis loops showed similar seasonal variation, with relatively smaller values occurring from May to September, which agreed well with the lifetime of plants and the period of rainy season at this site. About 62% and 23% of changes in the strength of measured ET-Ta and ET-VPD loops could be explained by the changes in the strength of simulated loops, respectively. Thus, the time lag between Rn and Ta/VPD is the most important factor generating and modulating the ET-Ta/VPD hysteresis, but plants and water status also contribute to the hysteresis response of ET. Our research confirmed the different hysteresis in the responses of ET to meteorological factors and proved the vital role of Rn in driving the diel course of ET.
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Steunou, Anne-Soisig; Jensen, Sheila I; Brecht, Eric; Becraft, Eric D; Bateson, Mary M; Kilian, Oliver; Bhaya, Devaki; Ward, David M; Peters, John W; Grossman, Arthur R; Kühl, Michael
2008-04-01
Nitrogen fixation, a prokaryotic, O2-inhibited process that reduces N2 gas to biomass, is of paramount importance in biogeochemical cycling of nitrogen. We analyzed the levels of nif transcripts of Synechococcus ecotypes, NifH subunit and nitrogenase activity over the diel cycle in the microbial mat of an alkaline hot spring in Yellowstone National Park. The results showed a rise in nif transcripts in the evening, with a subsequent decline over the course of the night. In contrast, immunological data demonstrated that the level of the NifH polypeptide remained stable during the night, and only declined when the mat became oxic in the morning. Nitrogenase activity was low throughout the night; however, it exhibited two peaks, a small one in the evening and a large one in the early morning, when light began to stimulate cyanobacterial photosynthetic activity, but O2 consumption by respiration still exceeded the rate of O2 evolution. Once the irradiance increased to the point at which the mat became oxic, the nitrogenase activity was strongly inhibited. Transcripts for proteins associated with energy-producing metabolisms in the cell also followed diel patterns, with fermentation-related transcripts accumulating at night, photosynthesis- and respiration-related transcripts accumulating during the day and late afternoon, respectively. These results are discussed with respect to the energetics and regulation of N2 fixation in hot spring mats and factors that can markedly influence the extent of N2 fixation over the diel cycle.
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Directory of Open Access Journals (Sweden)
Dongfeng Yang
Full Text Available Plants of the genus Salvia produce various types of phenolic compounds and tanshinones which are effective for treatment of coronary heart disease. Salvia miltiorrhiza and S. castanea Diels f. tomentosa Stib are two important members of the genus. In this study, metabolic profiles and cDNA-AFLP analysis of four samples were employed to identify novel genes potentially involved in phenolic compounds and tanshinones biosynthesis, including the red roots from the two species and two tanshinone-free roots from S. miltiorrhiza. The results showed that the red roots of S. castanea Diels f. tomentosa Stib produced high contents of rosmarinic acid (21.77 mg/g and tanshinone IIA (12.60 mg/g, but low content of salvianolic acid B (1.45 mg/g. The red roots of S. miltiorrhiza produced high content of salvianolic acid B (18.69 mg/g, while tanshinones accumulation in this sample was much less than that in S. castanea Diels f. tomentosa Stib. Tanshinones were not detected in the two tanshinone-free samples, which produced high contents of phenolic compounds. A cDNA-AFLP analysis with 128 primer pairs revealed that 2300 transcript derived fragments (TDFs were differentially expressed among the four samples. About 323 TDFs were sequenced, of which 78 TDFs were annotated with known functions through BLASTX searching the Genbank database and 14 annotated TDFs were assigned into secondary metabolic pathways through searching the KEGGPATHWAY database. The quantitative real-time PCR analysis indicated that the expression of 9 TDFs was positively correlated with accumulation of phenolic compounds and tanshinones. These TDFs additionally showed coordinated transcriptional response with 6 previously-identified genes involved in biosynthesis of tanshinones and phenolic compounds in S. miltiorrhiza hairy roots treated with yeast extract. The sequence data in the present work not only provided us candidate genes involved in phenolic compounds and tanshinones biosynthesis
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Partial diel migration: A facultative migration underpinned by long-term inter-individual variation.
Harrison, Philip M; Gutowsky, Lee F G; Martins, Eduardo G; Patterson, David A; Cooke, Steven J; Power, Michael
2017-09-01
The variations in migration that comprise partial diel migrations, putatively occur entirely as a consequence of behavioural flexibility. However, seasonal partial migrations are increasingly recognised to be mediated by a combination of reversible plasticity in response to environmental variation and individual variation due to genetic and environmental effects. Here, we test the hypothesis that while partial diel migration heterogeneity occurs primarily due to short-term within-individual flexibility in behaviour, long-term individual differences in migratory behaviour also underpin this migration variation. Specifically, we use a hierarchical behavioural reaction norm approach to partition within- and among-individual variation in depth use and diel plasticity in depth use, across short- and long-term time-scales, in a group of 47 burbot (Lota lota) tagged with depth-sensing acoustic telemetry transmitters. We found that within-individual variation at the among-dates-within-seasons and among-seasons scale, explained the dominant proportion of phenotypic variation. However, individuals also repeatedly differed in their expression of migration behaviour over the 2 year study duration. These results reveal that diel migration variation occurs primarily due to short-term within-individual flexibility in depth use and diel migration behaviour. However, repeatable individual differences also played a key role in mediating partial diel migration. These findings represent a significant advancement of our understanding of the mechanisms generating the important, yet poorly understood phenomena of partial diel migration. Moreover, given the pervasive occurrence of diel migrations across aquatic taxa, these findings indicate that individual differences have an important, yet previously unacknowledged role in structuring the temporal and vertical dynamics of aquatic ecosystems. © 2017 The Authors. Journal of Animal Ecology © 2017 British Ecological Society.
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Assessing diel variation of CH4 flux from rice paddies through temperature patterns
Centeno, Caesar Arloo R.; Alberto, Ma Carmelita R.; Wassmann, Reiner; Sander, Bjoern Ole
2017-10-01
The diel variation in methane (CH4) flux from irrigated rice was characterized during the dry and wet cropping seasons in 2013 and 2014 using the eddy covariance (EC) technique. The EC technique has the advantage of obtaining measurements of fluxes at an extremely high temporal resolution (10Hz), meaning it records 36,000 measurements per hour. The EC measurements can very well capture the temporal variations of the diel (both diurnal and nocturnal) fluxes of CH4 and the environmental factors (temperature, surface energy flux, and gross ecosystem photosynthesis) at 30-min intervals. The information generated by this technique is important to enhance our mechanistic understanding of the different factors affecting the landscape scale diel CH4 flux. Distinct diel patterns of CH4 flux were observed when the data were partitioned into different cropping periods (pre-planting, growth, and fallow). The temporal variations of the diel CH4 flux during the dry seasons were more pronounced than during the wet seasons because the latter had so much climatic disturbance from heavy monsoon rains and occasional typhoons. Pearson correlation analysis and Granger causality test were used to confirm if the environmental factors evaluated were not only correlated with but also Granger-causing the diel CH4 flux. Soil temperature at 2.5 cm depth (Ts 2.5 cm) can be used as simple proxy for predicting diel variations of CH4 fluxes in rice paddies using simple linear regression during both the dry and wet seasons. This simple site-specific temperature response function can be used for gap-filling CH4 flux data for improving the estimates of CH4 source strength from irrigated rice production.
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Reaction energetics on long-range corrected density functional theory: Diels-Alder reactions.
Singh, Raman K; Tsuneda, Takao
2013-02-15
The possibility of quantitative reaction analysis on the orbital energies of long-range corrected density functional theory (LC-DFT) is presented. First, we calculated the Diels-Alder reaction enthalpies that have been poorly given by conventional functionals including B3LYP functional. As a result, it is found that the long-range correction drastically improves the reaction enthalpies. The barrier height energies were also computed for these reactions. Consequently, we found that dispersion correlation correction is also crucial to give accurate barrier height energies. It is, therefore, concluded that both long-range exchange interactions and dispersion correlations are essentially required in conventional functionals to investigate Diels-Alder reactions quantitatively. After confirming that LC-DFT accurately reproduces the orbital energies of the reactant and product molecules of the Diels-Alder reactions, the global hardness responses, the halves of highest occupied molecular orbital (HOMO)-lowest unoccupied molecular orbital (LUMO) energy gaps, along the intrinsic reaction coordinates of two Diels-Alder reactions were computed. We noticed that LC-DFT results satisfy the maximum hardness rule for overall reaction paths while conventional functionals violate this rule on the reaction pathways. Furthermore, our results also show that the HOMO-LUMO gap variations are close to the reaction enthalpies for these Diels-Alder reactions. Based on these results, we foresee quantitative reaction analysis on the orbital energies. Copyright © 2012 Wiley Periodicals, Inc.
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The pentadehydro-Diels-Alder reaction.
Wang, Teng; Naredla, Rajasekhar Reddy; Thompson, Severin K; Hoye, Thomas R
2016-04-28
In the classic Diels-Alder [4 + 2] cycloaddition reaction, the overall degree of unsaturation (or oxidation state) of the 4π (diene) and 2π (dienophile) pairs of reactants dictates the oxidation state of the newly formed six-membered carbocycle. For example, in the classic Diels-Alder reaction, butadiene and ethylene combine to produce cyclohexene. More recent developments include variants in which the number of hydrogen atoms in the reactant pair and in the resulting product is reduced by, for example, four in the tetradehydro-Diels-Alder (TDDA) and by six in the hexadehydro-Diels-Alder (HDDA) reactions. Any oxidation state higher than tetradehydro (that is, lacking more than four hydrogens) leads to the production of a reactive intermediate that is more highly oxidized than benzene. This increases the power of the overall process substantially, because trapping of the reactive intermediate can be used to increase the structural complexity of the final product in a controllable and versatile manner. Here we report an unprecedented overall 4π + 2π cycloaddition reaction that generates a different, highly reactive intermediate known as an α,3-dehydrotoluene. This species is in the same oxidation state as a benzyne. Like benzynes, α,3-dehydrotoluenes can be captured by various trapping agents to produce structurally diverse products that are complementary to those arising from the HDDA process. We call this new cycloisomerization process a pentadehydro-Diels-Alder (PDDA) reaction-a nomenclature chosen for chemical taxonomic reasons rather than mechanistic ones. In addition to alkynes, nitriles (RC≡N), although non-participants in aza-HDDA reactions, readily function as the 2π component in PDDA cyclizations to produce, via trapping of the α,3-(5-aza)dehydrotoluene intermediates, pyridine-containing products.
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Application of the aza-Diels-Alder reaction in the synthesis of natural products.
Cao, Min-Hui; Green, Nicholas J; Xu, Sheng-Zhen
2017-04-11
The Diels-Alder reaction that involves a nitrogen atom in the diene or dienophile is termed the aza-Diels-Alder reaction. As well as the powerful all-carbon Diels-Alder reaction, the aza-Diels-Alder reaction has also played an important role in the total synthesis of natural products. Herein, we review various natural products using an aza-Diels-Alder reaction as a key step to their total synthesis, and divide the syntheses into inter- and intra-molecular aza-Diels-Alder reactions and a retro-aza-Diels-Alder reaction. Inter- and intra-molecular aza-Diels-Alder reactions involve an imine as an electron deficient dienophile and an imine as an electron deficient azadiene. The significance of the aza-Diels-Alder reaction for the construction of a six-membered ring containing nitrogen is tremendous, but the development of asymmetric, in particular catalytic enantioselective intramolecular aza-Diels-Alder reaction in the total synthesis of natural products remains highly challenging, and will no doubt see enormous advances in the future.
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Patterns of Diel Variation in Nitrate Concentrations in the Potomac River
Burns, D. A.; Miller, M. P.; Pellerin, B. A.; Capel, P. D.
2015-12-01
The Potomac River is the second largest source of nitrogen to Chesapeake Bay, where reducing nutrient loads has been a focus of efforts to improve estuarine trophic status. Two years of high frequency sensor measurements of nitrate (NO3-) concentrations in the Upper Potomac River at the Little Falls gage were analyzed to quantify seasonal variation in the magnitude and timing of the apparent loss of NO3- from the water column that results from diel-driven processes. In addition to broad seasonal and flow-driven variation in NO3- concentrations, clear diel patterns were evident in the river, especially during low flow conditions that follow stormflow by several days. Diel variation was about 0.01 mg N/L in winter and 0.02 to 0.03 mg N/L in summer with intermediate values during spring and fall. This variation was equivalent to 10% occurred during some summer days. Maximum diel concentrations occurred during mid- to late-morning in most seasons, with the most repeatable patterns in summer and wider variation in timing during fall and winter. Diel NO3- loss diminished loads by about 0.6% in winter and 1.3% in summer, and diel-driven processes were minor compared to estimates of total in-stream NO3- loss that averaged about one-third of the inferred groundwater NO3- contribution to the river network. The magnitude of diel NO3- variation was more strongly related to metrics based on water temperature and discharge than to metrics based on photosynthetically active radiation. Despite the fairly low diminishment of NO3- loads attributable to diel variation, estimates of diel NO3- uptake were fairly high compared to published values from smaller streams and rivers. The diel NO3- patterns observed in the Potomac River are consistent with photosynthesis of periphyton as a principal driver which may be linked to denitrification through the release of labile carbon. The extent to which these diel patterns are related to measures of aquatic metabolism are unknown as is the role
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Guaresti, O; García-Astrain, C; Aguirresarobe, R H; Eceiza, A; Gabilondo, N
2018-03-01
Stimuli-responsive chitosan-based hydrogels for biomedical applications using the Diels-Alder reaction were prepared. Furan modified chitosan (Cs-Fu) was cross-linked with polyetheramine derived bismaleimide at different equivalent ratios in order to determine the effect in the swelling and release properties on the final CsFu:BMI hydrogels. The Diels Alder cross-linking reaction was monitored by UV-vis spectroscopy and rheological measurements. Both the sol-gel transition value and the final storage modulus for the different formulations were similar and close to 40 min and 400 Pa, respectively. On the contrary, the swelling degree was found to be strongly dependent on the amount of bismaleimide, mainly in acidic medium, where the increased cross-linking reduced the swelling value in 25%, but maintaining the sustained drug release in the simulated gastrointestinal environment. Our study suggested that these DA-cross-linked chitosan hydrogels could be potential carriers for targeted drug administration. Copyright © 2017 Elsevier Ltd. All rights reserved.
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Bender, Sara J; Parker, Micaela S; Armbrust, E Virginia
2012-03-01
Diatoms are photoautotrophic organisms capable of growing on a variety of inorganic and organic nitrogen sources. Discovery of a complete urea cycle in diatoms was surprising, as this pathway commonly functions in heterotrophic organisms to rid cells of waste nitrogen. To determine how the urea cycle is integrated into cellular nitrogen metabolism and energy management, the centric diatom Thalassiosira pseudonana was maintained in semi-continuous batch cultures on nitrate, ammonium, or urea as the sole nitrogen source, under a 16: 8 light: dark cycle and at light intensities that were low, saturating, or high for growth. Steady-state transcript levels were determined for genes encoding enzymes linked to the urea cycle, urea hydrolysis, glutamine synthesis, pyrimidine synthesis, photorespiration, and energy storage. Transcript abundances were significantly affected by nitrogen source, light intensity and a diel cycle. The impact of N source on differential transcript accumulation was most apparent under the highest light intensity. Models of cellular metabolism under high light were developed based on changes in transcript abundance and predicted enzyme localizations. We hypothesize that the urea cycle is integrated into nitrogen metabolism through its connection to glutamine and in the eventual production of urea. These findings have important implications for nitrogen flow in the cell over diel cycles at surface ocean irradiances. Copyright © 2011 Elsevier GmbH. All rights reserved.
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Transcription Factor Functional Protein-Protein Interactions in Plant Defense Responses
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Murilo S. Alves
2014-03-01
Full Text Available Responses to biotic stress in plants lead to dramatic reprogramming of gene expression, favoring stress responses at the expense of normal cellular functions. Transcription factors are master regulators of gene expression at the transcriptional level, and controlling the activity of these factors alters the transcriptome of the plant, leading to metabolic and phenotypic changes in response to stress. The functional analysis of interactions between transcription factors and other proteins is very important for elucidating the role of these transcriptional regulators in different signaling cascades. In this review, we present an overview of protein-protein interactions for the six major families of transcription factors involved in plant defense: basic leucine zipper containing domain proteins (bZIP, amino-acid sequence WRKYGQK (WRKY, myelocytomatosis related proteins (MYC, myeloblastosis related proteins (MYB, APETALA2/ ETHYLENE-RESPONSIVE ELEMENT BINDING FACTORS (AP2/EREBP and no apical meristem (NAM, Arabidopsis transcription activation factor (ATAF, and cup-shaped cotyledon (CUC (NAC. We describe the interaction partners of these transcription factors as molecular responses during pathogen attack and the key components of signal transduction pathways that take place during plant defense responses. These interactions determine the activation or repression of response pathways and are crucial to understanding the regulatory networks that modulate plant defense responses.
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Solvent Effects in Asymmetric Hetero Diels-Alder and Ene Reactions
DEFF Research Database (Denmark)
Johannsen, Mogens; Jørgensen, Karl Anker
1996-01-01
The use of polar solvents such as nitromethane or 2-nitropropane leads to a significant improvement of the catalytic properties of a cationic copper-Lewis acid in the hetero Diels-Alder reaction of alkyl glyoxylates with dienes; The scope of a newly developed copper(II)-bisoxazoline catalyst...... for the hetero Diels-Alder reaction is demonstrated by the reaction of different dienes with alkyl glyoxylates in nitroalkane solvents with the formation of the hetero Diels-Alder adduct in high enantiomeric excess as the major product. The synthetic application of the reaction is exemplified by an improved...
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Gieling, Reinerus Gerardus
2003-01-01
This thesis deals with the conceivable transfer of the Diels Alder/retro-Diels Alder concept to the solid phase in order to broaden the scope of the methodology to a combinatorial level. In addition, based on this methodology the development of a traceless thermocleavable linking system for
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Directory of Open Access Journals (Sweden)
Xinguo Shi
Full Text Available Gene structure and expression regulation of form II RuBisCO (rbcII in dinoflagellates are still poorly understood. Here we isolated this gene (Pdrbc and investigated its diel expression pattern in a harmful algal bloom forming dinoflagellate Prorocentrum donghaiense. We obtained cDNA sequences with triple tandem repeats of the coding unit (CU; the 5' region has the sequence of a typical dinoflagellate plastid gene, encoding an N-terminus with two transmembrane regions separated by a plastid transit peptide. The CUs (1,455 bp except 1464 bp in last CU are connected through a 63 bp spacer. Phylogenetic analysis showed that rbcII CUs within species formed monophyletic clusters, indicative of intraspecific gene duplication or purifying evolution. Using quantitative PCR (qPCR we estimated 117±40 CUs of Pdrbc in the P. donghaiense genome. Although it is commonly believed that most dinoflagellate genes lack transcriptional regulation, our RT-qPCR analysis on synchronized cultures revealed remarkable diel rhythm of Pdrbc expression, showing significant correlations of transcript abundance with the timing of the dark-to-light transition and cell cycle G2M-phase. When the cultures were shifted to continuous light, Pdrbc expression remained significantly correlated with the G2M-phase. Under continuous darkness the cell cycle was arrested at the G1 phase, and the rhythm of Pdrbc transcription disappeared. Our results suggest that dinoflagellate rbcII 1 undergoes duplication or sequence purification within species, 2 is organized in tandem arrays in most species probably to facilitate efficient translation and import of the encoded enzyme, and 3 is regulated transcriptionally in a cell cycle-dependent fashion at least in some dinoflagellates.
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Stepwise radical cation Diels-Alder reaction via multiple pathways.
Shimizu, Ryo; Okada, Yohei; Chiba, Kazuhiro
2018-01-01
Herein we disclose the radical cation Diels-Alder reaction of aryl vinyl ethers by electrocatalysis, which is triggered by an oxidative SET process. The reaction clearly proceeds in a stepwise fashion, which is a rare mechanism in this class. We also found that two distinctive pathways, including "direct" and "indirect", are possible to construct the Diels-Alder adduct.
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Directory of Open Access Journals (Sweden)
Yu Guang
2011-01-01
Full Text Available Angelica sinensis (Oliv. Diels (Umbelliferae is a well-known medicinal plant mainly distributed in Gansu Province of China. Its local and global demand is significant because of its food and medicinal applications. However, the early bolting rate of Angelica sinensis (Oliv. Diels reaches 20%-60%, which seriously affects its food and medicinal qualities. Thus, differences in gene expression between the flower bud and sprout-shoot apical meristem underwent analysis, by means of cDNA-amplified restriction fragment length polymorphism, to better understand the flowering mechanism. 64 primer sets, each of which amplified to 60 transcript-derived fragments (TDFs, were used. Among these TDFs, 26 were expressed specifically in the flower bud. After cloning and sequencing, 32 distinct sequences were obtained from these 26 TDFs, and 25 were found with homologous sequences in databases. Confirmation of differential expression of 13 sequences was obtained by semi-quantitative RT-PCR, their showing higher expression levels in flower buds. These homologous sequences encode transposable elements, pentatricopeptide repeat-containing proteins, DNA-binding transcription factors, zinc finger (B-box type family proteins, NADP-dependent sorbitol 6-phosphate dehydrogenase (S6PDH, amongst others.
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DEFF Research Database (Denmark)
Steunou, Anne-Soisig; Jensen, Sheila I; Brecht, Eric
2008-01-01
Nitrogen fixation, a prokaryotic, O(2)-inhibited process that reduces N(2) gas to biomass, is of paramount importance in biogeochemical cycling of nitrogen. We analyzed the levels of nif transcripts of Synechococcus ecotypes, NifH subunit and nitrogenase activity over the diel cycle...... in the microbial mat of an alkaline hot spring in Yellowstone National Park. The results showed a rise in nif transcripts in the evening, with a subsequent decline over the course of the night. In contrast, immunological data demonstrated that the level of the NifH polypeptide remained stable during the night...
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Poiré, Richard; Wiese-Klinkenberg, Anika; Parent, Boris; Mielewczik, Michael; Schurr, Ulrich; Tardieu, François; Walter, Achim
2010-06-01
Diel (24 h) leaf growth patterns were differently affected by temperature variations and the circadian clock in several plant species. In the monocotyledon Zea mays, leaf elongation rate closely followed changes in temperature. In the dicotyledons Nicotiana tabacum, Ricinus communis, and Flaveria bidentis, the effect of temperature regimes was less obvious and leaf growth exhibited a clear circadian oscillation. These differences were related neither to primary metabolism nor to altered carbohydrate availability for growth. The effect of endogenous rhythms on leaf growth was analysed under continuous light in Arabidopsis thaliana, Ricinus communis, Zea mays, and Oryza sativa. No rhythmic growth was observed under continuous light in the two monocotyledons, while growth rhythmicity persisted in the two dicotyledons. Based on model simulations it is concluded that diel leaf growth patterns in mono- and dicotyledons result from the additive effects of both circadian-clock-controlled processes and responses to environmental changes such as temperature and evaporative demand. Apparently very distinct diel leaf growth behaviour of monocotyledons and dicotyledons can thus be explained by the different degrees to which diel temperature variations affect leaf growth in the two groups of species which, in turn, depends on the extent of the leaf growth control by internal clocks.
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Diel vertical migration of zooplankton in the Tanzanian waters of ...
African Journals Online (AJOL)
The diel vertical migration of zooplankton was studied in the Southern part of Lake Victoria in January and July 2002. A van dorn water sampler was used to collect zooplankton. In January 2002, zooplankton showed a pronounced diel vertical migration whereby zooplankton were moving upward at around sunset and ...
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Discriminative identification of transcriptional responses of promoters and enhancers after stimulus
Kleftogiannis, Dimitrios A.
2016-10-17
Promoters and enhancers regulate the initiation of gene expression and maintenance of expression levels in spatial and temporal manner. Recent findings stemming from the Cap Analysis of Gene Expression (CAGE) demonstrate that promoters and enhancers, based on their expression profiles after stimulus, belong to different transcription response subclasses. One of the most promising biological features that might explain the difference in transcriptional response between subclasses is the local chromatin environment. We introduce a novel computational framework, PEDAL, for distinguishing effectively transcriptional profiles of promoters and enhancers using solely histone modification marks, chromatin accessibility and binding sites of transcription factors and co-activators. A case study on data from MCF-7 cell-line reveals that PEDAL can identify successfully the transcription response subclasses of promoters and enhancers from two different stimulations. Moreover, we report subsets of input markers that discriminate with minimized classification error MCF-7 promoter and enhancer transcription response subclasses. Our work provides a general computational approach for identifying effectively cell-specific and stimulation-specific promoter and enhancer transcriptional profiles, and thus, contributes to improve our understanding of transcriptional activation in human.
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Intramolecular Diels-Alder reactions of pyrimidines, a synthetic and computational study
Stolle, W.A.W.
1992-01-01
This thesis deals with an investigation on the ringtransformation reactions of 2and 5-(ω-alkynyl)pyrimidine derivatives, which undergo upon heating an intramolecular Diels-Alder reaction and subsequently a spontaneous retro Diels- Alder reaction. To get a better insight into the
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The hexadehydro-Diels-Alder reaction.
Hoye, Thomas R; Baire, Beeraiah; Niu, Dawen; Willoughby, Patrick H; Woods, Brian P
2012-10-11
Arynes (aromatic systems containing, formally, a carbon-carbon triple bond) are among the most versatile of all reactive intermediates in organic chemistry. They can be 'trapped' to give products that are used as pharmaceuticals, agrochemicals, dyes, polymers and other fine chemicals. Here we explore a strategy that unites the de novo generation of benzynes-through a hexadehydro-Diels-Alder reaction-with their in situ elaboration into structurally complex benzenoid products. In the hexadehydro-Diels-Alder reaction, a 1,3-diyne is engaged in a [4+2] cycloisomerization with a 'diynophile' to produce the highly reactive benzyne intermediate. The reaction conditions for this simple, thermal transformation are notable for being free of metals and reagents. The subsequent and highly efficient trapping reactions increase the power of the overall process. Finally, we provide examples of how this de novo benzyne generation approach allows new modes of intrinsic reactivity to be revealed.
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Diels-Alder reactions of inert aromatic compounds within a self-assembled coordination cage.
Horiuchi, Shinnosuke; Murase, Takashi; Fujita, Makoto
2011-07-04
A self-assembled coordination cage serves as a nanometer-sized molecular flask to promote the Diels-Alder reactions of aromatic hydrocarbons with N-cyclohexylmaleimide. The coordination cage accelerated the Diels-Alder reaction of anthracene at the electronically unfavorable, terminal benzene ring to give a compact, cavity-restrained syn-adduct. Activation-parameter measurements for the reactions revealed considerable reduction in the entropy cost, and preorganization of the substrates is a dominant factor in the enhanced reactivity. Owing to this entropy-cost reduction, otherwise-unreactive aromatic compounds, such as naphthalenes or triphenylene, also underwent Diels-Alder reactions in a regio- and stereocontrolled fashion. In the naphthalene Diels-Alder reaction, X-ray crystallographic analysis of the guest-inclusion complex clarified the reinforced orientation and proximity of the substrate pairs before the reaction. A perylene Diels-Alder adduct was stabilized inside the cage and protected from aerial oxidation. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Asymmetric Diels-Alder reactions with 5-menthyloxy-2(5H)-furanones
Jong, Johannes Cornelis de
2006-01-01
At the beginning of the reseach described in this thesis the catalytic asymmetric Diels-Alder reaction had scarcely been investigated. No good catalytic processes with high enantiomeric excess were known at that time. At the same time the Diels-Alder reactions with chiral dienophiles needed further
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Diel dualism in the energy consumption of the European catfish Silurus glanis.
Slavík, O; Horký, P
2012-12-01
Twenty individuals of the largest European freshwater predator, the European catfish Silurus glanis, were tagged with electromyogram (EMG) physiological telemetry sensors. The fish were observed during diel cycles during the spring and summer in the Elbe and Berounka Rivers, Czech Republic. The purpose of this study was to determine whether diel dualism in the activity of S. glanis occurs naturally or is induced by the laboratory environment and by the conditions occurring in aquaculture. The results obtained from the riverine environment tended to show dualism in the use of the light and dark phases of the day because 35% of the individuals varied from a site-specific common diel activity pattern. The EMG values increased in accordance with the mass (M) of the fish. To eliminate the influence of M on individual energy consumption, the EMG records were analysed in terms of the EMG:M ratios. High individual variability was found in these ratios. The diel activity pattern of the individuals with relatively high energy consumption differed from the common diel activity pattern. In contrast, the fish that adopted the common diel activity pattern displayed relatively low energy consumption. The results of this study indicated that dualism and energy consumption are related. The EMG values also varied with the values of the environmental variables. Increasing temperature was associated with high EMG values, whereas the EMG values decreased with increasing flow. © 2012 The Authors. Journal of Fish Biology © 2012 The Fisheries Society of the British Isles.
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Diels-Alder reactions: The effects of catalyst on the addition reaction
Yilmaz, Özgür; Kus, Nermin Simsek; Tunç, Tuncay; Sahin, Ertan
2015-10-01
The reaction between 2,3-dimethyl-1,3-butadiene and dimethyl 7-oxabicyclo[2.2.1]hepta-2,5-diene-2,3-dicarboxylate is efficiently achieved with small amounts of catalyst, i.e. phenol, AcOH, nafion, and β-cyclodextrin. Exo-diastereoselective cycloaddition reactions were observed both without catalyst and different catalysts for 48 days. As a result, different products (tricyclicmolecule 5, retro-Diels-Alder product 6, and oxidation product 7) were obtained with different catalysts. In addition, we synthesized Diels-Alders product 8 and tricyclocyclitol 10 via Diels-Alder reaction. The structures of these products were characterized by 1H NMR, 13C NMR, MS and IR spectroscopy.
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Zhu, Shifa; Guo, Zhengjiang; Huang, Zhipeng; Jiang, Huanfeng
2014-02-24
A bioinsipred gold-catalyzed tandem Diels-Alder/Diels-Alder reaction of an enynal and a 1,3-diene, forming the highly-strained benzotricyclo[3.2.1.0(2,7) ]octane skeleton, was reported. In contrast, a Diels-Alder/Friedel-Crafts tandem reaction occurred instead when silver salts were used as the catalyst. Although both reactions experienced the similar Diels-Alder reaction of a pyrylium intermediate with a 1,3-diene, they have different reaction mechanisms. The former proceeded with a stepwise Diels-Alder reaction, while the latter one with a concerted one. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Estudio dieléctrico del envejecimiento físico
Hernández, M. C; Suárez, N; Puma, M
2006-01-01
La influencia del envejecimiento físico en las propiedades dieléctricas de un poliarilato y un policarbonato derivados de la tirosina: Poli(DTH succinato) y poli(DTO carbonato) respectivamente, es estudiada utilizando la técnica de Corrientes de Polarización Estimuladas Térmicamente (TSPC). La caracterización dieléctrica, utilizando electrodos de bloqueo, permite estudiar el efecto de los cambios estructurales del material sobre las relajaciones asociadas con la redistribución de cargas debid...
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Diel changes in metal concentrations in a geogenically acidic river: Rio Agrio, Argentina
Parker, Stephen R.; Gammons, Christopher H.; Pedrozo, Fernando L.; Wood, Scott A.
2008-12-01
Rio Agrio in Patagonia, Argentina is a geogenically acidic stream that derives its low-pH waters from condensation of acidic gases near its headwaters on the flanks of the active Copahue Volcano. This study reports the results of three diel (24-h) water samplings in three different pH regimes (3.2, 4.4 and 6.3) along the river. Changes in the concentration and speciation of Fe dominated the diel chemical changes at all three sites, although the timing and intensity of these cycles were different in each reach. At the two acidic sampling sites, total dissolved Fe and dissolved Fe(III) concentrations decreased during the day and increased at night, whereas dissolved Fe(II) showed the reverse pattern. These cycles are explained by Fe(III) photoreduction, as well as enhanced rates of precipitation of hydrous ferric oxide (HFO) during the warm afternoon hours. A strong correlation was observed between Fe(III) and As at the furthest upstream (pH 3.2) site, most likely due to co-precipitation of As with HFO. At the downstream (pH 6.3) location, Fe(II) concentrations increased at night, as did concentrations of rare earth elements and dissolved Al. Photoreduction does not appear to be an important process at pH 6.3, although it may be indirectly responsible for the observed diel cycle of Fe(II) due to advection of photochemically produced Fe(II) from acidic upstream waters. The results of this study of a naturally-acidic river are very similar to diel trends recently obtained from mining-impacted streams receiving acid rock drainage. The results are also used to explore the link between geochemistry and microbiology in acidic eco-systems. For example, Fe(III) photoreduction produces chemical potential energy (in the form of metastable Fe 2+) that helps support the bacterial community in this unique extreme environment.
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Modeling Diel Oxygen Dynamics and Ecosystem Metabolism in a Shallow, Eutrophic Estuary
Weeks Bay is a shallow eutrophic estuary that exhibits frequent summertime diel-cycling hypoxia and periods of dissolved oxygen (DO) oversaturation during the day. Diel DO dynamics in shallow estuaries like Weeks Bay are complex, and may be influenced by wind forcing, vertical an...
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Nandi, Sisir; Monesi, Alessandro; Drgan, Viktor; Merzel, Franci; Novič, Marjana
2013-10-30
In the present study, we show the correlation of quantum chemical structural descriptors with the activation barriers of the Diels-Alder ligations. A set of 72 non-catalysed Diels-Alder reactions were subjected to quantitative structure-activation barrier relationship (QSABR) under the framework of theoretical quantum chemical descriptors calculated solely from the structures of diene and dienophile reactants. Experimental activation barrier data were obtained from literature. Descriptors were computed using Hartree-Fock theory using 6-31G(d) basis set as implemented in Gaussian 09 software. Variable selection and model development were carried out by stepwise multiple linear regression methodology. Predictive performance of the quantitative structure-activation barrier relationship (QSABR) model was assessed by training and test set concept and by calculating leave-one-out cross-validated Q2 and predictive R2 values. The QSABR model can explain and predict 86.5% and 80% of the variances, respectively, in the activation energy barrier training data. Alternatively, a neural network model based on back propagation of errors was developed to assess the nonlinearity of the sought correlations between theoretical descriptors and experimental reaction barriers. A reasonable predictability for the activation barrier of the test set reactions was obtained, which enabled an exploration and interpretation of the significant variables responsible for Diels-Alder interaction between dienes and dienophiles. Thus, studies in the direction of QSABR modelling that provide efficient and fast prediction of activation barriers of the Diels-Alder reactions turn out to be a meaningful alternative to transition state theory based computation.
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DEFF Research Database (Denmark)
Jensen, Sheila I; Steunou, Anne-Soisig; Bhaya, Devaki
2011-01-01
The relative abundance of transcripts encoding proteins involved in inorganic carbon concentrating mechanisms (CCM), detoxification of reactive oxygen species (ROS) and photosynthesis in the thermophilic cyanobacterium Synechococcus OS-B' was measured in hot spring microbial mats over two diel...
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Identifying salt stress-responsive transcripts from Roselle ( Hibiscus ...
African Journals Online (AJOL)
Hibiscus sabdariffa L.). Identifying the potentially novel transcripts responsible for salt stress tolerance in roselle will increase knowledge of the molecular mechanism underlying salt stress responses. In this study, differential display reverse ...
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The asymmetric hetero-Diels-Alder reaction in the syntheses of biologically relevant compounds.
Eschenbrenner-Lux, Vincent; Kumar, Kamal; Waldmann, Herbert
2014-10-13
The hetero-Diels-Alder reaction is one of the most powerful transformations in the chemistry toolbox for the synthesis of aza- and oxa-heterocycles embodying multiple stereogenic centers. However, as compared to other cycloadditions, in particular the dipolar cycloadditions and the Diels-Alder reaction, the hetero-Diels-Alder reaction has been much less explored and exploited in organic synthesis. Nevertheless, this powerful transformation has opened up efficient and creative routes to biologically relevant small molecules and different natural products which contain six-membered oxygen or nitrogen ring systems. Recent developments in this field, in particular in the establishment of enantioselectively catalyzed hetero-Diels-Alder cycloadditions steered by a plethora of different catalysts and the application of the resulting small molecules in chemical biology and medicinal chemistry research, are highlighted in this Minireview. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Niobium Pentachloride Activation of Enone Derivatives: Diels-Alder and Conjugate Addition Products
Directory of Open Access Journals (Sweden)
Gil Valdo José da Silva
2002-05-01
Full Text Available Niobium pentachloride has proven to be a powerful activating agent for Diels-Alder or conjugate addition reactions of cycloenones. The Diels-Alder product was obtained only with an unsubstituted enone (cyclohexenone and the highly reactive diene cyclopentadiene; substituents in the b-position of enones seem to prevent Diels-Alder reaction: oxygenated substituents favor the formation of vinyl chlorides (ethyl ether or dichloromethane as solvents or enol ethers (ethyl acetate as solvent, while a methyl substituent prevents any kind of transformation with NbCl5. Less reactive dienes, furan and 2-methylfuran gave the conjugate addition products of the furan ring to the enone system.
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Cantín, Ángel; Gomez, M Victoria; de la Hoz, Antonio
2016-01-01
Diels-Alder cycloaddition between cyclopentadiene and p -benzoquinone has been studied in the confined space of a pure silica zeolite Beta and the impact on reaction rate due to the concentration effect within the pore and diffusion limitations are discussed. Introduction of Lewis or Brønsted acid sites on the walls of the zeolite strongly increases the reaction rate. However, contrary to what occurs with mesoporous molecular sieves (MCM-41), Beta zeolite does not catalyse the retro-Diels-Alder reaction, resulting in a highly selective catalyst for the cycloaddition reaction.
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Transcriptional profiling of the bovine hepatic response to experimentally induced E. coli mastitis
DEFF Research Database (Denmark)
Jørgensen, Hanne Birgitte Hede; Buitenhuis, Bart; Røntved, Christine Maria
2012-01-01
The mammalian liver works to keep the body in a state of homeostasis and plays an important role in systemic acute phase response to infections. In this study we investigated the bovine hepatic acute phase response at the gene transcription level in dairy cows with experimentally E. coli-induced ......The mammalian liver works to keep the body in a state of homeostasis and plays an important role in systemic acute phase response to infections. In this study we investigated the bovine hepatic acute phase response at the gene transcription level in dairy cows with experimentally E. coli......-induced mastitis. At time = 0, each of 16 periparturient dairy cows received 20-40 CFU of live E. coli in one front quarter of the udder. A time series of liver biopsies was collected at -144, 12, 24 and 192 hours relative to time of inoculation. Changes in transcription levels in response to E. coli inoculation...... were analyzed using the Bovine Genome Array and tested significant for 408 transcripts over the time series (adjusted p0.05; abs(fold-change)>2). After 2-D clustering, transcripts represented three distinct transcription profiles: 1) regulation of gene transcription and apoptosis, 2) responses...
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Physicochemical Properties and Fatty Acid Profiles of Elaeagnus mollis Diels Nut Oils.
Liang, Shaohua; Yang, Ruinan; Dong, Caiwen; Yang, Qingping
2015-01-01
The physicochemical properties, fatty acid profiles, content of tocopherol and sterol of the oils extracted from the nuts of Elaeagnus mollis Diels grown in different regions of China were studied in this work. The results indicated that the Elaeagnus mollis Diels nut oils contained about 0.2% sterols and the tocopherol contents were in the range of 119.6-128.6mg/100g. The nut oils were all rich in unsaturated fatty acids, especially oleic acid and linoleic acid. Furthermore, the main triacylglycerols species of the nut oils were all dilinoleoyl-monoolein (LOL), dioleoyl-monolinoleoyl (OLO) and trilinoleate (LLL). This work might be useful for developing applications for Elaeagnus mollis Diels nut oil.
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Diel variation in the catch of fishes and penaeid shrimps in a tropical estuary
Stoner, Allan W.
1991-07-01
In Laguna Joyuda, Puerto Rico, 24-h trawl surveys were conducted to test the hypothesis that there is no diel variation in the catch rate of fishes and penaeid shrimps in a turbid, microtidal estuary relatively free of visual predation. The null hypothesis was not rejected for the two most abundant fishes in the lagoon, Eucinostomus gula (Gerreidae) and Achirus lineatus (Bothidae). Conversely, the total number of fishes, Diapterus rhombeus (Gerreidae), and the engraulids Anchoa cubana and A. hepsetus were collected in significantly higher numbers during hours of darkness. Total penaeid catch was significantly higher in night than in day collections. The most abundant species were Penaeus notialis and P. subtilis, both of which appeared to be strong daytime burrowers. Small penaeids demonstrated greater diel variation in trawl capture rate than larger (subadult) shrimps. Diel variation in capture rate was related to habitat associations of individual species. Fauna resident in the very turbid lagoon demonstrated no diel variation in activity patterns and trawl susceptibility. Those species which spend only the early part of their lives in the lagoon, or live in both turbid and clear water, had significant diel variation in activity and trawl catchability.
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BLOKZIJL, W; BLANDAMER, MJ; ENGBERTS, JBFN
1991-01-01
Second-order rate constants and isobaric activation parameters for the intermolecular Diels-Alder reactions of cyclopentadiene with alkyl vinyl ketones (2a,b) and 5-substituted-1,4-naphthoquinones (3a-c) as well as for the intramolecular Diels-Alder reaction of N-furfuryl-N-methylmaleamic acid (4)
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The first organocatalytic, ortho-regioselective inverse-electron-demand hetero-Diels-Alder reaction.
Hejmanowska, Joanna; Jasiński, Marcin; Wojciechowski, Jakub; Mlostoń, Grzegorz; Albrecht, Łukasz
2017-10-17
The development of the unprecedented ortho-regioselective inverse-electron-demand hetero-Diels-Alder (IEDHDA) reaction is described. It has been demonstrated that by proper choice of reactants and reaction conditions the inverse-electron-demand hetero-Diels-Alder cycloaddition can be realized with unprecedented regioselectivity arising from the reaction between the terminal carbon atom of the dienophile and the heteroatom of the heterodiene.
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Theoretical study of the Diels-Alder reaction between o-benzoquinone and norbornadiene
Quijano-Quiñones, Ramiro F.; Quesadas-Rojas, M.; Cuevas, Gabriel; Mena-Rejón, Gonzalo J.
2013-06-01
The reaction between norbornadiene and o-benzoquinone is an important step in polyalicyclic rigid structures synthesis. It has been considered that this reaction is an example of Diels-Alder (DA) and hetero-Diels-Alder (HDA) cycloadditions with o-benzoquinone acting as diene (forming C-C bonds) and heterodiene (forming O-C bonds). We have performed a Density Functional Theory study of this reaction, employing B3LYP, mPW1PW91, and B1B95 functionals and 6-31G(d,p) and 6-31+G(d,p) Gaussian type basis sets. The results indicate that Diels-Alder is a feasible mechanism for both reactions, but should not be the main route to the formation of products with C-C bonds.
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Theoretical study of the Diels-Alder reaction between o-benzoquinone and norbornadiene
International Nuclear Information System (INIS)
Quijano-Quiñones, Ramiro F; Quesadas-Rojas, M; Mena-Rejón, Gonzalo J; Cuevas, Gabriel
2013-01-01
The reaction between norbornadiene and o-benzoquinone is an important step in polyalicyclic rigid structures synthesis. It has been considered that this reaction is an example of Diels-Alder (DA) and hetero-Diels-Alder (HDA) cycloadditions with o-benzoquinone acting as diene (forming C-C bonds) and heterodiene (forming O-C bonds). We have performed a Density Functional Theory study of this reaction, employing B3LYP, mPW1PW91, and B1B95 functionals and 6-31G(d,p) and 6-31+G(d,p) Gaussian type basis sets. The results indicate that Diels-Alder is a feasible mechanism for both reactions, but should not be the main route to the formation of products with C-C bonds.
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Bojanovič, Klara; D'Arrigo, Isotta; Long, Katherine S
2017-04-01
Bacteria cope with and adapt to stress by modulating gene expression in response to specific environmental cues. In this study, the transcriptional response of Pseudomonas putida KT2440 to osmotic, oxidative, and imipenem stress conditions at two time points was investigated via identification of differentially expressed mRNAs and small RNAs (sRNAs). A total of 440 sRNA transcripts were detected, of which 10% correspond to previously annotated sRNAs, 40% to novel intergenic transcripts, and 50% to novel transcripts antisense to annotated genes. Each stress elicits a unique response as far as the extent and dynamics of the transcriptional changes. Nearly 200 protein-encoding genes exhibited significant changes in all stress types, implicating their participation in a general stress response. Almost half of the sRNA transcripts were differentially expressed under at least one condition, suggesting possible functional roles in the cellular response to stress conditions. The data show a larger fraction of differentially expressed sRNAs than of mRNAs with >5-fold expression changes. The work provides detailed insights into the mechanisms through which P. putida responds to different stress conditions and increases understanding of bacterial adaptation in natural and industrial settings. IMPORTANCE This study maps the complete transcriptional response of P. putida KT2440 to osmotic, oxidative, and imipenem stress conditions at short and long exposure times. Over 400 sRNA transcripts, consisting of both intergenic and antisense transcripts, were detected, increasing the number of identified sRNA transcripts in the strain by a factor of 10. Unique responses to each type of stress are documented, including both the extent and dynamics of the gene expression changes. The work adds rich detail to previous knowledge of stress response mechanisms due to the depth of the RNA sequencing data. Almost half of the sRNAs exhibit significant expression changes under at least one
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Rund, Samuel S C; Yoo, Boyoung; Alam, Camille; Green, Taryn; Stephens, Melissa T; Zeng, Erliang; George, Gary F; Sheppard, Aaron D; Duffield, Giles E; Milenković, Tijana; Pfrender, Michael E
2016-08-18
Marine and freshwater zooplankton exhibit daily rhythmic patterns of behavior and physiology which may be regulated directly by the light:dark (LD) cycle and/or a molecular circadian clock. One of the best-studied zooplankton taxa, the freshwater crustacean Daphnia, has a 24 h diel vertical migration (DVM) behavior whereby the organism travels up and down through the water column daily. DVM plays a critical role in resource tracking and the behavioral avoidance of predators and damaging ultraviolet radiation. However, there is little information at the transcriptional level linking the expression patterns of genes to the rhythmic physiology/behavior of Daphnia. Here we analyzed genome-wide temporal transcriptional patterns from Daphnia pulex collected over a 44 h time period under a 12:12 LD cycle (diel) conditions using a cosine-fitting algorithm. We used a comprehensive network modeling and analysis approach to identify novel co-regulated rhythmic genes that have similar network topological properties and functional annotations as rhythmic genes identified by the cosine-fitting analyses. Furthermore, we used the network approach to predict with high accuracy novel gene-function associations, thus enhancing current functional annotations available for genes in this ecologically relevant model species. Our results reveal that genes in many functional groupings exhibit 24 h rhythms in their expression patterns under diel conditions. We highlight the rhythmic expression of immunity, oxidative detoxification, and sensory process genes. We discuss differences in the chronobiology of D. pulex from other well-characterized terrestrial arthropods. This research adds to a growing body of literature suggesting the genetic mechanisms governing rhythmicity in crustaceans may be divergent from other arthropod lineages including insects. Lastly, these results highlight the power of using a network analysis approach to identify differential gene expression and provide novel
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Diel Variation in Beaked Whale Diving Behavior
National Research Council Canada - National Science Library
Baird, Robin; Webster, Daniel L; Schorr, Gregory S; McSweeney, Daniel J
2008-01-01
...) occurred at similar rates during the day and night for Blainville's beaked whales (daymean=0.38 h-1; nightmean=0.46 h-1), and there were no significant diel differences in depths, durations, ascent or descent rates for deep dives...
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Is it true that polymerization of vegetable oil occurs through Diels-Alder reaction?
Diels-Alder reaction mechanism is known to be one of the major reaction mechanisms to produce dimers and polymers during heating process of vegetable oil. However, our NMR study showed no evidence for Diels-Alder products. Soybean oil oxidized at 180 °C for 24 hrs with 1.45 surface area-to-volume ...
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The Diels-Alder cyclization of ketenimines.
Erb, Jeremy; Strull, Jessica; Miller, David; He, Jean; Lectka, Thomas
2012-04-20
A Diels-Alder reaction between cyclopentadiene and a variety of ketenimines is reported. A copper(I)-bis(phosphine complex catalyzes the cycloaddition across the C═N bond of the ketenimine in a [4 + 2] reaction to give an enamine intermediate that is hydrolyzed upon purification to generate aminoketones. © 2012 American Chemical Society
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Metagenomic screening for aromatic compound-responsive transcriptional regulators.
Directory of Open Access Journals (Sweden)
Taku Uchiyama
Full Text Available We applied a metagenomics approach to screen for transcriptional regulators that sense aromatic compounds. The library was constructed by cloning environmental DNA fragments into a promoter-less vector containing green fluorescence protein. Fluorescence-based screening was then performed in the presence of various aromatic compounds. A total of 12 clones were isolated that fluoresced in response to salicylate, 3-methyl catechol, 4-chlorocatechol and chlorohydroquinone. Sequence analysis revealed at least 1 putative transcriptional regulator, excluding 1 clone (CHLO8F. Deletion analysis identified compound-specific transcriptional regulators; namely, 8 LysR-types, 2 two-component-types and 1 AraC-type. Of these, 9 representative clones were selected and their reaction specificities to 18 aromatic compounds were investigated. Overall, our transcriptional regulators were functionally diverse in terms of both specificity and induction rates. LysR- and AraC- type regulators had relatively narrow specificities with high induction rates (5-50 fold, whereas two-component-types had wide specificities with low induction rates (3 fold. Numerous transcriptional regulators have been deposited in sequence databases, but their functions remain largely unknown. Thus, our results add valuable information regarding the sequence-function relationship of transcriptional regulators.
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The transcriptional response of microbial communities in thawing Alaskan permafrost soils
Coolen, Marco J. L.; Orsi, William D.
2015-01-01
Thawing of permafrost soils is expected to stimulate microbial decomposition and respiration of sequestered carbon. This could, in turn, increase atmospheric concentrations of greenhouse gasses, such as carbon dioxide and methane, and create a positive feedback to climate warming. Recent metagenomic studies suggest that permafrost has a large metabolic potential for carbon processing, including pathways for fermentation and methanogenesis. Here, we performed a pilot study using ultrahigh throughput Illumina HiSeq sequencing of reverse transcribed messenger RNA to obtain a detailed overview of active metabolic pathways and responsible organisms in up to 70 cm deep permafrost soils at a moist acidic tundra location in Arctic Alaska. The transcriptional response of the permafrost microbial community was compared before and after 11 days of thaw. In general, the transcriptional profile under frozen conditions suggests a dominance of stress responses, survival strategies, and maintenance processes, whereas upon thaw a rapid enzymatic response to decomposing soil organic matter (SOM) was observed. Bacteroidetes, Firmicutes, ascomycete fungi, and methanogens were responsible for largest transcriptional response upon thaw. Transcripts indicative of heterotrophic methanogenic pathways utilizing acetate, methanol, and methylamine were found predominantly in the permafrost table after thaw. Furthermore, transcripts involved in acetogenesis were expressed exclusively after thaw suggesting that acetogenic bacteria are a potential source of acetate for acetoclastic methanogenesis in freshly thawed permafrost. Metatranscriptomics is shown here to be a useful approach for inferring the activity of permafrost microbes that has potential to improve our understanding of permafrost SOM bioavailability and biogeochemical mechanisms contributing to greenhouse gas emissions as a result of permafrost thaw. PMID:25852660
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The transcriptional response of microbial communities in thawing Alaskan permafrost soils
Directory of Open Access Journals (Sweden)
M J L Coolen
2015-03-01
Full Text Available Thawing of permafrost soils is expected to stimulate microbial decomposition and respiration of sequestered carbon. This could, in turn, increase atmospheric concentrations of greenhouse gases, such as carbon dioxide and methane, and create a positive feedback to climate warming. Recent metagenomic studies suggest that permafrost has a large metabolic potential for carbon processing, including pathways for fermentation and methanogenesis. Here, we performed a pilot study using ultrahigh throughput Illumina HiSeq sequencing of reverse transcribed messenger RNA to obtain a detailed overview of active metabolic pathways and responsible organisms in up to 70 cm deep permafrost soils at a moist acidic tundra location in Arctic Alaska. The transcriptional response of the permafrost microbial community was compared before and after eleven days of thaw. In general, the transcriptional profile under frozen conditions suggests a dominance of stress responses, survival strategies, and maintenance processes, whereas upon thaw a rapid enzymatic response to decomposing soil organic matter (SOM was observed. Bacteroidetes, Firmicutes, ascomycete fungi, and methanogens were responsible for largest transcriptional response upon thaw. Transcripts indicative of heterotrophic methanogenic pathways utilizing acetate, methanol, and methylamine were found predominantly in the permafrost table after thaw. Furthermore, transcripts involved in acetogenesis were expressed exclusively after thaw suggesting that acetogenic bacteria are a potential source of acetate for acetoclastic methanogenesis in freshly thawed permafrost. Metatranscriptomics is shown here to be a useful approach for inferring the activity of permafrost microbes that has potential to improve our understanding of permafrost SOM bioavailability and biogeochemical mechanisms contributing to greenhouse gas emissions as a result of permafrost thaw.
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Diel predator activity drives a dynamic landscape of fear
Kohl, Michel T.; Stahler, Daniel R.; Metz, Matthew C.; Forester, James D.; Kauffman, Matthew J.; Varley, Nathan; White, P.J.; Smith, Douglas W.; MacNulty, Daniel R.
2017-01-01
A "landscape of fear" (LOF) is a map that describes continuous spatial variation in an animal's perception of predation risk. The relief on this map reflects, for example, places that an animal avoids to minimize risk. Although the LOF concept is a potential unifying theme in ecology that is often invoked to explain the ecological and conservation significance of fear, quantified examples of a LOF over large spatial scales are lacking as is knowledge about the daily dynamics of a LOF. Despite theory and data to the contrary, investigators often assume, implicitly or explicitly, that a LOF is a static consequence of a predator's mere presence. We tested the prediction that a LOF in a large-scale, free-living system is a highly-dynamic map with "peaks" and "valleys" that alternate across the diel (24-hour) cycle in response to daily lulls in predator activity. We did so with extensive data from the case study of Yellowstone elk (Cervus elaphus) and wolves (Canis lupus) that was the original basis for the LOF concept. We quantified the elk LOF, defined here as spatial allocation of time away from risky places and times, across nearly 1000-km2 of northern Yellowstone National Park and found that it fluctuated with the crepuscular activity pattern of wolves, enabling elk to use risky places during wolf downtimes. This may help explain evidence that wolf predation risk has no effect on elk stress levels, body condition, pregnancy, or herbivory. The ability of free-living animals to adaptively allocate habitat use across periods of high and low predator activity within the diel cycle is an underappreciated aspect of animal behavior that helps explain why strong antipredator responses may trigger weak ecological effects, and why a LOF may have less conceptual and practical importance than direct killing.
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The Diels-Alder reaction: A powerful tool for the design of drug delivery systems and biomaterials.
Gregoritza, Manuel; Brandl, Ferdinand P
2015-11-01
Click reactions have the potential to greatly facilitate the development of drug delivery systems and biomaterials. These reactions proceed under mild conditions, give high yields, and form only inoffensive by-products. The Diels-Alder cycloaddition is one of the click reactions that do not require any metal catalyst; it is one of the most useful reactions in synthetic organic chemistry and material design. Herein, we highlight possible applications of the Diels-Alder reaction in pharmaceutics and biomedical engineering. Particular focus is placed on the synthesis of polymers and dendrimers for drug delivery, the preparation of functionalized surfaces, bioconjugation techniques, and applications of the Diels-Alder reaction in nanotechnology. Moreover, applications of the reaction for the preparation of hydrogels for drug delivery and tissue engineering are reviewed. A general introduction to the Diels-Alder reaction is presented, along with a discussion of potential pitfalls and challenges. At the end of the article, we provide a set of tools that may facilitate the application of the Diels-Alder reaction to solve important pharmaceutical or biomedical problems. Copyright © 2015 Elsevier B.V. All rights reserved.
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The Role of the Transcriptional Response to DNA Replication Stress.
Herlihy, Anna E; de Bruin, Robertus A M
2017-03-02
During DNA replication many factors can result in DNA replication stress. The DNA replication stress checkpoint prevents the accumulation of replication stress-induced DNA damage and the potential ensuing genome instability. A critical role for post-translational modifications, such as phosphorylation, in the replication stress checkpoint response has been well established. However, recent work has revealed an important role for transcription in the cellular response to DNA replication stress. In this review, we will provide an overview of current knowledge of the cellular response to DNA replication stress with a specific focus on the DNA replication stress checkpoint transcriptional response and its role in the prevention of replication stress-induced DNA damage.
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The Role of the Transcriptional Response to DNA Replication Stress
Herlihy, Anna E.; de Bruin, Robertus A.M.
2017-01-01
During DNA replication many factors can result in DNA replication stress. The DNA replication stress checkpoint prevents the accumulation of replication stress-induced DNA damage and the potential ensuing genome instability. A critical role for post-translational modifications, such as phosphorylation, in the replication stress checkpoint response has been well established. However, recent work has revealed an important role for transcription in the cellular response to DNA replication stress. In this review, we will provide an overview of current knowledge of the cellular response to DNA replication stress with a specific focus on the DNA replication stress checkpoint transcriptional response and its role in the prevention of replication stress-induced DNA damage. PMID:28257104
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Yang, Kai; Dang, Qun; Cai, Pei-Jun; Gao, Yang; Yu, Zhi-Xiang; Bai, Xu
2017-03-03
Catalytic inverse electron demand Diels-Alder (IEDDA) reactions of heterocyclic aza-dienes are rarely reported since highly reactive and electron-rich dienophiles are often found not compatible with strong acids such as Lewis acids. Herein, we disclose that TFA-catalyzed reactions of electron-deficient 1,3,5-triazines and electron-deficient aldehydes/ketones can take place. These reactions led to highly functionalized pyrimidines as products in fair to good yields. The reaction mechanism was carefully studied by the combination of experimental and computational studies. The reactions involve a cascade of stepwise inverse electron demand hetero-Diels-Alder (ihDA) reactions, followed by retro-Diels-Alder (rDA) reactions and elimination of water. An acid was required for both ihDA and rDA reactions. This mechanism was further verified by comparing the relative reactivity of aldehydes/ketones and their corresponding vinyl ethers in the current reaction system.
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Global transcriptional responses of Bacillus subtilis to xenocoumacin 1.
Zhou, T; Zeng, H; Qiu, D; Yang, X; Wang, B; Chen, M; Guo, L; Wang, S
2011-09-01
To determine the global transcriptional response of Bacillus subtilis to an antimicrobial agent, xenocoumacin 1 (Xcn1). Subinhibitory concentration of Xcn1 applied to B. subtilis was measured according to Hutter's method for determining optimal concentrations. cDNA microarray technology was used to study the global transcriptional response of B. subtilis to Xcn1. Real-time RT-PCR was employed to verify alterations in the transcript levels of six genes. The subinhibitory concentration was determined to be 1 μg ml(-1). The microarray data demonstrated that Xcn1 treatment of B. subtilis led to more than a 2.0-fold up-regulation of 480 genes and more than a 2.0-fold down-regulation of 479 genes (q ≤ 0.05). The transcriptional responses of B. subtilis to Xcn1 were determined, and several processes were affected by Xcn1. Additionally, cluster analysis of gene expression profiles after treatment with Xcn1 or 37 previously studied antibiotics indicated that Xcn1 has similar mechanisms of action to protein synthesis inhibitors. These microarray data showed alterations of gene expression in B. subtilis after exposure to Xcn1. From the results, we identified various processes affected by Xcn1. This study provides a whole-genome perspective to elucidate the action of Xcn1 as a potential antimicrobial agent. © 2011 The Authors. Journal of Applied Microbiology © 2011 The Society for Applied Microbiology.
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Circulating RNA transcripts identify therapeutic response in cystic fibrosis lung disease.
Saavedra, Milene T; Hughes, Grant J; Sanders, Linda A; Carr, Michelle; Rodman, David M; Coldren, Christopher D; Geraci, Mark W; Sagel, Scott D; Accurso, Frank J; West, James; Nick, Jerry A
2008-11-01
Circulating leukocyte RNA transcripts are systemic markers of inflammation, which have not been studied in cystic fibrosis (CF) lung disease. Although the standard assessment of pulmonary treatment response is FEV(1), a measure of airflow limitation, the lack of systemic markers to reflect changes in lung inflammation critically limits the testing of proposed therapeutics. We sought to prospectively identify and validate peripheral blood leukocyte genes that could mark resolution of pulmonary infection and inflammation using a model by which RNA transcripts could increase the predictive value of spirometry. Peripheral blood mononuclear cells were isolated from 10 patients with CF and acute pulmonary exacerbations before and after therapy. RNA expression profiling revealed that 10 genes significantly changed with treatment when compared with matched non-CF and control subjects with stable CF to establish baseline transcript abundance. Peripheral blood mononuclear cell RNA transcripts were prospectively validated, using real-time polymerase chain reaction amplification, in an independent cohort of acutely ill patients with CF (n = 14). Patients who responded to therapy were analyzed using general estimating equations and multiple logistic regression, such that changes in FEV(1)% predicted were regressed with transcript changes. Three genes, CD64, ADAM9, and CD36, were significant and independent predictors of a therapeutic response beyond that of FEV(1) alone (P < 0.05). In both cohorts, receiver operating characteristic analysis revealed greater accuracy when genes were combined with FEV(1). Circulating mononuclear cell transcripts characterize a response to the treatment of pulmonary exacerbations. Even in small patient cohorts, changes in gene expression in conjunction with FEV(1) may enhance current outcomes measures for treatment response.
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Barthel, Matthias; Hammerle, Albin; Sturm, Patrick; Baur, Thomas; Gentsch, Lydia; Knohl, Alexander
2011-12-01
Recent (13) CO(2) canopy pulse chase labeling studies revealed that photosynthesis influences the carbon isotopic composition of soil respired CO(2) (δ(13) C(SR)) even on a diel timescale. However, the driving mechanisms underlying these short-term responses remain unclear, in particular under drought conditions. The gas exchange of CO(2) isotopes of canopy and soil was monitored in drought/nondrought-stressed beech (Fagus sylvatica) saplings after (13) CO(2) canopy pulse labeling. A combined canopy/soil chamber system with gas-tight separated soil and canopy compartments was coupled to a laser spectrometer measuring mixing ratios and isotopic composition of CO(2) in air at high temporal resolution. The measured δ(13) C(SR) signal was then explained and substantiated by a mechanistic carbon allocation model. Leaf metabolism had a strong imprint on diel cycles in control plants, as a result of an alternating substrate supply switching between sugar and transient starch. By contrast, diel cycles in drought-stressed plants were determined by the relative contributions of autotrophic and heterotrophic respiration throughout the day. Drought reduced the speed of the link between photosynthesis and soil respiration by a factor of c. 2.5, depending on the photosynthetic rate. Drought slows the coupling between photosynthesis and soil respiration and alters the underlying mechanism causing diel variations of δ(13) C(SR). © 2011 The Authors. New Phytologist © 2011 New Phytologist Trust.
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Covalently crosslinked diels-alder polymer networks.
Energy Technology Data Exchange (ETDEWEB)
Bowman, Christopher (University of Colorado, Boulder, CO); Adzima, Brian J. (University of Colorado, Boulder, CO); Anderson, Benjamin John
2011-09-01
This project examines the utility of cycloaddition reactions for the synthesis of polymer networks. Cycloaddition reactions are desirable because they produce no unwanted side reactions or small molecules, allowing for the formation of high molecular weight species and glassy crosslinked networks. Both the Diels-Alder reaction and the copper-catalyzed azide-alkyne cycloaddition (CuAAC) were studied. Accomplishments include externally triggered healing of a thermoreversible covalent network via self-limited hysteresis heating, the creation of Diels-Alder based photoresists, and the successful photochemical catalysis of CuAAC as an alternative to the use of ascorbic acid for the generation of Cu(I) in click reactions. An analysis of the results reveals that these new methods offer the promise of efficiently creating robust, high molecular weight species and delicate three dimensional structures that incorporate chemical functionality in the patterned material. This work was performed under a Strategic Partnerships LDRD during FY10 and FY11 as part of a Sandia National Laboratories/University of Colorado-Boulder Excellence in Science and Engineering Fellowship awarded to Brian J. Adzima, a graduate student at UC-Boulder. Benjamin J. Anderson (Org. 1833) was the Sandia National Laboratories point-of-contact for this fellowship.
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Fe(II)/Fe(III)-Catalyzed Intramolecular Didehydro-Diels-Alder Reaction of Styrene-ynes.
Mun, Hyeon Jin; Seong, Eun Young; Ahn, Kwang-Hyun; Kang, Eun Joo
2018-02-02
The intramolecular didehydro-Diels-Alder reaction of styrene-ynes was catalyzed by Fe(II) and Fe(III) to produce various naphthalene derivatives under microwave heating conditions. Mechanistic calculations found that the Fe(II) catalyst activates the styrenyl diene in an inverse-electron-demand Diels-Alder reaction, and the consecutive dehydrogenation reaction can be promoted by either Fe(II)-catalyzed direct dehydrogenation or an Fe(III)-catalyzed rearomatization/dehydrogenation pathway.
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Fourfold Diels-Alder reaction of tetraethynylsilane.
Geyer, Florian L; Rode, Alexander; Bunz, Uwe H F
2014-12-08
A series of ethynylated silanes, including tetraethynylsilane, was treated with tetraphenylcyclopentadienone at 300 °C under microwave irradiation to give the aromatized Diels-Alder adducts as sterically encumbered mini-dendrimers with up to 20 benzene rings. The sterically most congested adducts display red-shifted emission through intramolecular π-π interactions in the excited state. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Synthetic studies on taxanes: A domino-enyne metathesis/Diels ...
Indian Academy of Sciences (India)
Abstract. A domino enyne cross-metathesis/intramolecular Diels-Alder reaction has been successfully used to synthesize a bicyclo[5.3.1] undecene, corresponding to AB-ring of taxol without the gem dimethyl group.
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Modified lignin: Preparation and use in reversible gel via Diels-Alder reaction.
Zhou, Wanpeng; Zhang, Hui; Chen, Fangeng
2018-02-01
In this study, popular soda lignin was modified with either furan or maleimide ring, and the modified lignins were subjected to reversible Diels-Alder reaction. A new process was proposed to prepare the functionalized lignin. A long chain was introduced to the hydroxyl groups of lignin, and then either the furan or maleimide ring was added to the other end of the chain. The test results confirmed that either the furan ring or the maleimide ring was bound to lignin. Furan- and maleimide-functionalized lignins were also combined to generate crosslinking via Diels-Alder [4+2] cycloaddition reaction. Under appropriate conditions, the formation of a gel was identified, which reverted to liquid state after retro Diels-Alder reaction upon heating at 120°C. This study reveals the significant versatility and potential of the developed strategy for the utilization of lignin-based recyclable networks. Copyright © 2017 Elsevier B.V. All rights reserved.
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Rosati, F.; Roelfes, J.G.
A structure-activity relationship study of the first generation ligands for the DNA-based asymmetric hydration of enones and Diels-Alder reaction in water is reported. The design of the ligand was optimized resulting in a maximum ee of 83% in the hydration reaction and 75% in the Diels-Alder
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Mata, D.; Amaral, M.; Fernandes, A. J. S.; Colaço, B.; Gama, A.; Paiva, M. C.; Gomes, P. S.; Silva, R. F.; Fernandes, M. H.
2015-05-01
The risk-benefit balance for carbon nanotubes (CNTs) dictates their clinical fate. To take a step forward at this crossroad it is compulsory to modulate the CNT in vivo biocompatibility and biodegradability via e.g. chemical functionalization. CNT membranes were functionalised combining a Diels-Alder cycloaddition reaction to generate cyclohexene (-C6H10) followed by a mild oxidisation to yield carboxylic acid groups (-COOH). In vitro proliferation and osteogenic differentiation of human osteoblastic cells were maximized on functionalized CNT membranes (p,f-CNTs). The in vivo subcutaneously implanted materials showed a higher biological reactivity, thus inducing a slighter intense inflammatory response compared to non-functionalized CNT membranes (p-CNTs), but still showing a reduced cytotoxicity profile. Moreover, the in vivo biodegradation of CNTs was superior for p,f-CNT membranes, likely mediated by the oxidation-induced myeloperoxidase (MPO) in neutrophil and macrophage inflammatory milieus. This proves the biodegradability faculty of functionalized CNTs, which potentially avoids long-term tissue accumulation and triggering of acute toxicity. On the whole, the proposed Diels-Alder functionalization accounts for the improved CNT biological response in terms of the biocompatibility and biodegradability profiles. Therefore, CNTs can be considered for use in bone tissue engineering without notable toxicological threats.The risk-benefit balance for carbon nanotubes (CNTs) dictates their clinical fate. To take a step forward at this crossroad it is compulsory to modulate the CNT in vivo biocompatibility and biodegradability via e.g. chemical functionalization. CNT membranes were functionalised combining a Diels-Alder cycloaddition reaction to generate cyclohexene (-C6H10) followed by a mild oxidisation to yield carboxylic acid groups (-COOH). In vitro proliferation and osteogenic differentiation of human osteoblastic cells were maximized on functionalized CNT
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Modularization and Response Curve Engineering of a Naringenin-Responsive Transcriptional Biosensor.
De Paepe, Brecht; Maertens, Jo; Vanholme, Bartel; De Mey, Marjan
2018-05-18
To monitor the intra- and extracellular environment of micro-organisms and to adapt their metabolic processes accordingly, scientists are reprogramming nature's myriad of transcriptional regulatory systems into transcriptional biosensors, which are able to detect small molecules and, in response, express specific output signals of choice. However, the naturally occurring response curve, the key characteristic of biosensor circuits, is typically not in line with the requirements for real-life biosensor applications. In this contribution, a natural LysR-type naringenin-responsive biosensor circuit is developed and characterized with Escherichia coli as host organism. Subsequently, this biosensor is dissected into a clearly defined detector and effector module without loss of functionality, and the influence of the expression levels of both modules on the biosensor response characteristics is investigated. Two collections of ten unique synthetic biosensors each are generated. Each collection demonstrates a unique diversity of response curve characteristics spanning a 128-fold change in dynamic and 2.5-fold change in operational ranges and 3-fold change in levels of Noise, fit for a wide range of applications, such as adaptive laboratory evolution, dynamic pathway control and high-throughput screening methods. The established biosensor engineering concepts, and the developed biosensor collections themselves, are of use for the future development and customization of biosensors in general, for the multitude of biosensor applications and as a compelling alternative for the commonly used LacI-, TetR- and AraC-based inducible circuits.
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Energy Technology Data Exchange (ETDEWEB)
Waltman, Peter H.; Guo, Jian; Reistetter, Emily Nahas; Purvine, Samuel; Ansong, Charles K.; van Baren, Marijke J.; Wong, Chee-Hong; Wei, Chia-Lin; Smith, Richard D.; Callister, Stephen J.; Stuart, Joshua M.; Worden, Alexandra Z.; Mills, Ken
2016-07-19
Micromonas is a unicellular green alga that belongs to the prasinophytes, a sister lineage to land plants. This picoeukaryotic (<2 μm diameter) alga is widespread in the marine environment but still not understood at the cellular level. Here, we examine the mRNA and protein level changes that take place over the course of the day-night cycle using mid-exponential nutrient replete cultures of Micromonas pusilla CCMP1545 grown and analyzed in biological triplicate. During the experiment, samples were collected at key transition points during the diel for evaluation using high-throughput LC-MS proteomics. We also sequenced matched mRNA samples from the same time points, using pair-ended directional Illumina RNA-Seq to investigate the dynamics and relationship between the mRNA and protein expression programs of M. pusilla. Similar to a prior study of the marine cyanobacterium Prochlorococcus, we found significant divergence in the mRNA and proteomics expression dynamics in response to the light:dark cycle. Additionally, expressional responses of genes and the proteins they encoded could also be variable within the same metabolic pathway, such as the oxygenic photosynthesis pathway. A regression framework was used to predict protein levels using both mRNA expression and gene-specific sequence-based features. Several features in the genome sequence were found to influence protein abundance including the codon usage and the length of the 3’ UTR. Collectively, our studies provide insights into the regulation of the proteome over a diel as relationships between the transcriptional and translational programs in the widespread marine green alga Micromonas.
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Directory of Open Access Journals (Sweden)
Peter H Waltman
Full Text Available Micromonas is a unicellular motile alga within the Prasinophyceae, a green algal group that is related to land plants. This picoeukaryote (<2 μm diameter is widespread in the marine environment but is not well understood at the cellular level. Here, we examine shifts in mRNA and protein expression over the course of the day-night cycle using triplicated mid-exponential, nutrient replete cultures of Micromonas pusilla CCMP1545. Samples were collected at key transition points during the diel cycle for evaluation using high-throughput LC-MS proteomics. In conjunction, matched mRNA samples from the same time points were sequenced using pair-ended directional Illumina RNA-Seq to investigate the dynamics and relationship between the mRNA and protein expression programs of M. pusilla. Similar to a prior study of the marine cyanobacterium Prochlorococcus, we found significant divergence in the mRNA and proteomics expression dynamics in response to the light:dark cycle. Additionally, expressional responses of genes and the proteins they encoded could also be variable within the same metabolic pathway, such as we observed in the oxygenic photosynthesis pathway. A regression framework was used to predict protein levels from both mRNA expression and gene-specific sequence-based features. Several features in the genome sequence were found to influence protein abundance including codon usage as well as 3' UTR length and structure. Collectively, our studies provide insights into the regulation of the proteome over a diel cycle as well as the relationships between transcriptional and translational programs in the widespread marine green alga Micromonas.
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Polansky, Leo; Douglas-Hamilton, Iain; Wittemyer, George
2013-01-01
Adaptive movement behaviors allow individuals to respond to fluctuations in resource quality and distribution in order to maintain fitness. Classically, studies of the interaction between ecological conditions and movement behavior have focused on such metrics as travel distance, velocity, home range size or patch occupancy time as the salient metrics of behavior. Driven by the emergence of very regular high frequency data, more recently the importance of interpreting the autocorrelation structure of movement as a behavioral metric has become apparent. Studying movement of a free ranging African savannah elephant population, we evaluated how two movement metrics, diel displacement (DD) and movement predictability (MP - the degree of autocorrelated movement activity at diel time scales), changed in response to variation in resource availability as measured by the Normalized Difference Vegetation Index. We were able to capitalize on long term (multi-year) yet high resolution (hourly) global positioning system tracking datasets, the sample size of which allows robust analysis of complex models. We use optimal foraging theory predictions as a framework to interpret our results, in particular contrasting the behaviors across changes in social rank and resource availability to infer which movement behaviors at diel time scales may be optimal in this highly social species. Both DD and MP increased with increasing forage availability, irrespective of rank, reflecting increased energy expenditure and movement predictability during time periods of overall high resource availability. However, significant interactions between forage availability and social rank indicated a stronger response in DD, and a weaker response in MP, with increasing social status. Relative to high ranking individuals, low ranking individuals expended more energy and exhibited less behavioral movement autocorrelation during lower forage availability conditions, likely reflecting sub-optimal movement
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Directory of Open Access Journals (Sweden)
Rui-Ru Ji
2009-09-01
Full Text Available The dose response curve is the gold standard for measuring the effect of a drug treatment, but is rarely used in genomic scale transcriptional profiling due to perceived obstacles of cost and analysis. One barrier to examining transcriptional dose responses is that existing methods for microarray data analysis can identify patterns, but provide no quantitative pharmacological information. We developed analytical methods that identify transcripts responsive to dose, calculate classical pharmacological parameters such as the EC50, and enable an in-depth analysis of coordinated dose-dependent treatment effects. The approach was applied to a transcriptional profiling study that evaluated four kinase inhibitors (imatinib, nilotinib, dasatinib and PD0325901 across a six-logarithm dose range, using 12 arrays per compound. The transcript responses proved a powerful means to characterize and compare the compounds: the distribution of EC50 values for the transcriptome was linked to specific targets, dose-dependent effects on cellular processes were identified using automated pathway analysis, and a connection was seen between EC50s in standard cellular assays and transcriptional EC50s. Our approach greatly enriches the information that can be obtained from standard transcriptional profiling technology. Moreover, these methods are automated, robust to non-optimized assays, and could be applied to other sources of quantitative data.
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Sela, Dotan; Chen, Lu; Martin-Brown, Skylar; Washburn, Michael P; Florens, Laurence; Conaway, Joan Weliky; Conaway, Ronald C
2012-06-29
The basic leucine zipper transcription factor ATF6α functions as a master regulator of endoplasmic reticulum (ER) stress response genes. Previous studies have established that, in response to ER stress, ATF6α translocates to the nucleus and activates transcription of ER stress response genes upon binding sequence specifically to ER stress response enhancer elements in their promoters. In this study, we investigate the biochemical mechanism by which ATF6α activates transcription. By exploiting a combination of biochemical and multidimensional protein identification technology-based mass spectrometry approaches, we have obtained evidence that ATF6α functions at least in part by recruiting to the ER stress response enhancer elements of ER stress response genes a collection of RNA polymerase II coregulatory complexes, including the Mediator and multiple histone acetyltransferase complexes, among which are the Spt-Ada-Gcn5 acetyltransferase (SAGA) and Ada-Two-A-containing (ATAC) complexes. Our findings shed new light on the mechanism of action of ATF6α, and they outline a straightforward strategy for applying multidimensional protein identification technology mass spectrometry to determine which RNA polymerase II transcription factors and coregulators are recruited to promoters and other regulatory elements to control transcription.
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Moeckel, Claudia; Macleod, Matthew; Hungerbühler, Konrad; Jones, Kevin C
2008-05-01
Short-term variability of concentrations of polybrominated diphenyl ethers (PBDEs) and chlordanes in air at a semirural site in England over a 5 day period is reported. Four-hour air samples were collected during a period dominated by a high pressure system that produced stable diel (24-h) patterns of meteorological conditions such as temperature and atmospheric boundary layer height. PBDE and chlordane concentrations showed clear diel variability with concentrations in the afternoon and evening being 1.9 - 2.7 times higher than in the early morning. The measurements are interpreted using a multimedia mass balance model parametrized with forcing functions representing local temperature, atmospheric boundary layer height, wind speed and hydroxyl radical concentrations. Model results indicate that reversible, temperature-controlled air-surface exchange is the primary driver of the diel concentration pattern observed for chlordanes and PBDE 28. For higher brominated PBDE congeners (47, 99 and 100), the effect of variable atmospheric mixing height in combination with irreversible deposition on aerosol particles is dominant and explains the diel patterns almost entirely. Higher concentrations of chlordanes and PBDEs in air observed at the end of the study period could be related to likely source areas using back trajectory analysis. This is the first study to clearly document diel variability in concentrations of PBDEs in air over a period of several days. Our model analysis indicates that high daytime and low nighttime concentrations of semivolatile organic chemicals can arise from different underlying driving processes, and are not necessarily evidence of reversible air-surface exchange on a 24-h time scale.
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AFSC/ABL: Gulf of Alaska Diel Trawl Survey, 2005-2006
National Oceanic and Atmospheric Administration, Department of Commerce — Diel epipelagic sampling for juvenile Pacific salmon (Oncorhynchus spp.), rockfish (Sebastes spp.), sablefish (Anoplopoma fimbria), and associated species was...
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Siadati, Seyyed Amir; Nami, Navabeh
2016-10-01
C20 fullerene, this novel species with all its pentagonal faces has displayed some unique operations in making fast pericyclic reactions. As an example, the high dienophile character of the C20 fullerene and the ability of this species in making an ultra-fast Diels-Alder reaction with 1,3-butadiene, has been recently reported. Moreover, new experimental reports claim that the C60 fullerene, one of the fullerene family, could make a Diels-Alder reaction with the central ring of anthracene and make the ring non-aromatic. These reports may encourage researchers to do more studies on the properties of this small carbon cage. To address this question, the present research has discussed all the reaction channels of the Diels-Alder cycloaddition of benzene molecule as a 1,3-diene with the C20 fullerene in order to answer this question: ;Is C20fullerene able to make a Diels-Alder reaction with this molecule?;.
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Transcriptional responses in honey bee larvae infected with chalkbrood fungus.
Aronstein, Katherine A; Murray, Keith D; Saldivar, Eduardo
2010-06-21
Diseases and other stress factors working synergistically weaken honey bee health and may play a major role in the losses of bee populations in recent years. Among a large number of bee diseases, chalkbrood has been on the rise. We present here the experimental identification of honey bee genes that are differentially expressed in response to infection of honey bee larvae with the chalkbrood fungus, Ascosphaera apis. We used cDNA-AFLP Technology to profile transcripts in infected and uninfected bee larvae. From 64 primer combinations, over 7,400 transcriptionally-derived fragments were obtained A total of 98 reproducible polymorphic cDNA-AFLP fragments were excised and sequenced, followed by quantitative real-time RT-PCR (qRT-PCR) analysis of these and additional samples.We have identified a number of differentially-regulated transcripts that are implicated in general mechanisms of stress adaptation, including energy metabolism and protein transport. One of the most interesting differentially-regulated transcripts is for a chitinase-like enzyme that may be linked to anti-fungal activities in the honey bee larvae, similarly to gut and fat-body specific chitinases found in mosquitoes and the red flour beetle. Surprisingly, we did not find many components of the well-characterized NF-kappaB intracellular signaling pathways to be differentially-regulated using the cDNA-AFLP approach. Therefore, utilizing qRT-PCR, we probed some of the immune related genes to determine whether the lack of up-regulation of their transcripts in our analysis can be attributed to lack of immune activation or to limitations of the cDNA-AFLP approach. Using a combination of cDNA-AFLP and qRT-PCR analyses, we were able to determine several key transcriptional events that constitute the overall effort in the honey bee larvae to fight natural fungal infection. Honey bee transcripts identified in this study are involved in critical functions related to transcriptional regulation, apoptotic
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Gat-Viks, Irit; Chevrier, Nicolas; Wilentzik, Roni; Eisenhaure, Thomas; Raychowdhury, Raktima; Steuerman, Yael; Shalek, Alex K; Hacohen, Nir; Amit, Ido; Regev, Aviv
2013-04-01
Individual genetic variation affects gene responsiveness to stimuli, often by influencing complex molecular circuits. Here we combine genomic and intermediate-scale transcriptional profiling with computational methods to identify variants that affect the responsiveness of genes to stimuli (responsiveness quantitative trait loci or reQTLs) and to position these variants in molecular circuit diagrams. We apply this approach to study variation in transcriptional responsiveness to pathogen components in dendritic cells from recombinant inbred mouse strains. We identify reQTLs that correlate with particular stimuli and position them in known pathways. For example, in response to a virus-like stimulus, a trans-acting variant responds as an activator of the antiviral response; using RNA interference, we identify Rgs16 as the likely causal gene. Our approach charts an experimental and analytic path to decipher the mechanisms underlying genetic variation in circuits that control responses to stimuli.
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Sex-related differences in murine hepatic transcriptional and proteomic responses to TCDD
International Nuclear Information System (INIS)
Prokopec, Stephenie D.; Watson, John D.; Lee, Jamie; Pohjanvirta, Raimo; Boutros, Paul C.
2015-01-01
2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is an environmental contaminant that produces myriad toxicities in most mammals. In rodents alone, there is a huge divergence in the toxicological response across species, as well as among different strains within a species. But there are also significant differences between males and females animals of a single strain. These differences are inconsistent across model systems: the severity of toxicity is greater in female rats than males, while male mice and guinea pigs are more sensitive than females. Because the specific events that underlie this difference remain unclear, we characterized the hepatic transcriptional response of adult male and female C57BL/6 mice to 500 μg/kg TCDD at multiple time-points. The transcriptional profile diverged significantly between the sexes. Female mice demonstrated a large number of altered transcripts as early as 6 h following treatment, suggesting a large primary response. Conversely, male animals showed the greatest TCDD-mediated response 144 h following exposure, potentially implicating significant secondary responses. Nr1i3 was statistically significantly induced at all time-points in the sensitive male animals. This mRNA encodes the constitutive androstane receptor (CAR), a transcription factor involved in the regulation of xenobiotic metabolism, lipid metabolism, cell cycle and apoptosis. Surprisingly though, changes at the protein level (aside from the positive control, CYP1A1) were modest, with only FMO3 showing clear induction, and no genes with sex-differences. Thus, while male and female mice show transcriptional differences in their response to TCDD, their association with TCDD-induced toxicities remains unclear. - Highlights: • Differences exist between the toxicity phenotypes to TCDD in male and female mice. • TCDD-mediated transcriptomic differences were identified between the sexes. • Resistant female mice displayed a large, early-onset, transcriptomic response.
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Sex-related differences in murine hepatic transcriptional and proteomic responses to TCDD
Energy Technology Data Exchange (ETDEWEB)
Prokopec, Stephenie D.; Watson, John D. [Informatics and Bio-computing Program, Ontario Institute for Cancer Research, Toronto (Canada); Lee, Jamie [Informatics and Bio-computing Program, Ontario Institute for Cancer Research, Toronto (Canada); Department of Pharmacology & Toxicology, University of Toronto, Toronto (Canada); Pohjanvirta, Raimo [Laboratory of Toxicology, National Institute for Health and Welfare, Kuopio Finland (Finland); Department of Food Hygiene and Environmental Health, University of Helsinki, Helsinki (Finland); Boutros, Paul C., E-mail: Paul.Boutros@oicr.on.ca [Informatics and Bio-computing Program, Ontario Institute for Cancer Research, Toronto (Canada); Department of Pharmacology & Toxicology, University of Toronto, Toronto (Canada); Department of Medical Biophysics, University of Toronto, Toronto (Canada)
2015-04-15
2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is an environmental contaminant that produces myriad toxicities in most mammals. In rodents alone, there is a huge divergence in the toxicological response across species, as well as among different strains within a species. But there are also significant differences between males and females animals of a single strain. These differences are inconsistent across model systems: the severity of toxicity is greater in female rats than males, while male mice and guinea pigs are more sensitive than females. Because the specific events that underlie this difference remain unclear, we characterized the hepatic transcriptional response of adult male and female C57BL/6 mice to 500 μg/kg TCDD at multiple time-points. The transcriptional profile diverged significantly between the sexes. Female mice demonstrated a large number of altered transcripts as early as 6 h following treatment, suggesting a large primary response. Conversely, male animals showed the greatest TCDD-mediated response 144 h following exposure, potentially implicating significant secondary responses. Nr1i3 was statistically significantly induced at all time-points in the sensitive male animals. This mRNA encodes the constitutive androstane receptor (CAR), a transcription factor involved in the regulation of xenobiotic metabolism, lipid metabolism, cell cycle and apoptosis. Surprisingly though, changes at the protein level (aside from the positive control, CYP1A1) were modest, with only FMO3 showing clear induction, and no genes with sex-differences. Thus, while male and female mice show transcriptional differences in their response to TCDD, their association with TCDD-induced toxicities remains unclear. - Highlights: • Differences exist between the toxicity phenotypes to TCDD in male and female mice. • TCDD-mediated transcriptomic differences were identified between the sexes. • Resistant female mice displayed a large, early-onset, transcriptomic response.
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Caarls, Lotte; Van der Does, Dieuwertje; Hickman, Richard; Jansen, Wouter; Verk, Marcel C Van; Proietti, Silvia; Lorenzo, Oscar; Solano, Roberto; Pieterse, Corné M J; Van Wees, Saskia C M
2017-02-01
Salicylic acid (SA) and jasmonic acid (JA) cross-communicate in the plant immune signaling network to finely regulate induced defenses. In Arabidopsis, SA antagonizes many JA-responsive genes, partly by targeting the ETHYLENE RESPONSE FACTOR (ERF)-type transcriptional activator ORA59. Members of the ERF transcription factor family typically bind to GCC-box motifs in the promoters of JA- and ethylene-responsive genes, thereby positively or negatively regulating their expression. The GCC-box motif is sufficient for SA-mediated suppression of JA-responsive gene expression. Here, we investigated whether SA-induced ERF-type transcriptional repressors, which may compete with JA-induced ERF-type activators for binding at the GCC-box, play a role in SA/JA antagonism. We selected ERFs that are transcriptionally induced by SA and/or possess an EAR transcriptional repressor motif. Several of the 16 ERFs tested suppressed JA-dependent gene expression, as revealed by enhanced JA-induced PDF1.2 or VSP2 expression levels in the corresponding erf mutants, while others were involved in activation of these genes. However, SA could antagonize JA-induced PDF1.2 or VSP2 in all erf mutants, suggesting that the tested ERF transcriptional repressors are not required for SA/JA cross-talk. Moreover, a mutant in the co-repressor TOPLESS, that showed reduction in repression of JA signaling, still displayed SA-mediated antagonism of PDF1.2 and VSP2. Collectively, these results suggest that SA-regulated ERF transcriptional repressors are not essential for antagonism of JA-responsive gene expression by SA. We further show that de novo SA-induced protein synthesis is required for suppression of JA-induced PDF1.2, pointing to SA-stimulated production of an as yet unknown protein that suppresses JA-induced transcription. © The Author 2016. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.
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Quinones as dienophiles in the Diels-Alder reaction: history and applications in total synthesis.
Nawrat, Christopher C; Moody, Christopher J
2014-02-17
In the canon of reactions available to the organic chemist engaged in total synthesis, the Diels-Alder reaction is among the most powerful and well understood. Its ability to rapidly generate molecular complexity through the simultaneous formation of two carbon-carbon bonds is almost unrivalled, and this is reflected in the great number of reported applications of this reaction. Historically, the use of quinones as dienophiles is highly significant, being the very first example investigated by Diels and Alder. Herein, we review the application of the Diels-Alder reaction of quinones in the total synthesis of natural products. The highlighted examples span some 60 years from the landmark syntheses of morphine (1952) and reserpine (1956) by Gates and Woodward, respectively, through to the present day examples, such as the tetracyclines. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Transcriptional response of kidney tissue after 177Lu-octreotate administration in mice
International Nuclear Information System (INIS)
Schüler, Emil; Rudqvist, Nils; Parris, Toshima Z.; Langen, Britta; Helou, Khalil; Forssell-Aronsson, Eva
2014-01-01
Introduction: The kidneys are one of the main dose limiting organs in 177 Lu-octreotate therapy of neuroendocrine tumors. Therefore, biomarkers for radiation damage would be of great importance in this type of therapy. The purpose of this study was to investigate the absorbed dose dependency on early transcriptional changes in the kidneys from 177 Lu-octreotate exposure. Methods: Female Balb/c nude mice were i.v. injected with 1.3, 3.6, 14, 45 or 140 MBq 177 Lu-octreotate. The animals were killed 24 h after injection followed by excision of the kidneys. The absorbed dose to the kidneys ranged between 0.13 and 13 Gy. Total RNA was extracted from separated renal tissue samples, and applied to Illumina MouseRef-8 Whole-Genome Expression Beadchips to identify regulated transcripts after irradiation. Nexus Expression 2.0 and Gene Ontology terms were used for data processing and to determine affected biological processes. Results: Distinct transcriptional responses were observed following 177 Lu-octreotate administration. A higher number of differentially expressed transcripts were observed in the kidney medulla (480) compared to cortex (281). In addition, 39 transcripts were regulated at all absorbed dose levels in the medulla, compared to 32 in the cortex. Three biological processes in the cortex and five in the medulla were also shared by all absorbed dose levels. Strong association to metabolism was found among the affected processes in both tissues. Furthermore, an association with cellular and developmental processes was prominent in kidney medulla, while transport and immune response were prominent in kidney cortex. Conclusion: Specific biological and dose-dependent responses were observed in both tissues. The number of affected transcripts and biological processes revealed distinct response differences between the absorbed doses delivered to the tissues
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Catalytic Asymmetric Total Synthesis of (+)- and (-)-Paeoveitol via a Hetero-Diels-Alder Reaction.
Li, Tian-Ze; Geng, Chang-An; Yin, Xiu-Juan; Yang, Tong-Hua; Chen, Xing-Long; Huang, Xiao-Yan; Ma, Yun-Bao; Zhang, Xue-Mei; Chen, Ji-Jun
2017-02-03
The first catalytic asymmetric total synthesis of (+)- and (-)-paeoveitol has been accomplished in 42% overall yield via a biomimetic hetero-Diels-Alder reaction. The chiral phosphoric acid catalyzed hetero-Diels-Alder reaction showed excellent diastereo- and enantioselectivity (>99:1 dr and 90% ee); two rings and three stereocenters were constructed in a single step to produce (-)-paeoveitol on a scale of 452 mg. This strategy enabled us to selectively synthesize both paeoveitol enantiomers from the same substrates by simply changing the enantiomer of the catalyst.
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Directory of Open Access Journals (Sweden)
Stewart T G Burgess
Full Text Available BACKGROUND: Sheep scab, caused by infestation with the ectoparasitic mite Psoroptes ovis, results in the rapid development of cutaneous inflammation and leads to the crusted skin lesions characteristic of the disease. We described previously the global host transcriptional response to infestation with P. ovis, elucidating elements of the inflammatory processes which lead to the development of a rapid and profound immune response. However, the mechanisms by which this response is instigated remain unclear. To identify novel methods of intervention a better understanding of the early events involved in triggering the immune response is essential. The objective of this study was to gain a clearer understanding of the mechanisms and signaling pathways involved in the instigation of the immediate pro-inflammatory response. RESULTS: Through a combination of transcription factor binding site enrichment and pathway analysis we identified key roles for a number of transcription factors in the instigation of cutaneous inflammation. In particular, defined roles were elucidated for the transcription factors NF-kB and AP-1 in the orchestration of the early pro-inflammatory response, with these factors being implicated in the activation of a suite of inflammatory mediators. CONCLUSIONS: Interrogation of the host temporal response to P. ovis infestation has enabled the further identification of the mechanisms underlying the development of the immediate host pro-inflammatory response. This response involves key regulatory roles for the transcription factors NF-kB and AP-1. Pathway analysis demonstrated that the activation of these transcription factors may be triggered following a host LPS-type response, potentially involving TLR4-signalling and also lead to the intriguing possibility that this could be triggered by a P. ovis allergen.
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De Domenico, Ivana; Zhang, Tian Y; Koening, Curry L; Branch, Ryan W; London, Nyall; Lo, Eric; Daynes, Raymond A; Kushner, James P; Li, Dean; Ward, Diane M; Kaplan, Jerry
2010-07-01
Hepcidin is a peptide hormone that regulates iron homeostasis and acts as an antimicrobial peptide. It is expressed and secreted by a variety of cell types in response to iron loading and inflammation. Hepcidin mediates iron homeostasis by binding to the iron exporter ferroportin, inducing its internalization and degradation via activation of the protein kinase Jak2 and the subsequent phosphorylation of ferroportin. Here we have shown that hepcidin-activated Jak2 also phosphorylates the transcription factor Stat3, resulting in a transcriptional response. Hepcidin treatment of ferroportin-expressing mouse macrophages showed changes in mRNA expression levels of a wide variety of genes. The changes in transcript levels for half of these genes were a direct effect of hepcidin, as shown by cycloheximide insensitivity, and dependent on the presence of Stat3. Hepcidin-mediated transcriptional changes modulated LPS-induced transcription in both cultured macrophages and in vivo mouse models, as demonstrated by suppression of IL-6 and TNF-alpha transcript and secreted protein. Hepcidin-mediated transcription in mice also suppressed toxicity and morbidity due to single doses of LPS, poly(I:C), and turpentine, which is used to model chronic inflammatory disease. Most notably, we demonstrated that hepcidin pretreatment protected mice from a lethal dose of LPS and that hepcidin-knockout mice could be rescued from LPS toxicity by injection of hepcidin. The results of our study suggest a new function for hepcidin in modulating acute inflammatory responses.
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Interpreting diel hysteresis between soil respiration and temperature
C. Phillips; N. Nickerson; D. Risk; B.J. Bond
2011-01-01
Increasing use of automated soil respiration chambers in recent years has demonstrated complex diel relationships between soil respiration and temperature that are not apparent from less frequent measurements. Soil surface flux is often lagged from soil temperature by several hours, which results in semielliptical hysteresis loops when surface flux is plotted as a...
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DEFF Research Database (Denmark)
Bojanovic, Klara; D'Arrigo, Isotta; Long, Katherine
2017-01-01
functional roles in the cellular response to stress conditions. The data show a larger fraction of differentially expressed sRNAs than of mRNAs with >5-fold expression changes. The work provides detailed insights into the mechanisms through which P. putida responds to different stress conditions...... intergenic and antisense transcripts, were detected, increasing the number of identified sRNA transcripts in the strain by a factor of 10. Unique responses to each type of stress are documented, including both the extent and dynamics of the gene expression changes. The work adds rich detail to previous......Bacteria cope with and adapt to stress by modulating gene expression in response to specific environmental cues. In this study, the transcriptional response of Pseudomonas putida KT2440 to osmotic, oxidative, and imipenem stress conditions at two time points was investigated via identification...
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Intramolecular inverse electron demand Diels-Alder reactions of pyrimidines
Frissen, A.E.
1990-01-01
This thesis deals with the intramolecular inverse electron demand Diels-Alder reaction of pyrimidines. The main objective of the study was to investigate the synthetic applicability of this reaction and to get more insight in the electronic and steric effects which determine the reactivity
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Global transcription profiling reveals comprehensive insights into hypoxic response in Arabidopsis.
Liu, Fenglong; Vantoai, Tara; Moy, Linda P; Bock, Geoffrey; Linford, Lara D; Quackenbush, John
2005-03-01
Plants have evolved adaptation mechanisms to sense oxygen deficiency in their environments and make coordinated physiological and structural adjustments to enhance their hypoxic tolerance. To gain insight into how plants respond to low-oxygen stress, gene expression profiling using whole-genome DNA amplicon microarrays was carried out at seven time points over 24 h, in wild-type and transgenic P(SAG12):ipt Arabidopsis (Arabidopsis thaliana) plants under normoxic and hypoxic conditions. Transcript levels of genes involved in glycolysis and fermentation pathways, ethylene synthesis and perception, calcium signaling, nitrogen utilization, trehalose metabolism, and alkaloid synthesis were significantly altered in response to oxygen limitation. Analysis based on gene ontology assignments suggested a significant down-regulation of genes whose functions are associated with cell walls, nucleosome structures, water channels, and ion transporters and a significant up-regulation of genes involved in transcriptional regulation, protein kinase activity, and auxin responses under conditions of oxygen shortage. Promoter analysis on a cluster of up-regulated genes revealed a significant overrepresentation of the AtMYB2-binding motif (GT motif), a sugar response element-like motif, and a G-box-related sequence, and also identified several putative anaerobic response elements. Finally, quantitative real-time polymerase chain reactions using 29 selected genes independently verified the microarray results. This study represents one of the most comprehensive analyses conducted to date investigating hypoxia-responsive transcriptional networks in plants.
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Acetaminophen modulates the transcriptional response to recombinant interferon-beta.
Directory of Open Access Journals (Sweden)
Aaron Farnsworth
Full Text Available BACKGROUND: Recombinant interferon treatment can result in several common side effects including fever and injection-site pain. Patients are often advised to use acetaminophen or other over-the-counter pain medications as needed. Little is known regarding the transcriptional changes induced by such co-administration. METHODOLOGY/PRINCIPAL FINDINGS: We tested whether the administration of acetaminophen causes a change in the response normally induced by interferon-beta treatment. CD-1 mice were administered acetaminophen (APAP, interferon-beta (IFN-beta or a combination of IFN-beta+APAP and liver and serum samples were collected for analysis. Differential gene expression was determined using an Agilent 22 k whole mouse genome microarray. Data were analyzed by several methods including Gene Ontology term clustering and Gene Set Enrichment Analysis. We observed a significant change in the transcription profile of hepatic cells when APAP was co-administered with IFN-beta. These transcriptional changes included a marked up-regulation of genes involved in signal transduction and cell differentiation and down-regulation of genes involved in cellular metabolism, trafficking and the IkappaBK/NF-kappaB cascade. Additionally, we observed a large decrease in the expression of several IFN-induced genes including Ifit-3, Isg-15, Oasl1, Zbp1 and predicted gene EG634650 at both early and late time points. CONCLUSIONS/SIGNIFICANCE: A significant change in the transcriptional response was observed following co-administration of IFN-beta+APAP relative to IFN-beta treatment alone. These results suggest that administration of acetaminophen has the potential to modify the efficacy of IFN-beta treatment.
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High stereoselectivity on low temperature Diels-Alder reactions
Directory of Open Access Journals (Sweden)
Invernize Paulo
2005-12-01
Full Text Available Abstract We have found that some of the usually poor dienophiles (2-cycloenones can undergo Diels-Alder reaction at -78°C with unusually high stereoselectivity in the presence of niobium pentachloride as a Lewis acid catalyst. A remarkable difference in reaction rates for unsubstituted and α- or β-methyl substituted 2-cycloenones was also observed.
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Pawlus, Matthew R; Hu, Cheng-Jun
2013-09-01
Hypoxia is a prevalent attribute of the solid tumor microenvironment that promotes the expression of genes through posttranslational modifications and stabilization of alpha subunits (HIF1α and HIF2α) of hypoxia-inducible factors (HIFs). Despite significant similarities, HIF1 (HIF1α/ARNT) and HIF2 (HIF2α/ARNT) activate common as well as unique target genes and exhibit different functions in cancer biology. More surprisingly, accumulating data indicates that the HIF1- and/or HIF2-mediated hypoxia responses can be oncogenic as well as tumor suppressive. While the role of HIF in the hypoxia response is well established, recent data support the concept that HIF is necessary, but not sufficient for the hypoxic response. Other transcription factors that are activated by hypoxia are also required for the HIF-mediated hypoxia response. HIFs, other transcription factors, co-factors and RNA poll II recruited by HIF and other transcription factors form multifactorial enhanceosome complexes on the promoters of HIF target genes to activate hypoxia inducible genes. Importantly, HIF1 or HIF2 requires distinct partners in activating HIF1 or HIF2 target genes. Because HIF enhanceosome formation is required for the gene activation and distinct functions of HIF1 and HIF2 in tumor biology, disruption of the HIF1 or HIF2 specific enhanceosome complex may prove to be a beneficial strategy in tumor treatment in which tumor growth is specifically dependent upon HIF1 or HIF2 activity. Copyright © 2013 Elsevier Inc. All rights reserved.
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Niobium(V) chloride as catalyst in Diels-Alder reaction of furan ring
International Nuclear Information System (INIS)
Santos, Deborah A. dos; Rodrigues, Ludmila R.; Arpini, Bruno H.; Lacerda Junior, Valdemar; Greco, Sandro J.; Santos, Reginaldo B. dos; Neto, Alvaro C.; Castro, Eustaquio V.R. de
2014-01-01
According to the relevant literature, the Diels-Alder reaction of furan without a catalyst can last several weeks and shows a low yield due to the diene’s low reactivity. The use of Lewis acid catalysts or high pressures is described as an effective method for improving the reaction yields. This paper describes our recent study on the use of niobium pentachloride as the catalyst in Diels-Alder reactions between furan and several reactive dienophiles, among which methyl acrylate showed good yields, especially at lower temperatures. Other dienophiles have shown lower yields because of problems such as byproduct formation and the high reversibility of the reaction. (author)
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Niobium(V) chloride as catalyst in Diels-Alder reaction of furan ring
Energy Technology Data Exchange (ETDEWEB)
Santos, Deborah A. dos; Rodrigues, Ludmila R.; Arpini, Bruno H.; Lacerda Junior, Valdemar; Greco, Sandro J.; Santos, Reginaldo B. dos; Neto, Alvaro C.; Castro, Eustaquio V.R. de, E-mail: vljuniorqui@gmail.com [Universidade Federal do Espirito Santo (UFES), Vitoria, ES (Brazil). Dept. de Quimica; Romao, Wanderson [Instituto Federal de Educacao, Ciencia e Tecnologia (IFES), Vila Velha, ES (Brazil)
2014-05-15
According to the relevant literature, the Diels-Alder reaction of furan without a catalyst can last several weeks and shows a low yield due to the diene’s low reactivity. The use of Lewis acid catalysts or high pressures is described as an effective method for improving the reaction yields. This paper describes our recent study on the use of niobium pentachloride as the catalyst in Diels-Alder reactions between furan and several reactive dienophiles, among which methyl acrylate showed good yields, especially at lower temperatures. Other dienophiles have shown lower yields because of problems such as byproduct formation and the high reversibility of the reaction. (author)
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DFT studies for the substituent effect on the diels-alder reaction of 1,4-diaza-1,3-butadienes
International Nuclear Information System (INIS)
Lee, Gab Yong
2001-01-01
DFT calculations have been performed on several substituted 1,4-diaza-1,3-butadienes (1,4-DABs) with electron donating and withdrawing groups at the terminal two nitrogens to investigate the reactivity of Diels-Alder reaction with acrolein. The calculated FMO (Frontier Molecular orbital) energies for the optimized 1,4-disubstituted-1,4DABs have been used to explain both normal and inverse electron demand Diels-Alder reactions. It is shown that the electron donating and withdrawing substituents lead to the normal(HOMO diene controlled) and inverse electron demand (LUMO diene controlled) Diels-Alder reactions, respectively
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Magnetic Field Fluctuations Due to Diel Vertical Migrations of Zooplankton
Dean, C.; Soloviev, A.
2016-12-01
Dean et al. (2016) have indicated that at high zooplankton concentrations, diel vertical migrations (DVM) cause velocity fluctuations and a respective increase of the dissipation rate of turbulent kinetic energy (TKE). In this work, we used a 3D non-hydrostatic computational fluid dynamics model with Lagrangian particle injections (a proxy for migrating organisms) via a discrete phase model to simulate the effect of turbulence generation by DVM. We tested a range of organism concentrations from 1000 to 10,000 organisms/m3. The simulation at an extreme concentration of zooplankton showed an increase in dissipation rate of TKE by two to three orders of magnitude during DVM over background turbulence, 10-8 W kg-1. At lower concentrations (Frank, J. Wood, 2016: Biomixing due to diel vertical migrations of zooplankton. Ocean Modelling 98, 51-64.
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Directory of Open Access Journals (Sweden)
Z. Stirn
2016-07-01
Full Text Available The Diels-Alder reaction between N-phenylmaleimide and benzoxazine bearing furan group was investigated for the purpose of successful appliance of self-healing in benzoxazine polymer networks. The reaction as a function of temperature/time was performed in molten state and in a solution, where also the kinetic study was performed. The Diels-Alder reaction leads to a mixture of two diastereomers: endo presented at lower cyclo-reversion temperature and exo at higher. Therefore, the conversion rates and exo/endo ratio were studied in detail for both systems. For instance, in molten state the Diels-Alder reaction was triggered by the temperature of the melting point at 60 °C with exo/endo ratio preferable to the endo adduct. The study of the kinetics in a solution revealed that the Diels-Alder reaction followed typical bimolecular reversible second-order reaction. The activation energies were close to the previous literature data; 48.4 and 51.9 kJ·mol–1 for Diels-Alder reaction, and 91.0 and 102.3 kJ·mol–1 for retro-Diels-Alder reaction, in acetonitrile and chloroform, respectively. The reaction equilibrium in a solution is much more affected by the retro-Diels-Alder reaction than in a molten state. This study shows detailed investigation of DA reaction and provides beneficial knowledge for further use in self-healing polymer networks.
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Early transcriptional response of soybean contrasting accessions to root dehydration.
Directory of Open Access Journals (Sweden)
José Ribamar Costa Ferreira Neto
Full Text Available Drought is a significant constraint to yield increase in soybean. The early perception of water deprivation is critical for recruitment of genes that promote plant tolerance. DeepSuperSAGE libraries, including one control and a bulk of six stress times imposed (from 25 to 150 min of root dehydration for drought-tolerant and sensitive soybean accessions, allowed to identify new molecular targets for drought tolerance. The survey uncovered 120,770 unique transcripts expressed by the contrasting accessions. Of these, 57,610 aligned with known cDNA sequences, allowing the annotation of 32,373 unitags. A total of 1,127 unitags were up-regulated only in the tolerant accession, whereas 1,557 were up-regulated in both as compared to their controls. An expression profile concerning the most representative Gene Ontology (GO categories for the tolerant accession revealed the expression "protein binding" as the most represented for "Molecular Function", whereas CDPK and CBL were the most up-regulated protein families in this category. Furthermore, particular genes expressed different isoforms according to the accession, showing the potential to operate in the distinction of physiological behaviors. Besides, heat maps comprising GO categories related to abiotic stress response and the unitags regulation observed in the expression contrasts covering tolerant and sensitive accessions, revealed the unitags potential for plant breeding. Candidate genes related to "hormone response" (LOX, ERF1b, XET, "water response" (PUB, BMY, "salt stress response" (WRKY, MYB and "oxidative stress response" (PER figured among the most promising molecular targets. Additionally, nine transcripts (HMGR, XET, WRKY20, RAP2-4, EREBP, NAC3, PER, GPX5 and BMY validated by RT-qPCR (four different time points confirmed their differential expression and pointed that already after 25 minutes a transcriptional reorganization started in response to the new condition, with important
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Specific transcripts are elevated in Saccharomyces cerevisiae in response to DNA damage
International Nuclear Information System (INIS)
McClanahan, T.; McEntee, K.
1984-01-01
Differential hybridization has been used to identify genes in Saccharomyces cerevisiae displaying increased transcript levels after treatment of cells with UV irradiation or with the mutagen/carcinogen 4-nitroquinoline-1-oxide (NQO). The authors describe the isolation and characterization of four DNA damage responsive genes obtained from screening ca. 9000 yeast genomic clones. Two of these clones, lambda 78A and pBR178C, contain repetitive elements in the yeast genome as shown by Southern hybridization analysis. Although the genomic hybridization pattern is distinct for each of these two clones, both of these sequences hybridize to large polyadenylated transcripts ca. 5 kilobases in length. Two other DNA damage responsive sequences, pBRA2 and pBR3016B, are single-copy genes and hybridize to 0.5- and 3.2-kilobase transcripts, respectively. Kinetic analysis of the 0.5-kilobase transcript homologous to pBRA2 indicates that the level of this RNA increases more than 15-fold within 20 min after exposure to 4-nitroquinoline-1-oxide. Moreover, the level of this transcript is significantly elevated in cells containing the rad52-1 mutation which are deficient in DNA strand break repair and gene conversion. These results provide some of the first evidence that DNA damage stimulates transcription of specific genes in eucaryotic cells
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Arabidopsis transcriptional responses differentiate between O3 and herbicides
Using published data based on Affymetrix ATH1 Gene-Chips we characterized the transcriptional response of Arabidopsis thaliana Columbia to O3 and a few other major environmental stresses including oxidative stress . A set of 101 markers could be extracted which provided a compo...
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Krivoruchko, Anastasia; Storey, Kenneth B
2013-11-01
The forkhead class O (FoxO) transcription factors are important regulators of multiple aspects of cellular metabolism. We hypothesized that activation of these transcription factors could play crucial roles in low oxygen survival in the anoxia-tolerant turtle, Trachemys scripta elegans. Two FoxOs, FoxO1 and FoxO3, were examined in turtle tissues in response to 5 and 20h of anoxic submergence using techniques of RT-PCR, western immunoblotting and DNA-binding assays to assess activation. Transcript levels of FoxO-responsive genes were also quantified using RT-PCR. FoxO1 was anoxia-responsive in the liver, with increases in transcript levels, protein levels, nuclear levels and DNA-binding of 1.7-4.8fold in response to anoxia. Levels of phosphorylated FoxO1 also decreased to 57% of control values in response to 5h of anoxia, indicating activation. FoxO3 was activated in the heart, kidney and liver in response to anoxia, with nuclear levels increasing by 1.5-3.7fold and DNA-binding activity increasing by 1.3-2.9fold. Transcript levels of two FoxO-target genes, p27kip1 and catalase, also rose by 2.4-2.5fold in the turtle liver under anoxia. The results suggest that the FoxO transcription factors are activated in response to anoxia in T. scripta elegans, potentially contributing to the regulation of stress resistance and metabolic depression. This study provides the first demonstration of activation of FoxOs in a natural model for vertebrate anoxia tolerance, further improving understanding of how tissues can survive without oxygen. © 2013.
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Unsaturated aldehydes as alkene equivalents in the Diels-Alder reaction
DEFF Research Database (Denmark)
Taarning, Esben; Madsen, Robert
2008-01-01
A one-pot procedure is described for using alpha,beta-unsaturated aldehydes as olefin equivalents in the Diels-Alder reaction. The method combines the normal electron demand cycloaddition with aldehyde dienophiles and the rhodium-catalyzed decarbonylation of aldehydes to afford cyclohexenes...
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Catalytic asymmetric diels-alder reaction of quinone imine ketals: a site-divergent approach.
Hashimoto, Takuya; Nakatsu, Hiroki; Maruoka, Keiji
2015-04-07
The catalytic asymmetric Diels-Alder reaction of quinone imine ketals with diene carbamates catalyzed by axially chiral dicarboxylic acids is reported herein. A variety of primary and secondary alkyl-substituted quinone derivatives which have not been applied in previous asymmetric quinone Diels-Alder reactions could be employed using this method. More importantly, we succeeded in developing a strategy to divert the reaction site in unsymmetrical 3-alkyl quinone imine ketals from the inherently favored unsubstituted C=C bond to the disfavored alkyl-substituted C=C bond. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Latorre, Mauricio; Ehrenfeld, Nicole; Cortés, María Paz; Travisany, Dante; Budinich, Marko; Aravena, Andrés; González, Mauricio; Bobadilla-Fazzini, Roberto A; Parada, Pilar; Maass, Alejandro
2016-01-01
In order to provide new information about the adaptation of Acidithiobacillus ferrooxidans during the bioleaching process, the current analysis presents the first report of the global transcriptional response of the native copper mine strain Wenelen (DSM 16786) oxidized under different sulfide minerals. Microarrays were used to measure the response of At. ferrooxidans Wenelen to shifts from iron supplemented liquid cultures (reference state) to the addition of solid substrates enriched in pyrite or chalcopyrite. Genes encoding for energy metabolism showed a similar transcriptional profile for the two sulfide minerals. Interestingly, four operons related to sulfur metabolism were over-expressed during growth on a reduced sulfur source. Genes associated with metal tolerance (RND and ATPases type P) were up-regulated in the presence of pyrite or chalcopyrite. These results suggest that At. ferrooxidans Wenelen presents an efficient transcriptional system developed to respond to environmental conditions, namely the ability to withstand high copper concentrations. Copyright © 2015 Elsevier Ltd. All rights reserved.
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Directory of Open Access Journals (Sweden)
Deyholos Michael K
2006-10-01
Full Text Available Abstract Background Roots are an attractive system for genomic and post-genomic studies of NaCl responses, due to their primary importance to agriculture, and because of their relative structural and biochemical simplicity. Excellent genomic resources have been established for the study of Arabidopsis roots, however, a comprehensive microarray analysis of the root transcriptome following NaCl exposure is required to further understand plant responses to abiotic stress and facilitate future, systems-based analyses of the underlying regulatory networks. Results We used microarrays of 70-mer oligonucleotide probes representing 23,686 Arabidopsis genes to identify root transcripts that changed in relative abundance following 6 h, 24 h, or 48 h of hydroponic exposure to 150 mM NaCl. Enrichment analysis identified groups of structurally or functionally related genes whose members were statistically over-represented among up- or down-regulated transcripts. Our results are consistent with generally observed stress response themes, and highlight potentially important roles for underappreciated gene families, including: several groups of transporters (e.g. MATE, LeOPT1-like; signalling molecules (e.g. PERK kinases, MLO-like receptors, carbohydrate active enzymes (e.g. XTH18, transcription factors (e.g. members of ZIM, WRKY, NAC, and other proteins (e.g. 4CL-like, COMT-like, LOB-Class 1. We verified the NaCl-inducible expression of selected transcription factors and other genes by qRT-PCR. Conclusion Micorarray profiling of NaCl-treated Arabidopsis roots revealed dynamic changes in transcript abundance for at least 20% of the genome, including hundreds of transcription factors, kinases/phosphatases, hormone-related genes, and effectors of homeostasis, all of which highlight the complexity of this stress response. Our identification of these transcriptional responses, and groups of evolutionarily related genes with either similar or divergent
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Intramolecular Diels-Alder Reactions in Organic Synthesis
Sizemore, Nicholas Blandford Luke
2014-01-01
Intramolecular Diels-Alder (IMDA) reactions are an important class of reactions in synthetic organic chemistry for the rapid construction of polycyclic frameworks. Three classes of IMDA reactions were investigated synthetically and computationally: 1) all-carbon type 1 IMDA reactions, 2) N-acylnitroso type 2 IMDA reactions, and 3) cyano-azadiene IMDA reactions. The first class was implemented in research toward the total synthesis of maoecrystal Z and isopalhinine A. The second class was stud...
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Scholl, Katie; Dillashaw, John; Timpy, Evan; Lam, Yu-Hong; DeRatt, Lindsey; Benton, Tyler R; Powell, Jacqueline P; Houk, Kendall N; Morgan, Jeremy B
2018-05-01
Diels-Alder reactions of tethered vinyl-metal species offer the opportunity to fashion highly functionalized diol intermediates for synthesis. We have developed the first enantioselective boron-tethered Diels-Alder reaction using quinine as a chiral promoter. Quinine recovery, enantioselectivity enhancement, and manipulation of the cyclohexene core are also investigated. DFT modeling calculations confirm the role of quinine as a bidentate ligand enhancing reaction rates. The enantioselectivity of the cycloaddition is proposed to originate from a boron-centered anomeric effect.
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Transcriptional profiling uncovers a network of cholesterol-responsive atherosclerosis target genes.
Directory of Open Access Journals (Sweden)
Josefin Skogsberg
2008-03-01
Full Text Available Despite the well-documented effects of plasma lipid lowering regimes halting atherosclerosis lesion development and reducing morbidity and mortality of coronary artery disease and stroke, the transcriptional response in the atherosclerotic lesion mediating these beneficial effects has not yet been carefully investigated. We performed transcriptional profiling at 10-week intervals in atherosclerosis-prone mice with human-like hypercholesterolemia and a genetic switch to lower plasma lipoproteins (Ldlr(-/-Apo(100/100Mttp(flox/flox Mx1-Cre. Atherosclerotic lesions progressed slowly at first, then expanded rapidly, and plateaued after advanced lesions formed. Analysis of lesion expression profiles indicated that accumulation of lipid-poor macrophages reached a point that led to the rapid expansion phase with accelerated foam-cell formation and inflammation, an interpretation supported by lesion histology. Genetic lowering of plasma cholesterol (e.g., lipoproteins at this point all together prevented the formation of advanced plaques and parallel transcriptional profiling of the atherosclerotic arterial wall identified 37 cholesterol-responsive genes mediating this effect. Validation by siRNA-inhibition in macrophages incubated with acetylated-LDL revealed a network of eight cholesterol-responsive atherosclerosis genes regulating cholesterol-ester accumulation. Taken together, we have identified a network of atherosclerosis genes that in response to plasma cholesterol-lowering prevents the formation of advanced plaques. This network should be of interest for the development of novel atherosclerosis therapies.
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Hadjichristidis, Nikolaos
2015-05-26
A novel strategy towards well-defined polymethylene-based co/terpolymers, by combining anthracene/maleimide Diels-Alder reaction with polyhomologation, is presented. For the synthesis of diblock copolymers the following approach was applied: a) synthesis of α-anthracene-ω-hydroxy- polymethylene by polyhomologation using tri (9-anthracene-methyl propyl ether) borane as initiator, b) synthesis of furan-protected-maleimide-terminated poly (ε-caprolactone) or polyethylene glycol and c). Diels-Alder reaction between the anthracene and maleimide-terminated polymers. In the case of triblock terpolymers the α-anthracene-ω-hydroxy-polymethylene was used as macroinitiator for the ring-opening polymerization of D, L-lactide to afford an anthracene-terminated PM-b-PLA copolymer, followed by Diels-Alder reaction with furan-protected maleimide-terminated poly (ε-caprolactone) or polyethylene glycol to give the triblock terpolymers. All intermediate and final products were characterized by SEC, 1H NMR, UV-VIS spectroscopy and DSC.
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Directory of Open Access Journals (Sweden)
Stephen L. McDaniel
2017-06-01
Full Text Available Set2-mediated histone methylation at H3K36 regulates diverse activities, including DNA repair, mRNA splicing, and suppression of inappropriate (cryptic transcription. Although failure of Set2 to suppress cryptic transcription has been linked to decreased lifespan, the extent to which cryptic transcription influences other cellular functions is poorly understood. Here, we uncover a role for H3K36 methylation in the regulation of the nutrient stress response pathway. We found that the transcriptional response to nutrient stress was dysregulated in SET2-deleted (set2Δ cells and was correlated with genome-wide bi-directional cryptic transcription that originated from within gene bodies. Antisense transcripts arising from these cryptic events extended into the promoters of the genes from which they arose and were associated with decreased sense transcription under nutrient stress conditions. These results suggest that Set2-enforced transcriptional fidelity is critical to the proper regulation of inducible and highly regulated transcription programs.
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Total Synthesis of (+)-Cytosporolide A via a Biomimetic Hetero-Diels-Alder Reaction.
Takao, Ken-Ichi; Noguchi, Shuji; Sakamoto, Shu; Kimura, Mizuki; Yoshida, Keisuke; Tadano, Kin-Ichi
2015-12-23
The first total synthesis of (+)-cytosporolide A was achieved by a biomimetic hetero-Diels-Alder reaction of (-)-fuscoatrol A with o-quinone methide generated from (+)-CJ-12,373. The dienophile, highly oxygenated caryophyllene sesquiterpenoid (-)-fuscoatrol A, was synthesized from the synthetic intermediate in our previous total synthesis of (+)-pestalotiopsin A. The o-quinone methide precursor, isochroman carboxylic acid (+)-CJ-12,373, was synthesized through a Kolbe-Schmitt reaction and an oxa-Pictet-Spengler reaction. The hetero-Diels-Alder reaction of these two compounds proceeded with complete chemo-, regio-, and stereoselectivity to produce the complicated pentacyclic ring system of the cytosporolide skeleton. This total synthesis unambiguously demonstrates that natural cytosporolide A has the structure previously suggested.
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Bmp indicator mice reveal dynamic regulation of transcriptional response.
Directory of Open Access Journals (Sweden)
Anna L Javier
Full Text Available Cellular responses to Bmp ligands are regulated at multiple levels, both extracellularly and intracellularly. Therefore, the presence of these growth factors is not an accurate indicator of Bmp signaling activity. While a common approach to detect Bmp signaling activity is to determine the presence of phosphorylated forms of Smad1, 5 and 8 by immunostaining, this approach is time consuming and not quantitative. In order to provide a simpler readout system to examine the presence of Bmp signaling in developing animals, we developed BRE-gal mouse embryonic stem cells and a transgenic mouse line that specifically respond to Bmp ligand stimulation. Our reporter identifies specific transcriptional responses that are mediated by Smad1 and Smad4 with the Schnurri transcription factor complex binding to a conserved Bmp-Responsive Element (BRE, originally identified among Drosophila, Xenopus and human Bmp targets. Our BRE-gal mES cells specifically respond to Bmp ligands at concentrations as low as 5 ng/ml; and BRE-gal reporter mice, derived from the BRE-gal mES cells, show dynamic activity in many cellular sites, including extraembryonic structures and mammary glands, thereby making this a useful scientific tool.
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Wang, Ben; Zha, Tian Shan; Jia, Xin; Gong, Jin Nan; Bourque, Charles; Feng, Wei; Tian, Yun; Wu, Bin; Qing Zhang, Yu; Peltola, Heli
2017-09-01
Explanations for the occurrence of hysteresis (asynchronicity) between diel soil respiration (Rs) and soil temperature (Ts) have evoked both biological and physical mechanisms. The specifics of these explanations, however, tend to vary with the particular ecosystem or biome being investigated. So far, the relative degree of control of biological and physical processes on hysteresis is not clear for drylands. This study examined the seasonal variation in diel hysteresis and its biological control in a desert-shrub ecosystem in northwest (NW) China. The study was based on continuous measurements of Rs, air temperature (Ta), temperature at the soil surface and below (Tsurf and Ts), volumetric soil water content (SWC), and photosynthesis in a dominant desert shrub (i.e., Artemisia ordosica) over an entire year in 2013. Trends in diel Rs were observed to vary with SWC over the growing season (April to October). Diel variations in Rs were more closely associated with variations in Tsurf than with photosynthesis as SWC increased, leading to Rs being in phase with Tsurf, particularly when SWC > 0.08 m3 m-3 (ratio of SWC to soil porosity = 0.26). However, as SWC decreased below 0.08 m3 m-3, diel variations in Rs were more closely related to variations in photosynthesis, leading to pronounced hysteresis between Rs and Tsurf. Incorporating photosynthesis into a Q10-function eliminated 84.2 % of the observed hysteresis, increasing the overall descriptive capability of the function. Our findings highlight a high degree of control by photosynthesis and SWC in regulating seasonal variation in diel hysteresis between Rs and temperature.
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Synthesis of a Phlorin from a Meso-Fused Anthriporphyrin by a Diels-Alder Strategy.
Aslam, Adil S; Hong, Jung-Ho; Shin, June-Ho; Cho, Dong-Gyu
2017-12-18
An anthracene-containing meso-fused carbaporphyrin, which has extended π-conjugation pathways as compared to the corresponding naphthalene-containing carbaporphyrin, has been synthesized. The weak global aromaticity of the anthriporphyrin also allowed its use as the diene for a Diels-Alder reaction with dimethyl acetylenedicarboxylate (DMAD). The resulting phlorin contains an interesting bicyclic structure. Moreover, to the best of our knowledge, this phlorin is the first Diels-Alder adduct of a diene forming part of the global π-conjugation pathway of an aromatic porphyrinoid. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Kotha, Sambasivarao; Chavan, Arjun S; Goyal, Deepti
2015-05-11
We describe diverse approaches to various dienes and their utilization in the Diels-Alder reaction to produce a variety of polycycles. The dienes covered here are prepared by simple alkylation reaction or via the Claisen rearrangement or by enyne metathesis of alkyne or enyne building blocks. Here, we have also included the Diels-Alder chemistry of dendralenes, a higher analog of cross-conjugated dienes. The present article is inclusive of o-xylylene derivatives that are generated in situ starting with benzosultine or benzosulfone derivatives. The Diels-Alder reaction of these dienes with various dienophiles gave diverse polycyclic systems and biologically important targets.
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Sato, Takeo; Maekawa, Shugo; Konishi, Mineko; Yoshioka, Nozomi; Sasaki, Yuki; Maeda, Haruna; Ishida, Tetsuya; Kato, Yuki; Yamaguchi, Junji; Yanagisawa, Shuichi
2017-01-29
Nitrate modulates growth and development, functioning as a nutrient signal in plants. Although many changes in physiological processes in response to nitrate have been well characterized as nitrate responses, the molecular mechanisms underlying the nitrate response are not yet fully understood. Here, we show that NLP transcription factors, which are key regulators of the nitrate response, directly activate the nitrate-inducible expression of BT1 and BT2 encoding putative scaffold proteins with a plant-specific domain structure in Arabidopsis. Interestingly, the 35S promoter-driven expression of BT2 partially rescued growth inhibition caused by reductions in NLP activity in Arabidopsis. Furthermore, simultaneous disruption of BT1 and BT2 affected nitrate-dependent lateral root development. These results suggest that direct activation of BT1 and BT2 by NLP transcriptional activators is a key component of the molecular mechanism underlying the nitrate response in Arabidopsis. Copyright © 2016 Elsevier Inc. All rights reserved.
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Thermally reversible rubber-toughened thermoset networks via Diels-Alder chemistry
Araya-Hermosilla, R.; Fortunato, G.; Pucci, A.; Raffa, P.; Polgar, L.; Broekhuis, A. A.; Pourhossein, P.; Lima, G. M. R.; Beljaars, M.; Picchioni, F.
In this work we present a reversible and toughened thermoset system based on the covalent incorporation of a furane functionalized ethylene-propylene rubber (EPM-Fu) into a thermoset furane functionalized polyketone (PK-Fu) via Diels-Alder (DA) reversible cross-linking with bismaleimide (b-MA).
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Directory of Open Access Journals (Sweden)
Peng Zhang
2014-03-01
Full Text Available Hypoxia-inducible factors (HIFs play key roles in the cellular response to hypoxia. It is widely accepted that whereas HIF-1 and HIF-2 function as transcriptional activators, HIF-3 inhibits HIF-1/2α action. Contrary to this idea, we show that zebrafish Hif-3α has strong transactivation activity. Hif-3α is degraded under normoxia. Mutation of P393, P493, and L503 inhibits this oxygen-dependent degradation. Transcriptomics and chromatin immunoprecipitation analyses identify genes that are regulated by Hif-3α, Hif-1α, or both. Under hypoxia or when overexpressed, Hif-3α binds to its target gene promoters and upregulates their expression. Dominant-negative inhibition and knockdown of Hif-3α abolish hypoxia-induced Hif-3α-promoter binding and gene expression. Hif-3α not only mediates hypoxia-induced growth and developmental retardation but also possesses hypoxia-independent activities. Importantly, transactivation activity is conserved and human HIF-3α upregulates similar genes in human cells. These findings suggest that Hif-3 is an oxygen-dependent transcription factor and activates a distinct transcriptional response to hypoxia.
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Stowe, G. Neil
2010-01-01
Conducting reactions using water as solvent is a highly prized goal for the organic chemist. Based upon recent literature and our continuing interest in the field of aqueous organocatalysis, we tested the scope of an enamine based Diels-Alder reaction using (±)-nornicotine, proline and a proline derivative as aqueous organocatalysts. Unfortunately, none of the examined catalysts under aqueous conditions proved useful, leaving the aqueous Diels-Alder reaction as an elusive goal. PMID:21516231
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Loke, Inga; Bentzinger, Guillaume; Holz, Julia; Raja, Aruna; Bhasin, Aman; Sasse, Florenz; Köhn, Andreas; Schobert, Rainer; Laschat, Sabine
2016-01-21
In order to construct the functionalized AB ring system of clifednamide, member of the class of macrocyclic tetramic acid lactams, a synthesis was developed which utilized an Ireland-Claisen rearrangement and an intramolecular Diels-Alder reaction. Starting from di-O-isopropylidene-d-mannitol the allyl carboxylate precursor for the sigmatropic rearrangement was prepared. This rearrangement proceeded diastereoselectively only in the presence of an allyl silyl ether instead of the parent enone in the side chain, as suggested by deuteration experiments. A subsequent Diels-Alder reaction yielded the target ethyl hexahydro-1H-indene-carboxylate with high diastereoselectivity. Quantum-chemical investigations of this intramolecular Diels-Alder reaction support the proposed configuration of the final product.
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Diel and Lunar Variations in Larval Fish Supply in Malindi Marine ...
African Journals Online (AJOL)
2Department of Fisheries and Aquatic Sciences, University of Eldoret, PO Box 1125, Eldoret, Kenya; ... in fish larval occurrence was thus studied in Malindi Marine Park, Kenya, to assess diel and lunar ..... New South Wales University Press,.
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Kaicharla, Trinadh; Bhojgude, Sachin Suresh; Biju, Akkattu T
2012-12-21
A new protocol for the efficient Diels-Alder reaction of 1,2-benzoquinones with arynes is reported. The aryne generated by the fluoride-induced 1,2-elimination of 2-(trimethylsilyl)aryl triflates undergoes a facile Diels-Alder reaction with 1,2-benzoquinones, affording the dioxobenzobicyclooctadienes in moderate to excellent yields. In addition, this methodology has been applied to the one-pot synthesis of benzoquinoxalinobarrelene and naphthalene derivatives.
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Puglisi, Edoardo
2010-04-06
We used a microarray targeting 3,524 genes to assess the transcriptional response of the actinomycete Rhodococcus aetherivorans I24 in minimal medium supplemented with various substrates (e. g., PCBs) and in both PCB-contaminated and non-contaminated sediment slurries. Relative to the reference condition (minimal medium supplemented with glucose), 408 genes were upregulated in the various treatments. In medium and in sediment, PCBs elicited the upregulation of a common set of 100 genes, including gene-encoding chaperones (groEL), a superoxide dismutase (sodA), alkyl hydroperoxide reductase protein C (ahpC), and a catalase/peroxidase (katG). Analysis of the R. aetherivorans I24 genome sequence identified orthologs of many of the genes in the canonical biphenyl pathway, but very few of these genes were upregulated in response to PCBs or biphenyl. This study is one of the first to use microarrays to assess the transcriptional response of a soil bacterium to a pollutant under conditions that more closely resemble the natural environment. Our results indicate that the transcriptional response of R. aetherivorans I24 to PCBs, in both medium and sediment, is primarily directed towards reducing oxidative stress, rather than catabolism. © 2010 Springer Science+Business Media, LLC.
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Transcriptional plant responses critical for resistance towards necrotrophic pathogens
Directory of Open Access Journals (Sweden)
Rainer P. Birkenbihl
2011-11-01
Full Text Available Plant defenses aimed at necrotrophic pathogens appear to be genetically complex. Despite the apparent lack of a specific recognition of such necrotrophs by products of major R genes, biochemical, molecular, and genetic studies, in particular using the model plant Arabidopsis, have uncovered numerous host components critical for the outcome of such interactions. Although the JA signaling pathway plays a central role in plant defense towards necrotrophs additional signaling pathways contribute to the plant response network. Transcriptional reprogramming is a vital part of the host defense machinery and several key regulators have recently been identified. Some of these transcription factors positively affect plant resistance whereas others play a role in enhancing host susceptibility towards these phytopathogens.
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Area-use patterns and diel movements of white steenbras ...
African Journals Online (AJOL)
The mean length of estuary used by the 15 individuals was 1 888 m (SD 666). There was a distinct diel activity pattern, with certain individuals utilising deeper parts of the estuary during the day and shallow regions at night. The results indicate that the shallow littoral zone is a critical habitat for juvenile white steenbras.
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Guan, Chao; Li, Xinrong; Zhang, Peng; Chen, Yongle
2018-01-01
Soil respiration induced by biological soil crusts (BSCs) is an important process in the carbon (C) cycle in arid and semi-arid ecosystems, where vascular plants are restricted by the harsh environment, particularly the limited soil moisture. However, the interaction between temperature and soil respiration remains uncertain because of the number of factors that control soil respiration, including temperature and soil moisture, especially in BSC-dominated areas. In this study, the soil respiration in moss-dominated crusts and lichen-dominated crusts was continuously measured using an automated soil respiration system over a one-year period from November 2015 to October 2016 in the Shapotou region of the Tengger Desert, northern China. The results indicated that over daily cycles, the half-hourly soil respiration rates in both types of BSC-covered areas were commonly related to the soil temperature. The observed diel hysteresis between the half-hourly soil respiration rates and soil temperature in the BSC-covered areas was limited by nonlinearity loops with semielliptical shapes, and soil temperature often peaked later than the half-hourly soil respiration rates in the BSC-covered areas. The average lag times between the half-hourly soil respiration rates and soil temperature for both types of BSC-covered areas were two hours over the diel cycles, and they were negatively and linearly related to the volumetric soil water content. Our results highlight the diel hysteresis phenomenon that occurs between soil respiration rates and soil temperatures in BSC-covered areas and the negative response of this phenomenon to soil moisture, which may influence total C budget evaluations. Therefore, the interactive effects of soil temperature and moisture on soil respiration in BSC-covered areas should be considered in global carbon cycle models of desert ecosystems.
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Diel cycle of iron, aluminum and other heavy metals in a volcano watershed in northern Taiwan
Kao, S.
2013-12-01
It is well known that heavy metals in surface water show diel (24-hr) changes in concentrations due to diel biogeochemical cycle. Accordingly, it is important to have a better sampling policy for monitoring the environmental impact of heavy metals of surface water, especially volcanic and mining areas. This study investigated Tatun Volcano watershed in northern Taiwan with a 24-h sampling operation to explore the diel cycle of arsenic concentrations and discuss on the corresponding biogeochemical processes. According to the previous studies, solar energy is the main factor of diel cycles, which could have strong effects on temperature, pH, dissolved oxygen, and many other water qualities. These changes produce a series of chain reactions and finally result in the change of heavy metal concentrations. In general, diel cycle of dissolved oxygen is dominated by metabolism of aquatic plants and sunlight photoreduction in acidic stream water; therefore, the Fe and Al contents would be accordingly changed. In addition, the concentrations of heavy metals will be simultaneously modified due to the high adsorption capacity of Fe and Al hydroxides. In this study, the results of hydro chemical analysis show that creek water is characterized by higher temperature, low pH value (3.0-4.5) and high SO4content(60-400 ppm) due to the mixing of hot spring. That the pH dramatically drops in the noon demonstrates that pH is highly dependent on photoreduction. This can be confirmed by the opposite trend of Fe concentration. The high Fe content in the noon also demonstrates that the precipitation of Fe hydroxides is not dominant in the day time and Fe is mainly in dissolved and/or colloid forms. Under the situation, heavy metals are supposed to have a similar trend with Fe. However, arsenic, aluminum and rare earth elements show a quite different diel cycle from Fe and other heavy metals. It concludes that arsenic and rare earth elements may be adsorbed by Al hydroxides instead of Fe
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Diels-Alder reactions of anthracenes with C-sulfonyldithioformates
DEFF Research Database (Denmark)
El-Sayed, I.; Ali, O.M.; Fischer, A.
2003-01-01
C-Sulfonyldithioformates (2) (R-1 = ArSO2, R 2 = ArS) readily add to anthracene and 9-methylanthracene (1) in a Diels-Alder fashion with formation of 9,10-dihydro-10,9-(epithiomethano)anthracenes (3) which in turn may suffer thermally induced elimination of arenesulfinic acid to yield the 9......-anthracenedithiocarboxylic esters (4). The reactions with the unsymmetrical diene 9-methylanthracene take place in a highly stereoselective fashion....
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Ubiquitin ligase activity of TFIIH and the transcriptional response to DNA damage.
Takagi, Yuichiro; Masuda, Claudio A; Chang, Wei-Hau; Komori, Hirofumi; Wang, Dong; Hunter, Tony; Joazeiro, Claudio A P; Kornberg, Roger D
2005-04-15
Core transcription factor (TF) IIH purified from yeast possesses an E3 ubiquitin (Ub) ligase activity, which resides, at least in part, in a RING finger (RNF) domain of the Ssl1 subunit. Yeast strains mutated in the Ssl1 RNF domain are sensitive to ultraviolet (UV) light and to methyl methanesulfonate (MMS). This increased sensitivity to DNA-damaging agents does not reflect a deficiency in nucleotide excision repair. Rather, it correlates with reduced transcriptional induction of genes involved in DNA repair, suggesting that the E3 Ub ligase activity of TFIIH mediates the transcriptional response to DNA damage.
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Chapin, T.P.; Nimick, D.A.; Gammons, C.H.; Wanty, R.B.
2007-01-01
Recent work has demonstrated that many trace metals undergo dramatic diel (24-h) cycles in near neutral pH streams with metal concentrations reproducibly changing up to 500% during the diel period (Nimick et al., 2003). To examine diel zinc cycles in streams affected by acid rock drainage, we have developed a novel instrument, the Zn-DigiScan, to continuously monitor in situ zinc concentrations in near real-time. Initial results from a 3-day deployment at Fisher Creek, Montana have demonstrated the ability of the Zn-DigiScan to record diel Zn cycling at levels below 100 ??g/l. Longer deployments of this instrument could be used to examine the effects of episodic events such as rainstorms and snowmelt pulses on zinc loading in streams affected by acid rock drainage. ?? Springer Science+Business Media B.V. 2006.
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Hooper, Joel F; James, Natalie C; Bozkurt, Esra; Aviyente, Viktorya; White, Jonathan M; Holland, Mareike C; Gilmour, Ryan; Holmes, Andrew B; Houk, K N
2015-12-18
The intramolecular Diels-Alder reaction has been used as a powerful method to access the tricyclic core of the eunicellin natural products from a number of 9-membered-ring precursors. The endo/exo selectivity of this reaction can be controlled through a remarkable organocatalytic approach, employing MacMillan's imidazolidinone catalysts, although the mechanistic origin of this selectivity remains unclear. We present a combined experimental and density functional theory investigation, providing insight into the effects of medium-ring constraints on the organocatalyzed intramolecular Diels-Alder reaction to form the isobenzofuran core of the eunicellins.
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Li, Yang; Barløse, Casper; Jørgensen, Julie; Carlsen, Bjørn Dreiø; Jørgensen, Karl Anker
2017-01-01
An asymmetric catalytic aza-Diels-Alder/ring-closing cascade reaction between acylhydrazones and in situ formed trienamines is presented. The reaction proceeds through a formal aza-Diels-Alder cycloaddition, followed by a ring-closing reaction forming the hemiaminal ring leading to chiral bicyclic azaheterocycles in moderate to good yield (up to 71 %), good enantio- (up to 92 % ee) and diastereoselectivity (up to >20:1 d.r.). Furthermore, transformations are presented to show the potential application of the formed product. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Zhang, Sheng; Cha, Lide; Li, Lijun; Hu, Yanbin; Li, Yanan; Zha, Zhenggen; Wang, Zhiyong
2016-04-15
A primary amine-catalyzed asymmetric formal aza-Diels-Alder reaction of trifluoromethyl hemiaminals with enones was developed via a chiral gem-diamine intermediate. This novel protocol allowed facile access to structurally diverse trifluoromethyl-substituted piperidine scaffolds with high stereoselectivity. The utility of this method was further demonstrated through a concise approach to biologically active 4-hydroxypiperidine. More importantly, a stepwise mechanism involving an asymmetric induction process was proposed to rationalize the positive correlation between the chirality of the gem-diamine intermediate and the formal aza-Diels-Alder product.
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The global transcriptional response of fission yeast to hydrogen sulfide.
Directory of Open Access Journals (Sweden)
Xu Jia
Full Text Available BACKGROUND: Hydrogen sulfide (H(2S is a newly identified member of the small family of gasotransmitters that are endogenous gaseous signaling molecules that have a fundamental role in human biology and disease. Although it is a relatively recent discovery and the mechanism of H(2S activity is not completely understood, it is known to be involved in a number of cellular processes; H(2S can affect ion channels, transcription factors and protein kinases in mammals. METHODOLOGY/PRINCIPAL FINDINGS: In this paper, we have used fission yeast as a model organism to study the global gene expression profile in response to H(2S by microarray. We initially measured the genome-wide transcriptional response of fission yeast to H(2S. Through the functional classification of genes whose expression profile changed in response to H(2S, we found that H(2S mainly influences genes that encode putative or known stress proteins, membrane transporters, cell cycle/meiotic proteins, transcription factors and respiration protein in the mitochondrion. Our analysis showed that there was a significant overlap between the genes affected by H(2S and the stress response. We identified that the target genes of the MAPK pathway respond to H(2S; we also identified that a number of transporters respond to H(2S, these include sugar/carbohydrate transporters, ion transporters, and amino acid transporters. We found many mitochondrial genes to be down regulated upon H(2S treatment and that H(2S can reduce mitochondrial oxygen consumption. CONCLUSION/SIGNIFICANCE: This study identifies potential molecular targets of the signaling molecule H(2S in fission yeast and provides clues about the identity of homologues human proteins and will further the understanding of the cellular role of H(2S in human diseases.
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Transcription-based prediction of response to IFNbeta using supervised computational methods.
Directory of Open Access Journals (Sweden)
Sergio E Baranzini
2005-01-01
Full Text Available Changes in cellular functions in response to drug therapy are mediated by specific transcriptional profiles resulting from the induction or repression in the activity of a number of genes, thereby modifying the preexisting gene activity pattern of the drug-targeted cell(s. Recombinant human interferon beta (rIFNbeta is routinely used to control exacerbations in multiple sclerosis patients with only partial success, mainly because of adverse effects and a relatively large proportion of nonresponders. We applied advanced data-mining and predictive modeling tools to a longitudinal 70-gene expression dataset generated by kinetic reverse-transcription PCR from 52 multiple sclerosis patients treated with rIFNbeta to discover higher-order predictive patterns associated with treatment outcome and to define the molecular footprint that rIFNbeta engraves on peripheral blood mononuclear cells. We identified nine sets of gene triplets whose expression, when tested before the initiation of therapy, can predict the response to interferon beta with up to 86% accuracy. In addition, time-series analysis revealed potential key players involved in a good or poor response to interferon beta. Statistical testing of a random outcome class and tolerance to noise was carried out to establish the robustness of the predictive models. Large-scale kinetic reverse-transcription PCR, coupled with advanced data-mining efforts, can effectively reveal preexisting and drug-induced gene expression signatures associated with therapeutic effects.
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Herdegen, Samantha; Holmes, Geraldine; Cyriac, Ashly; Calin-Jageman, Irina E; Calin-Jageman, Robert J
2014-12-01
We used a custom-designed microarray and quantitative PCR to characterize the rapid transcriptional response to long-term sensitization training in the marine mollusk Aplysia californica. Aplysia were exposed to repeated noxious shocks to one side of the body, a procedure known to induce a long-lasting, transcription-dependent increase in reflex responsiveness that is restricted to the side of training. One hour after training, pleural ganglia from the trained and untrained sides of the body were harvested; these ganglia contain the sensory nociceptors which help mediate the expression of long-term sensitization memory. Microarray analysis from 8 biological replicates suggests that long-term sensitization training rapidly regulates at least 81 transcripts. We used qPCR to test a subset of these transcripts and found that 83% were confirmed in the same samples, and 86% of these were again confirmed in an independent sample. Thus, our new microarray design shows strong convergent and predictive validity for analyzing the transcriptional correlates of memory in Aplysia. Fully validated transcripts include some previously identified as regulated in this paradigm (ApC/EBP and ApEgr) but also include novel findings. Specifically, we show that long-term sensitization training rapidly up-regulates the expression of transcripts which may encode Aplysia homologs of a C/EBPγ transcription factor, a glycine transporter (GlyT2), and a vacuolar-protein-sorting-associated protein (VPS36). Copyright © 2014 Elsevier Inc. All rights reserved.
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Zeituni, Erin M; Wilson, Meredith H; Zheng, Xiaobin; Iglesias, Pablo A; Sepanski, Michael A; Siddiqi, Mahmud A; Anderson, Jennifer L; Zheng, Yixian; Farber, Steven A
2016-11-04
Responding to a high-fat meal requires an interplay between multiple digestive tissues, sympathetic response pathways, and the gut microbiome. The epithelial enterocytes of the intestine are responsible for absorbing dietary nutrients and preparing them for circulation to distal tissues, which requires significant changes in cellular activity, including both morphological and transcriptional responses. Following a high-fat meal, we observe morphological changes in the enterocytes of larval zebrafish, including elongation of mitochondria, formation and expansion of lipid droplets, and the rapid and transient ruffling of the nuclear periphery. Dietary and pharmacological manipulation of zebrafish larvae demonstrated that these subcellular changes are specific to triglyceride absorption. The transcriptional changes that occur simultaneously with these morphological changes were determined using RNA sequencing, revealing a cohort of up-regulated genes associated with lipid droplet formation and lipid transport via lipoprotein particles. Using a microsomal triglyceride transfer protein (MTP) inhibitor to block β-lipoprotein particle formation, we demonstrate that the transcriptional response to a high-fat meal is associated with the transfer of ER triglyceride to nascent β-lipoproteins, possibly through the activation of Creb3l3/cyclic AMP-responsive element-binding protein. These data suggest that a transient increase in ER lipids is the likely mediator of the initial physiological response of intestinal enterocytes to dietary lipid. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.
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Zeituni, Erin M.; Wilson, Meredith H.; Zheng, Xiaobin; Iglesias, Pablo A.; Sepanski, Michael A.; Siddiqi, Mahmud A.; Anderson, Jennifer L.; Zheng, Yixian; Farber, Steven A.
2016-01-01
Responding to a high-fat meal requires an interplay between multiple digestive tissues, sympathetic response pathways, and the gut microbiome. The epithelial enterocytes of the intestine are responsible for absorbing dietary nutrients and preparing them for circulation to distal tissues, which requires significant changes in cellular activity, including both morphological and transcriptional responses. Following a high-fat meal, we observe morphological changes in the enterocytes of larval zebrafish, including elongation of mitochondria, formation and expansion of lipid droplets, and the rapid and transient ruffling of the nuclear periphery. Dietary and pharmacological manipulation of zebrafish larvae demonstrated that these subcellular changes are specific to triglyceride absorption. The transcriptional changes that occur simultaneously with these morphological changes were determined using RNA sequencing, revealing a cohort of up-regulated genes associated with lipid droplet formation and lipid transport via lipoprotein particles. Using a microsomal triglyceride transfer protein (MTP) inhibitor to block β-lipoprotein particle formation, we demonstrate that the transcriptional response to a high-fat meal is associated with the transfer of ER triglyceride to nascent β-lipoproteins, possibly through the activation of Creb3l3/cyclic AMP-responsive element-binding protein. These data suggest that a transient increase in ER lipids is the likely mediator of the initial physiological response of intestinal enterocytes to dietary lipid. PMID:27655916
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Directory of Open Access Journals (Sweden)
Regla Bustos
2010-09-01
Full Text Available Plants respond to different stresses by inducing or repressing transcription of partially overlapping sets of genes. In Arabidopsis, the PHR1 transcription factor (TF has an important role in the control of phosphate (Pi starvation stress responses. Using transcriptomic analysis of Pi starvation in phr1, and phr1 phr1-like (phl1 mutants and in wild type plants, we show that PHR1 in conjunction with PHL1 controls most transcriptional activation and repression responses to phosphate starvation, regardless of the Pi starvation specificity of these responses. Induced genes are enriched in PHR1 binding sequences (P1BS in their promoters, whereas repressed genes do not show such enrichment, suggesting that PHR1(-like control of transcriptional repression responses is indirect. In agreement with this, transcriptomic analysis of a transgenic plant expressing PHR1 fused to the hormone ligand domain of the glucocorticoid receptor showed that PHR1 direct targets (i.e., displaying altered expression after GR:PHR1 activation by dexamethasone in the presence of cycloheximide corresponded largely to Pi starvation-induced genes that are highly enriched in P1BS. A minimal promoter containing a multimerised P1BS recapitulates Pi starvation-specific responsiveness. Likewise, mutation of P1BS in the promoter of two Pi starvation-responsive genes impaired their responsiveness to Pi starvation, but not to other stress types. Phylogenetic footprinting confirmed the importance of P1BS and PHR1 in Pi starvation responsiveness and indicated that P1BS acts in concert with other cis motifs. All together, our data show that PHR1 and PHL1 are partially redundant TF acting as central integrators of Pi starvation responses, both specific and generic. In addition, they indicate that transcriptional repression responses are an integral part of adaptive responses to stress.
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Ghosh Dasgupta, Modhumita; Dharanishanthi, Veeramuthu
2017-09-05
Ecophysiological studies in Eucalyptus have shown that water is the principal factor limiting stem growth. Effect of water deficit conditions on physiological and biochemical parameters has been extensively reported in Eucalyptus. The present study was conducted to identify major polyethylene glycol induced water stress responsive transcripts in Eucalyptus grandis using gene co-expression network. A customized array representing 3359 water stress responsive genes was designed to document their expression in leaves of E. grandis cuttings subjected to -0.225MPa of PEG treatment. The differentially expressed transcripts were documented and significantly co-expressed transcripts were used for construction of network. The co-expression network was constructed with 915 nodes and 3454 edges with degree ranging from 2 to 45. Ninety four GO categories and 117 functional pathways were identified in the network. MCODE analysis generated 27 modules and module 6 with 479 nodes and 1005 edges was identified as the biologically relevant network. The major water responsive transcripts represented in the module included dehydrin, osmotin, LEA protein, expansin, arabinogalactans, heat shock proteins, major facilitator proteins, ARM repeat proteins, raffinose synthase, tonoplast intrinsic protein and transcription factors like DREB2A, ARF9, AGL24, UNE12, WLIM1 and MYB66, MYB70, MYB 55, MYB 16 and MYB 103. The coordinated analysis of gene expression patterns and coexpression networks developed in this study identified an array of transcripts that may regulate PEG induced water stress responses in E. grandis. Copyright © 2017 Elsevier B.V. All rights reserved.
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Innate immune responses: Crosstalk of signaling and regulation of gene transcription
International Nuclear Information System (INIS)
Zhong Bo; Tien Po; Shu Hongbing
2006-01-01
Innate immune responses to pathogens such as bacteria and viruses are triggered by recognition of specific structures of invading pathogens called pathogen-associated molecular patterns (PAMPs) by cellular pattern recognition receptors (PRRs) that are located at plasma membrane or inside cells. Stimulation of different PAMPs activates Toll-like receptor (TLR)-dependent and -independent signaling pathways that lead to activation of transcription factors nuclear factor-κB (NF-κB), interferon regulatory factor 3/7 (IRF3/7) and/or activator protein-1 (AP-1), which collaborate to induce transcription of a large number of downstream genes. This review focuses on the rapid progress that has recently improved our understanding of the crosstalk among the pathways and the precise regulation of transcription of the downstream genes
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Levi-Zada, Anat; Fefer, Daniela; David, Maayan; Eliyahu, Miriam; Franco, José Carlos; Protasov, Alex; Dunkelblum, Ezra; Mendel, Zvi
2014-08-01
The diel periodicity of sex pheromone release was monitored in two mealybug species, Planococcus citri and Planococcus ficus (Hemiptera; Pseudococcidae), using sequential SPME/GCMS analysis. A maximal release of 2 ng/h pheromone by 9-12-day-old P. citri females occurred 1-2 h before the beginning of photophase. The highest release of pheromone by P. ficus females was 1-2 ng/2 h of 10-20-day-old females, approximately 2 h after the beginning of photophase. Mating resulted in termination of the pheromone release in both mealybug species. The temporal flight activity of the males was monitored in rearing chambers using pheromone baited delta traps. Males of both P. citri and P. ficus displayed the same flight pattern and began flying at 06:00 hours when the light was turned on, reaching a peak during the first and second hour of the photophase. Our results suggest that other biparental mealybug species display also diel periodicities of maximal pheromone release and response. Direct evaluation of the diel periodicity of the pheromone release by the automatic sequential analysis is convenient and will be very helpful in optimizing the airborne collection and identification of other unknown mealybug pheromones and to study the calling behavior of females. Considering this behavior pattern may help to develop more effective pheromone-based management strategies against mealybugs.
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Lo, Miranda; Cordwell, Stuart J; Bulach, Dieter M; Adler, Ben
2009-12-08
Leptospirosis is a global zoonosis affecting millions of people annually. Transcriptional changes in response to temperature were previously investigated using microarrays to identify genes potentially expressed upon host entry. Past studies found that various leptospiral outer membrane proteins are differentially expressed at different temperatures. However, our microarray studies highlighted a divergence between protein abundance and transcript levels for some proteins. Given the abundance of post-transcriptional expression control mechanisms, this finding highlighted the importance of global protein analysis systems. To complement our previous transcription study, we evaluated differences in the proteins of the leptospiral outer membrane fraction in response to temperature upshift. Outer membrane protein-enriched fractions from Leptospira interrogans grown at 30 degrees C or overnight upshift to 37 degrees C were isolated and the relative abundance of each protein was determined by iTRAQ analysis coupled with two-dimensional liquid chromatography and tandem mass spectrometry (2-DLC/MS-MS). We identified 1026 proteins with 99% confidence; 27 and 66 were present at elevated and reduced abundance respectively. Protein abundance changes were compared with transcriptional differences determined from the microarray studies. While there was some correlation between the microarray and iTRAQ data, a subset of genes that showed no differential expression by microarray was found to encode temperature-regulated proteins. This set of genes is of particular interest as it is likely that regulation of their expression occurs post-transcriptionally, providing an opportunity to develop hypotheses about the molecular dynamics of the outer membrane of Leptospira in response to changing environments. This is the first study to compare transcriptional and translational responses to temperature shift in L. interrogans. The results thus provide an insight into the mechanisms used by L
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Directory of Open Access Journals (Sweden)
Miranda Lo
Full Text Available BACKGROUND: Leptospirosis is a global zoonosis affecting millions of people annually. Transcriptional changes in response to temperature were previously investigated using microarrays to identify genes potentially expressed upon host entry. Past studies found that various leptospiral outer membrane proteins are differentially expressed at different temperatures. However, our microarray studies highlighted a divergence between protein abundance and transcript levels for some proteins. Given the abundance of post-transcriptional expression control mechanisms, this finding highlighted the importance of global protein analysis systems. METHODOLOGY/PRINCIPAL FINDINGS: To complement our previous transcription study, we evaluated differences in the proteins of the leptospiral outer membrane fraction in response to temperature upshift. Outer membrane protein-enriched fractions from Leptospira interrogans grown at 30 degrees C or overnight upshift to 37 degrees C were isolated and the relative abundance of each protein was determined by iTRAQ analysis coupled with two-dimensional liquid chromatography and tandem mass spectrometry (2-DLC/MS-MS. We identified 1026 proteins with 99% confidence; 27 and 66 were present at elevated and reduced abundance respectively. Protein abundance changes were compared with transcriptional differences determined from the microarray studies. While there was some correlation between the microarray and iTRAQ data, a subset of genes that showed no differential expression by microarray was found to encode temperature-regulated proteins. This set of genes is of particular interest as it is likely that regulation of their expression occurs post-transcriptionally, providing an opportunity to develop hypotheses about the molecular dynamics of the outer membrane of Leptospira in response to changing environments. CONCLUSIONS/SIGNIFICANCE: This is the first study to compare transcriptional and translational responses to temperature
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Recent applications of intramolecular Diels-Alder reactions to natural product synthesis
DEFF Research Database (Denmark)
Juhl, M.; Tanner, David Ackland
2009-01-01
This tutorial review presents some recent examples of intramolecular Diels-Alder (IMDA) reactions as key complexity-generating steps in the total synthesis of structurally intricate natural products. The opportunities afforded by transannular (TADA) versions of the IMDA reaction in complex molecu...... comprehensive, reviews....
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Diels-Alder reactions in water : Enforced hydrophobic interaction and hydrogen bonding
Engberts, Jan B.F.N.
1995-01-01
Second-order rate constants have been measured for the Diels-Alder (DA) reactions of cyclopentadiene with dienophiles of varying hydrophobicity and hydrogen-bond acceptor capacity in water, in a series of organic solvents and in alcohol-water mixtures. The intramolecular DA reaction of
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DIELS-ALDER REACTIONS IN WATER - ENFORCED HYDROPHOBIC INTERACTION AND HYDROGEN-BONDING
Engberts, J.B.F.N.
Second-order rate constants have been measured for the Diels-Alder (DA) reactions of cyclopentadiene with dienophiles of varying hydrophobicity and hydrogen-bond acceptor capacity in water, in a series of organic solvents and in alcohol-water mixtures. The intramolecular DA reaction of
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Servant, Géraldine; Pinson, Benoit; Tchalikian-Cosson, Aurélie; Coulpier, Fanny; Lemoine, Sophie; Pennetier, Carole; Bridier-Nahmias, Antoine; Todeschini, Anne Laure; Fayol, Hélène; Daignan-Fornier, Bertrand; Lesage, Pascale
2012-07-01
Transposable elements play a fundamental role in genome evolution. It is proposed that their mobility, activated under stress, induces mutations that could confer advantages to the host organism. Transcription of the Ty1 LTR-retrotransposon of Saccharomyces cerevisiae is activated in response to a severe deficiency in adenylic nucleotides. Here, we show that Ty2 and Ty3 are also stimulated under these stress conditions, revealing the simultaneous activation of three active Ty retrotransposon families. We demonstrate that Ty1 activation in response to adenylic nucleotide depletion requires the DNA-binding transcription factor Tye7. Ty1 is transcribed in both sense and antisense directions. We identify three Tye7 potential binding sites in the region of Ty1 DNA sequence where antisense transcription starts. We show that Tye7 binds to Ty1 DNA and regulates Ty1 antisense transcription. Altogether, our data suggest that, in response to adenylic nucleotide reduction, TYE7 is induced and activates Ty1 mRNA transcription, possibly by controlling Ty1 antisense transcription. We also provide the first evidence that Ty1 antisense transcription can be regulated by environmental stress conditions, pointing to a new level of control of Ty1 activity by stress, as Ty1 antisense RNAs play an important role in regulating Ty1 mobility at both the transcriptional and post-transcriptional stages.
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Chk2 regulates transcription-independent p53-mediated apoptosis in response to DNA damage
International Nuclear Information System (INIS)
Chen Chen; Shimizu, Shigeomi; Tsujimoto, Yoshihide; Motoyama, Noboru
2005-01-01
The tumor suppressor protein p53 plays a central role in the induction of apoptosis in response to genotoxic stress. The protein kinase Chk2 is an important regulator of p53 function in mammalian cells exposed to ionizing radiation (IR). Cells derived from Chk2-deficient mice are resistant to the induction of apoptosis by IR, and this resistance has been thought to be a result of the defective transcriptional activation of p53 target genes. It was recently shown, however, that p53 itself and histone H1.2 translocate to mitochondria and thereby induces apoptosis in a transcription-independent manner in response to IR. We have now examined whether Chk2 also regulates the transcription-independent induction of apoptosis by p53 and histone H1.2. The reduced ability of IR to induce p53 stabilization in Chk2-deficient thymocytes was associated with a marked impairment of p53 and histone H1 translocation to mitochondria. These results suggest that Chk2 regulates the transcription-independent mechanism of p53-mediated apoptosis by inducing stabilization of p53 in response to IR
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Diel and seasonal variation in food habits of Atlantic salmon parr in a small stream
Grader, M.; Letcher, B.H.
2006-01-01
The diel and seasonal food habits of young-of-year (YOY) and post-young-of-year (PYOY) Atlantic salmon (Salmo salar) parr were assayed over the course of 11 months in the West Brook, Massachusetts USA. Gut fullness of YOY salmon did not vary significantly among months. PYOY salmon exhibited significant seasonal differences in gut fullness, with peak fullness occurring in the spring and late fall. Significant diel differences in PYOY gut fullness occurred in June and April, with peak fullness always occurring at dawn. Prey composition varied substantially among months. Dominant prey items of PYOY salmon were baetid mayflies in June, July, and August, limnephilid caddisflies in October and November, and ephemerellid mayflies in February and April. Few differences in prey composition between PYOY and YOY salmon were observed. Fish growth was unrelated to prey availability, but gut fullness explained up to 97% of growth variation across seasons. Results suggest that spring and fall are critical periods of feeding for PYOY salmon and that diel feeding intensity shifts seasonally.
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Lewis acid catalysis of a Diels-Alder reaction in water
Otto, S; Bertoncin, F; Engberts, JBFN
1996-01-01
Here we report the first detailed study of a Diels-Alder (DA) reaction that is catalyzed by Lewis acids in water. The effect of Co2+, Ni2+, Cu2+ and Zn2+ ions as Lewis acid catalysts on the rate and endo-exo selectivity of the DA reaction between the bidentate dienophiles
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Diels-Alder Reactions in Water. Effects of Hydrophobicity and Hydrogen Bonding
Otto, Sijbren; Blokzijl, Wilfried; Engberts, Jan B.F.N.
1994-01-01
In order to check whether the activated complex for the Diels-Alder reactions of 5-substituted 1,4-naphthoquinones with cyclopentadiene is more polar in water than in other solvents, we have determined the substituent effects in seven different solvents. The substituent effects gradually decrease
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Micellar Catalysis of Diels-Alder Reactions : Substrate Positioning in the Micelle
Rispens, Theo; Engberts, Jan B.F.N.
2002-01-01
We have studied the kinetics of the Diels-Alder reactions of cyclopentadiene, sorbyl alcohol, and sorbyltrimethylammonium bromide with a series of N-substituted maleimides in micellar media. Micellar rate constants have been determined and were found to be 20-40 times lower than the respective
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Lee, Jong-Soo
2007-09-01
Mutations in the ATM (ataxia-telangiectasia mutated) gene, which encodes a 370 kd protein with a kinase catalytic domain, predisposes people to cancers, and these mutations are also linked to ataxia-telangiectasia (A-T). The histone acetylaion/deacetylation- dependent chromatin remodeling can activate the ATM kinase-mediated DNA damage signal pathway (in an accompanying work, Lee, 2007). This has led us to study whether this modification can impinge on the ATM-mediated DNA damage response via transcriptional modulation in order to understand the function of ATM in the regulation of gene transcription. To identify the genes whose expression is regulated by ATM in response to histone deaceylase (HDAC) inhibition, we performed an analysis of oligonucleotide microarrays with using the appropriate cell lines, isogenic A-T (ATM(-)) and control (ATM(+)) cells, following treatment with a HDAC inhibitor TSA. Treatment with TSA reprograms the differential gene expression profile in response to HDAC inhibition in ATM(-) cells and ATM(+) cells. We analyzed the genes that are regulated by TSA in the ATM-dependent manner, and we classified these genes into different functional categories, including those involved in cell cycle/DNA replication, DNA repair, apoptosis, growth/differentiation, cell- cell adhesion, signal transduction, metabolism and transcription. We found that while some genes are regulated by TSA without regard to ATM, the patterns of gene regulation are differentially regulated in an ATM-dependent manner. Taken together, these finding indicate that ATM can regulate the transcription of genes that play critical roles in the molecular response to DNA damage, and this response is modulated through an altered HDAC inhibition-mediated gene expression.
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Nishikawa, Yasuhiro; Nakano, Saki; Tahira, Yuu; Terazawa, Kanako; Yamazaki, Ken; Kitamura, Chitoshi; Hara, Osamu
2016-05-06
Chiral pyridinium phosphoramide 1·HX was designed to be a new class of chiral Brønsted acid catalyst in which both the pyridinium proton and the adjacent imide-like proton activated by the electron-withdrawing pyridinium moiety could work cooperatively as strong dual proton donors. The potential of 1·HX was shown in the enantioselective Diels-Alder reactions of 1-amino dienes with various dienophiles including N-unsubstituted maleimide, which has yet to be successfully used in an asymmetric Diels-Alder reaction.
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Primo, Ana Lígia; Azeiteiro, Ulisses M.; Marques, Sónia C.; Ré, Pedro; Pardal, Miguel A.
2012-07-01
Vertical distribution and migration pattern of ichthyoplankton assemblage in the Mondego estuary were investigated in relation to diel and tidal cycle. Summer and winter communities were sampled, at surface and bottom, over a diel cycle during spring and neap tides at a fixed station at the mouth of the estuary. Summer presented higher larvae density mainly of Pomatoschistus spp., Gobius niger and Parablennius pilicornis. Main species in winter assemblages were Pomatoschistus spp. and Sardina pilchardus. There were no differences between depth stratums across diel or tide cycle. Nevertheless, main species larval densities showed significant periodic variation associated with tide (M2) and diel (K1) cycles presenting generally, higher density at night and around low tide. Conversely, vertical patterns observed could not be related with diel or tidal cycle. Tough, main species presented some extent of vertical migration. Vertical patterns observed appear to be related to seasonal stratification and river flow, increasing amplitude during periods of less stratification and lower water currents. Present study provides a better understanding of ichthyoplankton vertical movement patterns and of small scale dynamics at the interface of two coastal European systems.
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Heat shock factor-1 modulates p53 activity in the transcriptional response to DNA damage
Logan, Ian R.; McNeill, Hesta V.; Cook, Susan; Lu, Xiaohong; Meek, David W.; Fuller-Pace, Frances V.; Lunec, John; Robson, Craig N.
2009-01-01
Here we define an important role for heat shock factor 1 (HSF1) in the cellular response to genotoxic agents. We demonstrate for the first time that HSF1 can complex with nuclear p53 and that both proteins are co-operatively recruited to p53-responsive genes such as p21. Analysis of natural and synthetic cis elements demonstrates that HSF1 can enhance p53-mediated transcription, whilst depletion of HSF1 reduces the expression of p53-responsive transcripts. We find that HSF1 is required for optimal p21 expression and p53-mediated cell-cycle arrest in response to genotoxins while loss of HSF1 attenuates apoptosis in response to these agents. To explain these novel properties of HSF1 we show that HSF1 can complex with DNA damage kinases ATR and Chk1 to effect p53 phosphorylation in response to DNA damage. Our data reveal HSF1 as a key transcriptional regulator in response to genotoxic compounds widely used in the clinical setting, and suggest that HSF1 will contribute to the efficacy of these agents. PMID:19295133
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Liu, Fenglong; VanToai, Tara; Moy, Linda P.; Bock, Geoffrey; Linford, Lara D.; Quackenbush, John
2005-01-01
Plants have evolved adaptation mechanisms to sense oxygen deficiency in their environments and make coordinated physiological and structural adjustments to enhance their hypoxic tolerance. To gain insight into how plants respond to low-oxygen stress, gene expression profiling using whole-genome DNA amplicon microarrays was carried out at seven time points over 24 h, in wild-type and transgenic PSAG12:ipt Arabidopsis (Arabidopsis thaliana) plants under normoxic and hypoxic conditions. Transcript levels of genes involved in glycolysis and fermentation pathways, ethylene synthesis and perception, calcium signaling, nitrogen utilization, trehalose metabolism, and alkaloid synthesis were significantly altered in response to oxygen limitation. Analysis based on gene ontology assignments suggested a significant down-regulation of genes whose functions are associated with cell walls, nucleosome structures, water channels, and ion transporters and a significant up-regulation of genes involved in transcriptional regulation, protein kinase activity, and auxin responses under conditions of oxygen shortage. Promoter analysis on a cluster of up-regulated genes revealed a significant overrepresentation of the AtMYB2-binding motif (GT motif), a sugar response element-like motif, and a G-box-related sequence, and also identified several putative anaerobic response elements. Finally, quantitative real-time polymerase chain reactions using 29 selected genes independently verified the microarray results. This study represents one of the most comprehensive analyses conducted to date investigating hypoxia-responsive transcriptional networks in plants. PMID:15734912
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Genome wide analysis of stress responsive WRKY transcription factors in Arabidopsis thaliana
Directory of Open Access Journals (Sweden)
Shaiq Sultan
2016-04-01
Full Text Available WRKY transcription factors are a class of DNA-binding proteins that bind with a specific sequence C/TTGACT/C known as W-Box found in promoters of genes which are regulated by these WRKYs. From previous studies, 43 different stress responsive WRKY transcription factors in Arabidopsis thaliana, identified and then categorized in three groups viz., abiotic, biotic and both of these stresses. A comprehensive genome wide analysis including chromosomal localization, gene structure analysis, multiple sequence alignment, phylogenetic analysis and promoter analysis of these WRKY genes was carried out in this study to determine the functional homology in Arabidopsis. This analysis led to the classification of these WRKY family members into 3 major groups and subgroups and showed evolutionary relationship among these groups on the base of their functional WRKY domain, chromosomal localization and intron/exon structure. The proposed groups of these stress responsive WRKY genes and annotation based on their position on chromosomes can also be explored to determine their functional homology in other plant species in relation to different stresses. The result of the present study provides indispensable genomic information for the stress responsive WRKY transcription factors in Arabidopsis and will pave the way to explain the precise role of various AtWRKYs in plant growth and development under stressed conditions.
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New Insights into the Diels-Alder Reaction of Graphene Oxide.
Brisebois, Patrick P; Kuss, Christian; Schougaard, Steen B; Izquierdo, Ricardo; Siaj, Mohamed
2016-04-18
Graphene oxide is regarded as a major precursor for graphene-based materials. The development of graphene oxide based derivatives with new functionalities requires a thorough understanding of its chemical reactivity, especially for canonical synthetic methods such as the Diels-Alder cycloaddition. The Diels-Alder reaction has been successfully extended with graphene oxide as a source of diene by using maleic anhydride as a dienophile, thereby outlining the presence of the cis diene present in the graphene oxide framework. This reaction provides fundamental information for understanding the exact structure and chemical nature of graphene oxide. On the basis of high-resolution (13) C-SS NMR spectra, we show evidence for the formation of new sp(3) carbon centers covalently bonded to graphene oxide following hydrolysis of the reaction product. DFT calculations are also used to show that the presence of a cis dihydroxyl and C vacancy on the surface of graphene oxide are promoting the reaction with significant negative reaction enthalpies. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Diel Variations in Optical Properties of Micromonas pusilla, a Prasinophyte
DuRand, Michele D.; Green, Rebecca E.; Sosik, Heidi M.; Olson, Robert J.
2001-01-01
A laboratory experiment was conducted on cultures of Micromonas pusilla, a marine prasinophyte, to investigate how cell growth and division affect the optical properties over the light:dark cycle. Measurements were made of cell size and concentration, attenuation and absorption coefficients, flow cytometric light scattering (in forward and side directions), chlorophyll and carbon content. Refractive index was calculated using the anomalous diffraction approximation Cells were about 1.5 micrometers in diameter and exhibited phased division, with the major division burst occurring during the night. Typical diel variations were observed, with cells increasing in size and light scattering during the day as they photosynthesize and decreasing at night upon division. The cells were in ultradian growth, with more than one division per day, at a light level of 120 Mu-mol photons m/sq/sec. Since these cells are similar in size to small phytoplankton that are typically abundant in field samples, these results can be used in the interpretation of diel variations in light scattering in natural populations of phytoplankton.
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Functional analysis of jasmonate-responsive transcription factors in Arabidopsis thaliana
Zarei, Adel
2007-01-01
The aim of the studies described in this thesis was the functional analysis of JA-responsive transcription factors in Arabidopsis with an emphasis on the interaction with the promoters of their target genes. In short, the following new results were obtained. The promoter of the PDF1.2 gene contains
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Kuang, Jian-Fei; Chen, Jian-Ye; Liu, Xun-Cheng; Han, Yan-Chao; Xiao, Yun-Yi; Shan, Wei; Tang, Yang; Wu, Ke-Qiang; He, Jun-Xian; Lu, Wang-Jin
2017-04-01
Fruit ripening is a complex, genetically programmed process involving the action of critical transcription factors (TFs). Despite the established significance of dehydration-responsive element binding (DREB) TFs in plant abiotic stress responses, the involvement of DREBs in fruit ripening is yet to be determined. Here, we identified four genes encoding ripening-regulated DREB TFs in banana (Musa acuminata), MaDREB1, MaDREB2, MaDREB3, and MaDREB4, and demonstrated that they play regulatory roles in fruit ripening. We showed that MaDREB1-MaDREB4 are nucleus-localized, induced by ethylene and encompass transcriptional activation activities. We performed a genome-wide chromatin immunoprecipitation and high-throughput sequencing (ChIP-Seq) experiment for MaDREB2 and identified 697 genomic regions as potential targets of MaDREB2. MaDREB2 binds to hundreds of loci with diverse functions and its binding sites are distributed in the promoter regions proximal to the transcriptional start site (TSS). Most of the MaDREB2-binding targets contain the conserved (A/G)CC(G/C)AC motif and MaDREB2 appears to directly regulate the expression of a number of genes involved in fruit ripening. In combination with transcriptome profiling (RNA sequencing) data, our results indicate that MaDREB2 may serve as both transcriptional activator and repressor during banana fruit ripening. In conclusion, our study suggests a hierarchical regulatory model of fruit ripening in banana and that the MaDREB TFs may act as transcriptional regulators in the regulatory network. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.
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Transcriptional responses of Arabidopsis thaliana plants to As (V stress
Directory of Open Access Journals (Sweden)
Yuan Joshua S
2008-08-01
Full Text Available Abstract Background Arsenic is toxic to plants and a common environmental pollutant. There is a strong chemical similarity between arsenate [As (V] and phosphate (Pi. Whole genome oligonucleotide microarrays were employed to investigate the transcriptional responses of Arabidopsis thaliana plants to As (V stress. Results Antioxidant-related genes (i.e. coding for superoxide dismutases and peroxidases play prominent roles in response to arsenate. The microarray experiment revealed induction of chloroplast Cu/Zn superoxide dismutase (SOD (at2g28190, Cu/Zn SOD (at1g08830, as well as an SOD copper chaperone (at1g12520. On the other hand, Fe SODs were strongly repressed in response to As (V stress. Non-parametric rank product statistics were used to detect differentially expressed genes. Arsenate stress resulted in the repression of numerous genes known to be induced by phosphate starvation. These observations were confirmed with qRT-PCR and SOD activity assays. Conclusion Microarray data suggest that As (V induces genes involved in response to oxidative stress and represses transcription of genes induced by phosphate starvation. This study implicates As (V as a phosphate mimic in the cell by repressing genes normally induced when available phosphate is scarce. Most importantly, these data reveal that arsenate stress affects the expression of several genes with little or unknown biological functions, thereby providing new putative gene targets for future research.
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Discriminative identification of transcriptional responses of promoters and enhancers after stimulus
Kleftogiannis, Dimitrios A.; Kalnis, Panos; Arner, Erik; Bajic, Vladimir B.
2016-01-01
factors and co-activators. A case study on data from MCF-7 cell-line reveals that PEDAL can identify successfully the transcription response subclasses of promoters and enhancers from two different stimulations. Moreover, we report subsets of input markers
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Diel changes in water chemistry in an arsenic-rich stream and treatment-pond system
Gammons, C.H.; Grant, T.M.; Nimick, D.A.; Parker, S.R.; DeGrandpre, M.D.
2007-01-01
Arsenic concentrations are elevated in surface waters of the Warm Springs Ponds Operable Unit (WSPOU), located at the head of the upper Clark Fork River Superfund site, Montana, USA. Arsenic is derived from historical deposition of smelter emissions (Mill and Willow Creeks) and historical mining and milling wastes (Silver Bow Creek). Although long-term monitoring has characterized the general seasonal and flow-related trends in As concentrations in these streams and the pond system used to treat Silver Bow Creek water, little is known about solubility controls and sorption processes that influence diel cycles in As concentrations. Diel (24-h) sampling was conducted in July 2004 and August 2005 at the outlet of the treatment ponds, at two locations along a nearby reconstructed stream channel that diverts tributary water around the ponds, and at Silver Bow Creek 2??km below the ponds. Dissolved As concentration increased up to 51% during the day at most of the stream sites, whereas little or no diel change was displayed at the treatment-pond outlet. The strong cycle in streams is explained by pH- and temperature-dependent sorption of As onto hydrous metal oxides or biofilms on the streambed. Concentrations of dissolved Ca2+ and HCO3- at the stream sites showed a diel temporal pattern opposite to that of As, and geochemical modeling supports the hypothesis that the concentrations of Ca2+ and HCO3- were controlled by precipitation of calcite during the warm afternoon hours when pH rose above 9.0. Nightly increases in dissolved Mn and Fe(II) concentrations were out of phase with concentrations of other divalent cations and are more likely explained by redox phenomena. ?? 2007 Elsevier B.V. All rights reserved.
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Diels-Alder cycloaddition strategy for kinetic resolution of chiral pyrazolidinones.
Sibi, Mukund P; Kawashima, Keisuke; Stanley, Levi M
2009-09-03
A rare example of the application of a catalytic, enantioselective Diels-Alder cycloaddition to affect a kinetic resolution has been developed. Chiral pyrazolidinones are resolved with high selectivity through a process that utilizes a relay of stereochemical information from a permanent chiral center to a fluxional chiral center to enhance the inherent selectivity of the chiral Lewis acid catalyst.
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Cooperative binding of transcription factors promotes bimodal gene expression response.
Directory of Open Access Journals (Sweden)
Pablo S Gutierrez
Full Text Available In the present work we extend and analyze the scope of our recently proposed stochastic model for transcriptional regulation, which considers an arbitrarily complex cis-regulatory system using only elementary reactions. Previously, we determined the role of cooperativity on the intrinsic fluctuations of gene expression for activating transcriptional switches, by means of master equation formalism and computer simulation. This model allowed us to distinguish between two cooperative binding mechanisms and, even though the mean expression levels were not affected differently by the acting mechanism, we showed that the associated fluctuations were different. In the present generalized model we include other regulatory functions in addition to those associated to an activator switch. Namely, we introduce repressive regulatory functions and two theoretical mechanisms that account for the biphasic response that some cis-regulatory systems show to the transcription factor concentration. We have also extended our previous master equation formalism in order to include protein production by stochastic translation of mRNA. Furthermore, we examine the graded/binary scenarios in the context of the interaction energy between transcription factors. In this sense, this is the first report to show that the cooperative binding of transcription factors to DNA promotes the "all-or-none" phenomenon observed in eukaryotic systems. In addition, we confirm that gene expression fluctuation levels associated with one of two cooperative binding mechanism never exceed the fluctuation levels of the other.
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Weiss, Julia; Terry, Marta I; Martos-Fuentes, Marina; Letourneux, Lisa; Ruiz-Hernández, Victoria; Fernández, Juan A; Egea-Cortines, Marcos
2018-02-14
Cowpea (Vigna unguiculata) is an important source of protein supply for animal and human nutrition. The major storage globulins VICILIN and LEGUMIN (LEG) are synthesized from several genes including LEGA, LEGB, LEGJ and CVC (CONVICILIN). The current hypothesis is that the plant circadian core clock genes are conserved in a wide array of species and that primary metabolism is to a large extent controlled by the plant circadian clock. Our aim was to investigate a possible link between gene expression of storage proteins and the circadian clock. We identified cowpea orthologues of the core clock genes VunLHY, VunTOC1, VunGI and VunELF3, the protein storage genes VunLEG, VunLEGJ, and VunCVC as well as nine candidate reference genes used in RT-PCR. ELONGATION FACTOR 1-A (ELF1A) resulted the most suitable reference gene. The clock genes VunELF3, VunGI, VunTOC1 and VunLHY showed a rhythmic expression profile in leaves with a typical evening/night and morning/midday phased expression. The diel patterns were not completely robust and only VungGI and VungELF3 retained a rhythmic pattern under free running conditions of darkness. Under field conditions, rhythmicity and phasing apparently faded during early pod and seed development and was regained in ripening pods for VunTOC1 and VunLHY. Mature seeds showed a rhythmic expression of VunGI resembling leaf tissue under controlled growth chamber conditions. Comparing time windows during developmental stages we found that VunCVC and VunLEG were significantly down regulated during the night in mature pods as compared to intermediate ripe pods, while changes in seeds were non-significant due to high variance. The rhythmic expression under field conditions was lost under growth chamber conditions. The core clock gene network is conserved in cowpea leaves showing a robust diel expression pattern except VunELF3 under growth chamber conditions. There appears to be a clock transcriptional reprogramming in pods and seeds compared to
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Metal-catalyzed Asymmetric Hetero-Diels-Alder Reactions of Unactivated Dienes with Glyoxylates
DEFF Research Database (Denmark)
Johannsen, Mogens; Yao, Sulan; Graven, Anette
1998-01-01
The development of a catalytic asymmetric hetero-Diels-Alder methodology for the reaction of unactivated dienes with glyoxylates is presented. Several different asymmetric catalysts can be used, but copper-bisoxazolines and aluminium-BINOL give the highest yield, and the best chemo...
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Synthesis of 3-Alkenyl-1-azaanthraquinones via Diels-Alder and Electron Transfer Reactions
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Patrice Vanelle
2002-12-01
Full Text Available A convenient route to 3-alkenyl-1-azaanthraquinones via a hetero Diels-Alder reaction between an azadiene and naphthoquinone, a free radical chlorination and an electron transfer reaction is reported.
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Palmer, David R. J.
2004-01-01
The Diels-Alder reaction is used as an example for showing the integration of computational and preparative techniques, which help in demonstrating the physical organic concepts in synthetic organic chemistry. These experiments show that the students should not accept the computational results without questioning them and in many Diels-Alder…
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WRKY transcription factors in plant responses to stresses.
Jiang, Jingjing; Ma, Shenghui; Ye, Nenghui; Jiang, Ming; Cao, Jiashu; Zhang, Jianhua
2017-02-01
The WRKY gene family is among the largest families of transcription factors (TFs) in higher plants. By regulating the plant hormone signal transduction pathway, these TFs play critical roles in some plant processes in response to biotic and abiotic stress. Various bodies of research have demonstrated the important biological functions of WRKY TFs in plant response to different kinds of biotic and abiotic stresses and working mechanisms. However, very little summarization has been done to review their research progress. Not just important TFs function in plant response to biotic and abiotic stresses, WRKY also participates in carbohydrate synthesis, senescence, development, and secondary metabolites synthesis. WRKY proteins can bind to W-box (TGACC (A/T)) in the promoter of its target genes and activate or repress the expression of downstream genes to regulate their stress response. Moreover, WRKY proteins can interact with other TFs to regulate plant defensive responses. In the present review, we focus on the structural characteristics of WRKY TFs and the research progress on their functions in plant responses to a variety of stresses. © 2016 Institute of Botany, Chinese Academy of Sciences.
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Nimick, D.A.; Harper, D.D.; Farag, A.M.; Cleasby, T.E.; MacConnell, Elizabeth; Skaar, D.
2007-01-01
Extrapolating results of laboratory bioassays to streams is difficult, because conditions such as temperature and dissolved metal concentrations can change substantially on diel time scales. Field bioassays conducted for 96 h in two mining-affected streams compared the survival of hatchery-raised, metal-nai??ve westslope cutthroat trout (Oncorhynchus clarki lewisi) exposed to dissolved (0.1-??m filtration) metal concentrations that either exhibited the diel variation observed in streams or were controlled at a constant value. Cadmium and Zn concentrations in these streams increased each night by as much as 61 and 125%, respectively, and decreased a corresponding amount the next day, whereas Cu did not display a diel concentration cycle. In High Ore Creek (40 km south of Helena, MT, USA), survival (33%) after exposure to natural diel-fluctuating Zn concentrations (range, 214-634 ??g/L; mean, 428 ??g/L) was significantly (p = 0.008) higher than survival (14%) after exposure to a controlled, constant Zn concentration (422 ??g/L). Similarly, in Dry Fork Belt Creek (70 km southeast of Great Falls, MT, USA), survival (75%) after exposure to diel-fluctuating Zn concentrations (range, 266-522 ??g/L; mean, 399 ??g/L) was significantly (p = 0.022) higher than survival (50%) in the constant-concentration treatment (392 ??g/L). Survival likely was greater in these diel treatments, both because the periods of lower metal concentrations provided some relief for the fish and because toxicity during periods of higher metal concentrations was lessened by the simultaneous occurrence each night of lower water temperatures, which reduce the rate of metal uptake. Based on the present study, current water-quality criteria appear to be protective for streams with diel concentration cycles of Zn (and, perhaps, Cd) for the hydrologie conditions tested. ?? 2007 SETAC.
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Directory of Open Access Journals (Sweden)
Cicolani Bruno
2011-04-01
Full Text Available Abstract Background Although most freshwater planarias are well known photonegative organisms, their diel rhythms have never been quantified. Differences in daily activity rhythms may be particularly important for temperate-climate, freshwater planarias, which tend to overlap considerably in spatial distribution and trophic requirements. Methods Activity of stress-free, individually tested young adults of three common planarian species was recorded at 3-h intervals in a 10-d experiment under natural sunlight and photoperiod during autumnal equinox (D:L ~12:12. Individual activity status was averaged over the 10-d experiment, each tested individual thus serving as a true replicate. Twelve individuals per species were tested. Food was provided every 36 h, resulting in alternating day- and nighttime feeding events. Activity during the first post-feeding h was recorded and analyzed separately. Statistical procedures included ANOVAs, correlations, and second-order analyses of angles. Results Dugesia (= Girardia tigrina Girard 1850 exhibited clear nocturnal behavior, Dugesia (= Schmidtea polychroa Schmidt 1861 was predominantly but not exclusively nocturnal, and Polycelis tenuis Ijima 1884 was relatively more active from midnight through noon. Species-specific activity peaks were statistically similar, with peaks at dawn for P. tenuis and just before midnight for the two dugesiids; however, D. tigrina was comparatively more active in the early night hours, while D. polychroa was more active than D. tigrina during daytime. D. tigrina also responded less readily to daytime food addition. P. tenuis remained poorly active and unresponsive throughout the experiment. Individual variability in diel behavior was highest for D. polychroa and lowest for D. tigrina. P. tenuis's general low degree of activity and late activity peak in the experiment may be related to a strong reliance on external stimuli. Conclusions The tested species are mainly nocturnal
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Directory of Open Access Journals (Sweden)
Felicia Megumi Ito
2009-09-01
Full Text Available The present study aimed to evaluate the ability for biotransformation of the Diels-Alder adduct tricyclo[6.2.1.0(2,7]undeca-4,9-dien-3,6-dione (1 and two synthetic derivatives by the saprobe fungus Mucor ramosissimus Samutsevitsch. Products from oxidation, isomerization and, regioselective and enantioselective reduction were achieved.Neste trabalho avaliou-se a capacidade de biotransformação do aduto de Diels-Alder triciclo[6.2.1.0(2-7]undeca-4,9-dien-3,6-diona (1 e dois derivados sintéticos pelo fungo sapróbio Mucor ramosissimus Samutsevitsch. Produtos de oxidação, isomerização e redução regiosseletiva e enantiosseletiva foram obtidos.
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Benton, Michael G; Somasundaram, Swetha; Glasner, Jeremy D; Palecek, Sean P
2006-12-01
One of the most crucial tasks for a cell to ensure its long term survival is preserving the integrity of its genetic heritage via maintenance of DNA structure and sequence. While the DNA damage response in the yeast Saccharomyces cerevisiae, a model eukaryotic organism, has been extensively studied, much remains to be elucidated about how the organism senses and responds to different types and doses of DNA damage. We have measured the global transcriptional response of S. cerevisiae to multiple doses of two representative DNA damaging agents, methyl methanesulfonate (MMS) and gamma radiation. Hierarchical clustering of genes with a statistically significant change in transcription illustrated the differences in the cellular responses to MMS and gamma radiation. Overall, MMS produced a larger transcriptional response than gamma radiation, and many of the genes modulated in response to MMS are involved in protein and translational regulation. Several clusters of coregulated genes whose responses varied with DNA damaging agent dose were identified. Perhaps the most interesting cluster contained four genes exhibiting biphasic induction in response to MMS dose. All of the genes (DUN1, RNR2, RNR4, and HUG1) are involved in the Mec1p kinase pathway known to respond to MMS, presumably due to stalled DNA replication forks. The biphasic responses of these genes suggest that the pathway is induced at lower levels as MMS dose increases. The genes in this cluster with a threefold or greater transcriptional response to gamma radiation all showed an increased induction with increasing gamma radiation dosage. Analyzing genome-wide transcriptional changes to multiple doses of external stresses enabled the identification of cellular responses that are modulated by magnitude of the stress, providing insights into how a cell deals with genotoxicity.
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Directory of Open Access Journals (Sweden)
Glasner Jeremy D
2006-12-01
Full Text Available Abstract Background One of the most crucial tasks for a cell to ensure its long term survival is preserving the integrity of its genetic heritage via maintenance of DNA structure and sequence. While the DNA damage response in the yeast Saccharomyces cerevisiae, a model eukaryotic organism, has been extensively studied, much remains to be elucidated about how the organism senses and responds to different types and doses of DNA damage. We have measured the global transcriptional response of S. cerevisiae to multiple doses of two representative DNA damaging agents, methyl methanesulfonate (MMS and gamma radiation. Results Hierarchical clustering of genes with a statistically significant change in transcription illustrated the differences in the cellular responses to MMS and gamma radiation. Overall, MMS produced a larger transcriptional response than gamma radiation, and many of the genes modulated in response to MMS are involved in protein and translational regulation. Several clusters of coregulated genes whose responses varied with DNA damaging agent dose were identified. Perhaps the most interesting cluster contained four genes exhibiting biphasic induction in response to MMS dose. All of the genes (DUN1, RNR2, RNR4, and HUG1 are involved in the Mec1p kinase pathway known to respond to MMS, presumably due to stalled DNA replication forks. The biphasic responses of these genes suggest that the pathway is induced at lower levels as MMS dose increases. The genes in this cluster with a threefold or greater transcriptional response to gamma radiation all showed an increased induction with increasing gamma radiation dosage. Conclusion Analyzing genome-wide transcriptional changes to multiple doses of external stresses enabled the identification of cellular responses that are modulated by magnitude of the stress, providing insights into how a cell deals with genotoxicity.
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Kirby, Tyler J; Patel, Rooshil M; McClintock, Timothy S; Dupont-Versteegden, Esther E; Peterson, Charlotte A; McCarthy, John J
2016-03-01
Myofibers increase size and DNA content in response to a hypertrophic stimulus, thus providing a physiological model with which to study how these factors affect global transcription. Using 5-ethynyl uridine (EU) to metabolically label nascent RNA, we measured a sevenfold increase in myofiber transcription during early hypertrophy before a change in cell size and DNA content. The typical increase in myofiber DNA content observed at the later stage of hypertrophy was associated with a significant decrease in the percentage of EU-positive myonuclei; however, when DNA content was held constant by preventing myonuclear accretion via satellite cell depletion, both the number of transcriptionally active myonuclei and the amount of RNA generated by each myonucleus increased. During late hypertrophy, transcription did not scale with cell size, as smaller myofibers (transcriptional activity. Finally, transcription was primarily responsible for changes in the expression of genes known to regulate myofiber size. These findings show that resident myonuclei possess a significant reserve capacity to up-regulate transcription during hypertrophy and that myofiber transcription is responsive to DNA content but uncoupled from cell size during hypertrophy. © 2016 Kirby et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).
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Arumugam, Selvanathan; Orski, Sara V; Locklin, Jason; Popik, Vladimir V
2012-01-11
Reactive polymer brushes grown on silicon oxide surfaces were derivatized with photoreactive 3-(hydroxymethyl)naphthalene-2-ol (NQMP) moieties. Upon 300 or 350 nm irradiation, NQMP efficiently produces o-naphthoquinone methide (oNQM), which in turn undergoes very rapid Diels-Alder addition to vinyl ether groups attached to a substrate, resulting in the covalent immobilization of the latter. Any unreacted oNQM groups rapidly add water to regenerate NQMP. High-resolution surface patterning is achieved by irradiating NQMP-derivatized surfaces using photolithographic methods. The Diels-Alder photoclick reaction is orthogonal to azide-alkyne click chemistry, enabling sequential photoclick/azide-click derivatizations to generate complex surface functionalities. © 2011 American Chemical Society
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Pessanha, André Luiz Machado; Araújo, Francisco Gerson
2003-08-01
Fish assemblages from two beaches, one in the inner and the other in the outer Sepetiba Bay (latitude: 22°54'-23°04'S; longitude: 43°34'-44°10'W), Southeast Brazil, were sampled by beach seine net, simultaneously, on both seasonal and diel scales, between August 1998 and June 1999. Sites were selected to encompass different environmental conditions which reflect the two bay zones, thus providing a comprehensive assessment of the factors influencing surf zone fish assemblages, and their spatial, seasonal and diel variations. A total of 55 fish species was recorded, mostly young-of-the-year. Anchoa tricolor, Micropogonias furnieri, Gerres aprion, Diapterus rhombeus, Harengula clupeola, Atherinella brasiliensis and Mugil liza were numerically dominant and contributed to 95.2% of the total fish catches. Strong differences in fish assemblages were observed between the two areas, with higher number of species in the outer bay. Increases in fish numbers occurred in winter, while the highest biomass occurred in winter and summer. Transparency, followed by salinity, was responsible for most of the spatial variability and played an important role in structuring fish assemblages. Overall, diel patterns did not reveal any significant trends; however, if we consider each season separately, an increase in fish numbers during the day with peak at sunset was observed in winter, and a higher biomass occurred at night in winter and summer. Species preferences for various combinations of environmental variables are responsible for shifts in the structure and overall abundance of assemblages and dictated some patterns. The sciaenid M. furnieri, the second most abundant species, occurred only in the inner zone, being more abundant in winter. The species of Engraulidae were more abundant in the outer zone in winter/spring during the day. The gerreids G. aprion and D. rhombeus occurred mainly in summer. Overall, temporal fluctuations act more at a specific level than at a structural
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Pous, Jonathan; Courant, Thibaut; Bernadat, Guillaume; Iorga, Bogdan I; Blanchard, Florent; Masson, Géraldine
2015-09-23
Chiral phosphoric acid-catalyzed asymmetric nitroso-Diels-Alder reaction of nitrosoarenes with carbamate-dienes afforded cis-3,6-disubstituted dihydro-1,2-oxazines in high yields with excellent regio-, diastereo-, and enantioselectivities. Interestingly, we observed that the catalyst is able not only to control the enantioselectivity but also to reverse the regioselectivity of the noncatalyzed nitroso-Diels-Alder reaction. The regiochemistry reversal and asynchronous concerted mechanism were confirmed by DFT calculations.
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Tripathi, Prateek; Rabara, Roel C; Rushton, Paul J
2014-02-01
Drought is one of the major challenges affecting crop productivity and yield. However, water stress responses are notoriously multigenic and quantitative with strong environmental effects on phenotypes. It is also clear that water stress often does not occur alone under field conditions but rather in conjunction with other abiotic stresses such as high temperature and high light intensities. A multidisciplinary approach with successful integration of a whole range of -omics technologies will not only define the system, but also provide new gene targets for both transgenic approaches and marker-assisted selection. Transcription factors are major players in water stress signaling and some constitute major hubs in the signaling webs. The main transcription factors in this network include MYB, bHLH, bZIP, ERF, NAC, and WRKY transcription factors. The role of WRKY transcription factors in abiotic stress signaling networks is just becoming apparent and systems biology approaches are starting to define their places in the signaling network. Using systems biology approaches, there are now many transcriptomic analyses and promoter analyses that concern WRKY transcription factors. In addition, reports on nuclear proteomics have identified WRKY proteins that are up-regulated at the protein level by water stress. Interactomics has started to identify different classes of WRKY-interacting proteins. What are often lacking are connections between metabolomics, WRKY transcription factors, promoters, biosynthetic pathways, fluxes and downstream responses. As more levels of the system are characterized, a more detailed understanding of the roles of WRKY transcription factors in drought responses in crops will be obtained.
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Comportamiento dieléctrico de compuestos epoxi/aluminio/BaTiO3
Directory of Open Access Journals (Sweden)
Castro, M. S.
2009-06-01
Full Text Available In order to improve the dielectric behaviour of epoxi/BaTiO3, in this work the influence of micrometric aluminum metal flakes (Al, on the dielectric properties of epoxy / BaTiO3 composites was studied. Epoxy resin, Al and BaTiO3 were mixed using an ultrasonic mixer and composites were deposited onto glass substrates by dipping technique. Obtained materials presented good dielectric properties at room temperature, and relaxation process appeared due to the resin behaviour. Obtained results were compared with those reported in literature for similar systems.Con el objetivo de mejorar el comportamiento dieléctrico de los compuestos epoxi/BaTiO3, en este trabajo se estudió la influencia de partículas metálicas de aluminio (Al, con forma de escamas y tamaño micrométrico, sobre las propiedades dieléctricas de sistemas epoxi / BaTiO3. El material compuesto fue obtenido por la técnica de inmersión o “dipping”. La mezcla de los componentes fue llevado a cabo en mezclador ultrasónica y la deposición se realizó sobre sustratos de vidrio. Los materiales obtenidos presentaron buenas propiedades dieléctricas a temperatura ambiente, sin alcanzar el límite de percolación, y los fenómenos de relajación fueron generados por los dominios de la resina. Los valores obtenidos fueron comparados con los reportados en la bibliografía para sistemas similares.
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Sekita, Hiroko; Adachi, Kyohei; Kobayashi, Ippei; Sato, Yusuke; Nakada, Masahisa
2017-05-05
An enantio- and stereoselective construction of the atisane scaffold via organocatalytic intramolecular Michael reaction and Diels-Alder reaction is described. The organocatalytic intramolecular Michael reaction has been found to stereoselectively generate a trans-stereodiad comprising an all-carbon quaternary and a tertiary stereogenic centers. Use of the chiral secondary amine bearing thiourea with benzoic acid as additive is the key to obtaining the desired product with excellent ee in synthetically acceptable yield. The prepared chiral building block has been successfully converted to the compound including the atisane scaffold via the highly stereoselective intramolecular Diels-Alder reaction.
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A damage-responsive DNA binding protein regulates transcription of the yeast DNA repair gene PHR1
International Nuclear Information System (INIS)
Sebastian, J.; Sancar, G.B.
1991-01-01
The PHR1 gene of Saccharomyces cerevisiae encodes the DNA repair enzyme photolyase. Transcription of PHR1 increases in response to treatment of cells with 254-nm radiation and chemical agents that damage DNA. The authors here the identification of a damage-responsive DNA binding protein, termed photolyase regulatory protein (PRP), and its cognate binding site, termed the PHR1 transcription after DNA damage. PRP activity, monitored by electrophoretic-mobility-shift assay, was detected in cells during normal growth but disappeared within 30 min after irradiation. Copper-phenanthroline footprinting of PRP-DNA complexes revealed that PRP protects a 39-base-pair region of PHR1 5' flanking sequence beginning 40 base pairs upstream from the coding sequence. Thus these observations establish that PRP is a damage-responsive repressor of PHR1 transcription
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Transcriptional, proteomic, and metabolic responses to lithium in galactose-grown yeast cells
DEFF Research Database (Denmark)
Bro, Christoffer; Regenberg, Birgitte; Lagniel, G.
2003-01-01
Lithium is highly toxic to yeast when grown in galactose medium mainly because phosphoglucomutase, a key enzyme of galactose metabolism, is inhibited. We studied the global protein and gene expression profiles of Saccharomyces cerevisiae grown in galactose in different time intervals after addition...... of lithium. These results were related to physiological studies where both secreted and intracellular metabolites were determined. Microarray analysis showed that 664 open reading frames were down-regulated and 725 up-regulated in response to addition of lithium. Genes involved in transcription, translation......-regulated proteins were also identified as being changed on the mRNA level. Functional clusters obtained from proteome data were coincident with transcriptional clusters. Physiological studies showed that acetate, glycerol, and glycogen accumulate in response to lithium, as reflected in expression data, whereas...
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Caarls, Lotte; van der Does, Adriana; Hickman, Richard; Jansen, Wouter; van Verk, Marcel; Proietti, Silvia; Lorenzo, Oscar; Solano, Roberto; Pieterse, Corné M J; Van Wees, Saskia C M
2017-01-01
Salicylic acid (SA) and jasmonic acid (JA) cross-communicate in the plant immune signaling network to finely regulate induced defenses. In Arabidopsis, SA antagonizes many JA-responsive genes, partly by targeting the ETHYLENE RESPONSE FACTOR (ERF)-type transcriptional activator ORA59. Members of the
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Using chiral ionic liquid additives to enhance asymmetric induction in a Diels-Alder reaction.
Goodrich, P; Nimal Gunaratne, H Q; Hall, L; Wang, Y; Jin, L; Muldoon, M J; Ribeiro, A P C; Pombeiro, A J L; Pârvulescu, V I; Davey, P; Hardacre, C
2017-01-31
A bis-oxazoline ligand has been complexed using Cu(ii) and Zn(ii) trifluoromethanesulfonate and a range of chiral ionic liquid (CIL) additives based on natural products were used as a co-catalyst for a Diels-Alder reaction. The catalytic performance of these systems was compared for the asymmetric Diels-Alder reaction between N-acryloyloxazolidinone and cyclopentadiene with and without the presence of a CIL additive. In the absence of the CIL, both catalysts resulted in low enantioselectivities in conventional solvents and ionic liquids. However, whilst only a minor effect of the CIL was observed for the Cu based catalyst, in the case of the Zn based catalyst, significant enhancements in endo enantioselectivity of up to 50% were found on the addition of a CIL.
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Weng, Chia-Hao; Hsu, Day-Shin; Liao, Chun-Chen
2016-11-18
Total syntheses of ent-penicillones A (ent-1) and B (ent-2) from 3,5-dimethylcatechol (3) were accomplished in 10 and 9 synthetic steps, respectively. A carbohydrate-templated asymmetric intramolecular Diels-Alder reaction of a masked o-benzoquinone (MOB) 9 and an aqueous acid-catalyzed intramolecular aldol reaction are the key synthetic steps. In addition, the absolute configurations of the bicyclo[2.2.2]oct-5-en-2-one core obtained from the per-O-benzylated α-d-glucopyranosyl as a carbohydrate template in the intramolecular Diels-Alder reaction of MOBs were revised.
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Pfeifer, Johannes; Mielewczik, Michael; Friedli, Michael; Kirchgessner, Norbert; Walter, Achim
2018-01-01
Present-day high-resolution leaf growth measurements provide exciting insights into diel (24-h) leaf growth rhythms and their control by the circadian clock, which match photosynthesis with oscillating environmental conditions. However, these methods are based on measurements of leaf area or elongation and neglect diel changes of leaf thickness. In contrast, the influence of various environmental stress factors to which leaves are exposed to during growth on the final leaf thickness has been studied extensively. Yet, these studies cannot elucidate how variation in leaf area and thickness are simultaneously regulated and influenced on smaller time scales. Only few methods are available to measure the thickness of young, growing leaves non-destructively. Therefore, we evaluated X-ray computed tomography to simultaneously and non-invasively record diel changes and growth of leaf thickness and area. Using conventional imaging and X-ray computed tomography leaf area, thickness and volume growth of young soybean leaves were simultaneously and non-destructively monitored at three cardinal time points during night and day for a period of 80 h under non-stressful growth conditions. Reference thickness measurements on paperboards were in good agreement to CT measurements. Comparison of CT with leaf mass data further proved the consistency of our method. Exploratory analysis showed that measurements were accurate enough for recording and analyzing relative diel changes of leaf thickness, which were considerably different to those of leaf area. Relative growth rates of leaf area were consistently positive and highest during 'nights', while diel changes in thickness fluctuated more and were temporarily negative, particularly during 'evenings'. The method is suitable for non-invasive, accurate monitoring of diel variation in leaf volume. Moreover, our results indicate that diel rhythms of leaf area and thickness show some similarity but are not tightly coupled. These
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Jasmonate-responsive transcription factors regulating plant secondary metabolism.
Zhou, Meiliang; Memelink, Johan
2016-01-01
Plants produce a large variety of secondary metabolites including alkaloids, glucosinolates, terpenoids and phenylpropanoids. These compounds play key roles in plant-environment interactions and many of them have pharmacological activity in humans. Jasmonates (JAs) are plant hormones which induce biosynthesis of many secondary metabolites. JAs-responsive transcription factors (TFs) that regulate the JAs-induced accumulation of secondary metabolites belong to different families including AP2/ERF, bHLH, MYB and WRKY. Here, we give an overview of the types and functions of TFs that have been identified in JAs-induced secondary metabolite biosynthesis, and highlight their similarities and differences in regulating various biosynthetic pathways. We review major recent developments regarding JAs-responsive TFs mediating secondary metabolite biosynthesis, and provide suggestions for further studies. Copyright © 2016 Elsevier Inc. All rights reserved.
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Boersma, A.J.; Feringa, B.L.; Roelfes, G.
2007-01-01
alpha,beta-Unsaturated 2-acyl imidazoles are a novel and practical class of dienophiles for the DNA-based catalytic asymmetric Diels-Alder reaction in water. The Diels-Alder products are obtained with very high diastereoselectivities and enantioselectivities in the range of 83-98%. The catalytic
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Puglisi, Edoardo; Cahill, Matt J.; Lessard, Philip A.; Capri, Ettore; Sinskey, Anthony John; Archer, John A.C.; Boccazzi, Paolo
2010-01-01
the natural environment. Our results indicate that the transcriptional response of R. aetherivorans I24 to PCBs, in both medium and sediment, is primarily directed towards reducing oxidative stress, rather than catabolism. © 2010 Springer Science
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Genome wide transcriptional response of Saccharomyces cerevisiae to stress-induced perturbations
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Hilal eTaymaz-Nikerel
2016-02-01
Full Text Available Cells respond to environmental and/or genetic perturbations in order to survive and proliferate. Characterization of the changes after various stimuli at different -omics levels is crucial to comprehend the adaptation of cells to changing conditions. Genome wide quantification and analysis of transcript levels, the genes affected by perturbations, extends our understanding of cellular metabolism by pointing out the mechanisms that play role in sensing the stress caused by those perturbations and related signaling pathways, and in this way guides us to achieve endeavors such as rational engineering of cells or interpretation of disease mechanisms. Saccharomyces cerevisiae as a model system has been studied in response to different perturbations and corresponding transcriptional profiles were followed either statically or/and dynamically, short- and long- term. This review focuses on response of yeast cells to diverse stress inducing perturbations including nutritional changes, ionic stress, salt stress, oxidative stress, osmotic shock, as well as to genetic interventions such as deletion and over-expression of genes. It is aimed to conclude on common regulatory phenomena that allow yeast to organize its transcriptomic response after any perturbation under different external conditions.
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Misra, Rajesh Chandra; Maiti, Protiti; Chanotiya, Chandan Singh; Shanker, Karuna; Ghosh, Sumit
2014-01-01
Sweet basil (Ocimum basilicum) is well known for its diverse pharmacological properties and has been widely used in traditional medicine for the treatment of various ailments. Although a variety of secondary metabolites with potent biological activities are identified, our understanding of the biosynthetic pathways that produce them has remained largely incomplete. We studied transcriptional changes in sweet basil after methyl jasmonate (MeJA) treatment, which is considered an elicitor of secondary metabolites, and identified 388 candidate MeJA-responsive unique transcripts. Transcript analysis suggests that in addition to controlling its own biosynthesis and stress responses, MeJA up-regulates transcripts of the various secondary metabolic pathways, including terpenoids and phenylpropanoids/flavonoids. Furthermore, combined transcript and metabolite analysis revealed MeJA-induced biosynthesis of the medicinally important ursane-type and oleanane-type pentacyclic triterpenes. Two MeJA-responsive oxidosqualene cyclases (ObAS1 and ObAS2) that encode for 761- and 765-amino acid proteins, respectively, were identified and characterized. Functional expressions of ObAS1 and ObAS2 in Saccharomyces cerevisiae led to the production of β-amyrin and α-amyrin, the direct precursors of oleanane-type and ursane-type pentacyclic triterpenes, respectively. ObAS1 was identified as a β-amyrin synthase, whereas ObAS2 was a mixed amyrin synthase that produced both α-amyrin and β-amyrin but had a product preference for α-amyrin. Moreover, transcript and metabolite analysis shed light on the spatiotemporal regulation of pentacyclic triterpene biosynthesis in sweet basil. Taken together, these results will be helpful in elucidating the secondary metabolic pathways of sweet basil and developing metabolic engineering strategies for enhanced production of pentacyclic triterpenes. PMID:24367017
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Integrative modeling of transcriptional regulation in response to antirheumatic therapy
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Thiesen Hans-Juergen
2009-08-01
Full Text Available Abstract Background The investigation of gene regulatory networks is an important issue in molecular systems biology and significant progress has been made by combining different types of biological data. The purpose of this study was to characterize the transcriptional program induced by etanercept therapy in patients with rheumatoid arthritis (RA. Etanercept is known to reduce disease symptoms and progression in RA, but the underlying molecular mechanisms have not been fully elucidated. Results Using a DNA microarray dataset providing genome-wide expression profiles of 19 RA patients within the first week of therapy we identified significant transcriptional changes in 83 genes. Most of these genes are known to control the human body's immune response. A novel algorithm called TILAR was then applied to construct a linear network model of the genes' regulatory interactions. The inference method derives a model from the data based on the Least Angle Regression while incorporating DNA-binding site information. As a result we obtained a scale-free network that exhibits a self-regulating and highly parallel architecture, and reflects the pleiotropic immunological role of the therapeutic target TNF-alpha. Moreover, we could show that our integrative modeling strategy performs much better than algorithms using gene expression data alone. Conclusion We present TILAR, a method to deduce gene regulatory interactions from gene expression data by integrating information on transcription factor binding sites. The inferred network uncovers gene regulatory effects in response to etanercept and thus provides useful hypotheses about the drug's mechanisms of action.
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Mechanistic Insight into the Dehydro-Diels-Alder Reaction of Styrene-Ynes.
Kocsis, Laura S; Kagalwala, Husain N; Mutto, Sharlene; Godugu, Bhaskar; Bernhard, Stefan; Tantillo, Dean J; Brummond, Kay M
2015-12-04
The Diels-Alder reaction represents one of the most thoroughly studied and well-understood synthetic transformations for the assembly of six-membered rings. Although intramolecular dehydro-Diels-Alder (IMDDA) reactions have previously been employed for the preparation of naphthalene and dihydronaphthalene substrates, low yields and product mixtures have reduced the impact and scope of this reaction. Through the mechanistic studies described within, we have confirmed that the thermal IMDDA reaction of styrene-ynes produces a naphthalene product via loss of hydrogen gas from the initially formed cycloadduct, a tetraenyl intermediate. Alternatively, the dihydronaphthalene product is afforded from the same tetraenyl intermediate via a radical isomerization process. Moreover, we have identified conditions that can be used to achieve efficient, high-yielding, and selective IMDDA reactions of styrene-ynes to form either naphthalene or dihydronaphthalene products. The operational simplicity and retrosynthetic orthogonality of this method for the preparation of naphthalenes and dihydronaphthalenes makes this transformation appealing for the synthesis of medicinal and material targets. The mechanistic studies within may impact the development of other thermal transformations.
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The Hexadehydro-Diels-Alder Cycloisomerization Reaction Proceeds by a Stepwise Mechanism.
Wang, Tao; Niu, Dawen; Hoye, Thomas R
2016-06-29
We report here experiments showing that the hexadehydro-Diels-Alder (HDDA) cycloisomerization reaction proceeds in a stepwise manner-i.e., via a diradical intermediate. Judicious use of substituent effects was decisive. We prepared (i) a series of triyne HDDA substrates that differed only in the R group present on the remote terminus of the diynophilic alkyne and (ii) an analogous series of dienophilic alkynes (n-C7H15COC≡CR) for use in classical Diels-Alder (DA) reactions (with 1,3-cyclopentadiene). The R groups were CF3, CHO, COMe/Et, CO2Me, CONMe2/Et2, H, and 1-propynyl. The relative rates of both the HDDA cyclization reactions and the simple DA cycloadditions were measured. The reactivity trends revealed a dramatic difference in the behaviors of the CF3 (slowest HDDA and nearly fastest DA) and 1-propynyl (fastest HDDA and slowest DA) containing members of each series. These differences can be explained by invoking radical-stabilizing energies rather than electron-withdrawing effects as the dominating feature of the HDDA reaction.
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Willand, J.E.; McCravy, K.W.
2006-01-01
Diel activities of carabids (Coleoptera: Carabidae) associated with a coal mine remnant and surrounding soybean field were studied in west-central Illinois from June through October 2002. A total of 1,402 carabids, representing 29 species and 17 genera, were collected using pitfall traps. Poecilus chalcites (Say) demonstrated roughly equal diurnal and nocturnal activity in June, but greater diurnal activity thereafter. Pterostichus permundus (Say), Cyclotrachelus seximpressus (LeConte), Amara obesa (Say), and Scarites quadriceps Chaudoir showed significant nocturnal activity. Associations between habitat and diel activity were found for three species: P. chalcites associated with the remnant and edge habitats showed greater diurnal activity than those associated with the soybean field; C. seximpressus was most active diurnally in the remnant, and Harpalus pensylvanicus (DeGeer) showed the greatest nocturnal activity in the remnant and edge habitats. We found significant temporal and habitat-related variation in diel activity among carabid species inhabiting agricultural areas in west-central Illinois.
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Li, Hui; Li, Junjie; Ke, Wendong; Ge, Zhishen
2015-10-01
Near-infrared light (NIR) possesses great advantages for light-responsive controllable drug release, such as deep tissue penetration and low damage to healthy tissues. Herein, a NIR-responsive drug delivery system is developed based on a NIR dye, indocyanine green (ICG), and anticancer drug, doxorubicin (DOX)-loaded thermoresponsive block copolymer micelles, in which the drug release can be controlled via NIR irradiation. First, block copolymers, poly(oligo(ethylene glycol) methacrylate)-block-poly(furfuryl methacrylate) (POEGMA-b-PFMA), are synthesized by sequential reversible addition-fragmentation chain-transfer (RAFT) polymerization, followed by modification with N-octyl maleimide through Diels-Alder (DA) reaction to produce POEGMA-b-POMFMA. The self-assembly of POEGMA-b-POMFMA by nano-precipitation in aqueous solution affords the polymeric micelles which are used to simultaneously encapsulate ICG and DOX. Upon irradiation by NIR light (805 nm), the loaded DOX is released rapidly from the micelles due to partial retro DA reaction and local temperature increase-induced faster drug diffusion by the photothermal effect. Cytotoxicity evaluation and intracellular distribution observation demonstrate significant synergistic effects of NIR-triggered drug release, photothermal, and chemotherapy toward cancer cells under NIR irradiation. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Jouha, Jabrane; Buttard, Floris; Lorion, Magali; Berthonneau, Clément; Khouili, Mostafa; Hiebel, Marie-Aude; Guillaumet, Gérald; Brière, Jean-François; Suzenet, Franck
2017-09-15
A straightforward domino aza-Michael-inverse-electron-demand-hetero-Diels-Alder/retro-Diels-Alder reaction between primary and secondary propargylamine derivatives and 3-vinyl-1,2,4-triazines is developed highlighting not only the uniqueness of this dual-heterocyclic platform but also a novel and unprecedented path to polysubstituted tetrahydro-1,6-naphthyridine scaffolds.
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Directory of Open Access Journals (Sweden)
Bojan Tamburic
Full Text Available A matrix of photobioreactors integrated with metabolic sensors was used to examine the combined impact of light and temperature variations on the growth and physiology of the biofuel candidate microalgal species Nannochloropsis oculata. The experiments were performed with algal cultures maintained at a constant 20 °C versus a 15 °C to 25 °C diel temperature cycle, where light intensity also followed a diel cycle with a maximum irradiance of 1920 µmol photons m(-2 s(-1. No differences in algal growth (Chlorophyll a were found between the two environmental regimes; however, the metabolic processes responded differently throughout the day to the change in environmental conditions. The variable temperature treatment resulted in greater damage to photosystem II due to the combined effect of strong light and high temperature. Cellular functions responded differently to conditions before midday as opposed to the afternoon, leading to strong hysteresis in dissolved oxygen concentration, quantum yield of photosystem II and net photosynthesis. Overnight metabolism performed differently, probably as a result of the temperature impact on respiration. Our photobioreactor matrix has produced novel insights into the physiological response of Nannochloropsis oculata to simulated environmental conditions. This information can be used to predict the effectiveness of deploying Nannochloropsis oculata in similar field conditions for commercial biofuel production.
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Julio A. Alonso
2013-02-01
Full Text Available Density Functional Theory has been used to model the Diels-Alder reactions of the fullerene fragments triindenetriphenilene and pentacyclopentacorannulene with ethylene and 1,3-butadiene. The purpose is to prove the feasibility of using Diels-Alder cycloaddition reactions to grow fullerene fragments step by step, and to dimerize fullerene fragments, as a way to obtain C60. The dienophile character of the fullerene fragments is dominant, and the reaction of butadiene with pentacyclopentacorannulene is favored.
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Mancini, Pedro M. E.; Kneeteman, María N.; Cainelli, Mauro; Ormachea, Carla M.; Domingo, Luis R.
2017-11-01
The behaviors of N-tosylnitropyrroles acting as electrophilic dienophiles in polar Diels-Alder reactions joint to different dienes of increeased nucleophilicity are analyzed. The reactions were developed under microwave irradiation using toluene or protic ionic liquids (PILs) as solvents and in free solvent conditions. In all the cases explored we observed good yields in short reaction times. For these reactions, the free solvent condition and the use of protic ionic liquids as solvents offer similar results. However, the free solvent conditions favor environmental sustainability. The role of PILs in these polar Diels-Alder reactions has been theoretically studied within the Molecular Electron Density Theory.
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Sequential aminodiene Diels-Alder approach to the ergoline skeleton.
Padwa, Albert; Bur, Scott K; Zhang, Hongjun
2005-08-19
Through a novel sequence of aminodiene Diels-Alder reactions, several substituted amidofurans were readily converted to tricyclic ketones in good yield. The formation of the tricyclic ketone system is the result of a ring opening and dehydration of a transient oxabicyclic adduct formed by an intramolecular Diels-Alder cycloaddition of an amidofuran with a cyclohexenone moiety tethered such that it participates in the cycloaddition as the 2pi component. A convenient way to construct the cyclohexenone is to make use of some aminodiene chemistry developed by Rawal. An angular carbomethoxy group is required in order to activate the olefin toward cycloaddition with Rawal's diene. The presence of this activating group not only prevents the isomerization of the advanced ergoline intermediate to a naphthalene but can also be leveraged for an oxidation to provide Uhle's ketone (13). The easily formed Kornfeld ketone analogue 25 was readily transformed into the corresponding triflate 41 by the action of triflic anhydride and a base. Oxidative addition of vinyl triflate 41 to Pd(0) and the ability of the resulting vinyl palladium species to undergo cross-coupling with terminal alkynes prompted us to devise an expeditious route to lysergic acid. Unfortunately, our inability to carry out a regioselective Heck reaction using vinyl triflate 41 and the methylene amino acrylate ester 48 thwarted the completion of the synthesis of lysergic acid.
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Della Rosa, Claudia D.; Mancini, Pedro M. E.; Kneeteman, Maria N.; Lopez Baena, Anna F.; Suligoy, Melisa A.; Domingo, Luis R.
2015-01-01
The reactions between 2- and 3-nitrobenzothiophenes with three dienes of different nucleophilicity, 1-methoxy-3-trimethylsilyloxy-1,3-butadiene, 1-trimethylsilyloxy-1,3-butadiene and isoprene developed in anhydrous benzene and alternative under microwave irradiation with molecular solvents or in free solvent conditions, respectively, for produce dibenzothiophenes permit to conclude that both nitroheterocycles act as electrophile with the cited dienes. In the cases of the dienes 1-methoxy-3-trimethylsilyloxy-1,3-butadiene and 1-trimethylsilyloxy-1,3-butadiene which posses major nucleophilicity the observed product is the normal cycloaddition one. However when the diene is isoprene the product with both electrophiles follow the hetero Diels-Alder way. These reactions are considered polar cycloaddition reactions and the yields are reasonables. Moreover the polar Diels-Alder reactions of nitrobenzothiophenes with electron rich dienes 1-trimethylsilyloxy-1,3-butadiene have been theoretically studied using DFT methods.
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Wang, Cheng; Dong, Da; Strong, P J; Zhu, Weijing; Ma, Zhuang; Qin, Yong; Wu, Weixiang
2017-08-16
Animal manure is a reservoir of antibiotic resistance genes (ARGs) that pose a potential health risk globally, especially for resistance to the antibiotics commonly used in livestock production (such as tetracycline, sulfonamide, and fluoroquinolone). Currently, the effects of biological treatment (composting) on the transcriptional response of manure ARGs and their microbial hosts are not well characterized. Composting is a dynamic process that consists of four distinct phases that are distinguished by the temperature resulting from microbial activity, namely the mesophilic, thermophilic, cooling, and maturing phases. In this study, changes of resistome expression were determined and related to active microbiome profiles during the dynamic composting process. This was achieved by integrating metagenomic and time series metatranscriptomic data for the evolving microbial community during composting. Composting noticeably reduced the aggregated expression level of the manure resistome, which primarily consisted of genes encoding for tetracycline, vancomycin, fluoroquinolone, beta-lactam, and aminoglycoside resistance, as well as efflux pumps. Furthermore, a varied transcriptional response of resistome to composting at the ARG levels was highlighted. The expression of tetracycline resistance genes (tetM-tetW-tetO-tetS) decreased during composting, where distinctive shifts in the four phases of composting were related to variations in antibiotic concentration. Composting had no effect on the expression of sulfonamide and fluoroquinolone resistance genes, which increased slightly during the thermophilic phase and then decreased to initial levels. As indigenous populations switched greatly throughout the dynamic composting, the core resistome persisted and their reservoir hosts' composition was significantly correlated with dynamic active microbial phylogenetic structure. Hosts for sulfonamide and fuoroquinolone resistance genes changed notably in phylognetic structure
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Limited transcriptional responses of Rickettsia rickettsii exposed to environmental stimuli.
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Damon W Ellison
Full Text Available Rickettsiae are strict obligate intracellular pathogens that alternate between arthropod and mammalian hosts in a zoonotic cycle. Typically, pathogenic bacteria that cycle between environmental sources and mammalian hosts adapt to the respective environments by coordinately regulating gene expression such that genes essential for survival and virulence are expressed only upon infection of mammals. Temperature is a common environmental signal for upregulation of virulence gene expression although other factors may also play a role. We examined the transcriptional responses of Rickettsia rickettsii, the agent of Rocky Mountain spotted fever, to a variety of environmental signals expected to be encountered during its life cycle. R. rickettsii exposed to differences in growth temperature (25 degrees C vs. 37 degrees C, iron limitation, and host cell species displayed nominal changes in gene expression under any of these conditions with only 0, 5, or 7 genes, respectively, changing more than 3-fold in expression levels. R. rickettsii is not totally devoid of ability to respond to temperature shifts as cold shock (37 degrees C vs. 4 degrees C induced a change greater than 3-fold in up to 56 genes. Rickettsiae continuously occupy a relatively stable environment which is the cytosol of eukaryotic cells. Because of their obligate intracellular character, rickettsiae are believed to be undergoing reductive evolution to a minimal genome. We propose that their relatively constant environmental niche has led to a minimal requirement for R. rickettsii to respond to environmental changes with a consequent deletion of non-essential transcriptional response regulators. A minimal number of predicted transcriptional regulators in the R. rickettsii genome is consistent with this hypothesis.
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Pai, Chen-Chun; Kishkevich, Anastasiya; Deegan, Rachel S; Keszthelyi, Andrea; Folkes, Lisa; Kearsey, Stephen E; De León, Nagore; Soriano, Ignacio; de Bruin, Robertus Antonius Maria; Carr, Antony M; Humphrey, Timothy C
2017-09-12
Chromatin modification through histone H3 lysine 36 methylation by the SETD2 tumor suppressor plays a key role in maintaining genome stability. Here, we describe a role for Set2-dependent H3K36 methylation in facilitating DNA replication and the transcriptional responses to both replication stress and DNA damage through promoting MluI cell-cycle box (MCB) binding factor (MBF)-complex-dependent transcription in fission yeast. Set2 loss leads to reduced MBF-dependent ribonucleotide reductase (RNR) expression, reduced deoxyribonucleoside triphosphate (dNTP) synthesis, altered replication origin firing, and a checkpoint-dependent S-phase delay. Accordingly, prolonged S phase in the absence of Set2 is suppressed by increasing dNTP synthesis. Furthermore, H3K36 is di- and tri-methylated at these MBF gene promoters, and Set2 loss leads to reduced MBF binding and transcription in response to genotoxic stress. Together, these findings provide new insights into how H3K36 methylation facilitates DNA replication and promotes genotoxic stress responses in fission yeast. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.
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Directory of Open Access Journals (Sweden)
Chen-Chun Pai
2017-09-01
Full Text Available Chromatin modification through histone H3 lysine 36 methylation by the SETD2 tumor suppressor plays a key role in maintaining genome stability. Here, we describe a role for Set2-dependent H3K36 methylation in facilitating DNA replication and the transcriptional responses to both replication stress and DNA damage through promoting MluI cell-cycle box (MCB binding factor (MBF-complex-dependent transcription in fission yeast. Set2 loss leads to reduced MBF-dependent ribonucleotide reductase (RNR expression, reduced deoxyribonucleoside triphosphate (dNTP synthesis, altered replication origin firing, and a checkpoint-dependent S-phase delay. Accordingly, prolonged S phase in the absence of Set2 is suppressed by increasing dNTP synthesis. Furthermore, H3K36 is di- and tri-methylated at these MBF gene promoters, and Set2 loss leads to reduced MBF binding and transcription in response to genotoxic stress. Together, these findings provide new insights into how H3K36 methylation facilitates DNA replication and promotes genotoxic stress responses in fission yeast.
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Yu, Lu; Zhang, Wenliang; Wang, Lingling; Yang, Jian; Liu, Tao; Peng, Junping; Leng, Wenchuan; Chen, Lihong; Li, Ruoyu; Jin, Qi
2007-01-01
Trichophyton rubrum is a pathogenic filamentous fungus of increasing medical concern. Two antifungal agents, ketoconazole (KTC) and amphotericin B (AMB), have specific activity against dermatophytes. To identify the mechanisms of action of KTC and AMB against T. rubrum, a cDNA microarray was constructed from the expressed sequence tags of the cDNA library from different developmental stages, and transcriptional profiles of the responses to KTC and AMB were determined. T. rubrum was exposed to subinhibitory concentrations of KTC and AMB for 12 h, and microarray analysis was used to examine gene transcription. KTC exposure induced transcription of genes involved in lipid, fatty acid, and sterol metabolism, including ERG11, ERG3, ERG25, ERG6, ERG26, ERG24, ERG4, CPO, INO1, DW700960, CPR, DW696584, DW406350, and ATG15. KTC also increased transcription of the multidrug resistance gene ABC1. AMB exposure increased transcription of genes involved in lipid, fatty acid, and sterol metabolism (DW696584, EB801458, IVD, DW694010, DW688343, DW684992), membrane transport (Git1, DW706156, DW684040, DMT, DW406136, CCH1, DW710650), and stress-related responses (HSP70, HSP104, GSS, AOX, EB801455, EB801702, TDH1, UBI4) but reduced transcription of genes involved in maintenance of cell wall integrity and signal transduction pathways (FKS1, SUN4, DW699324, GAS1, DW681613, SPS1, DW703091, STE7, DW703091, DW695308) and some ribosomal proteins. This is the first report of the use of microarray analysis to determine the effects of drug action in T. rubrum. PMID:17060531
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Avramova, Zoya
2015-07-01
Drought, salinity, extreme temperature variations, pathogen and herbivory attacks are recurring environmental stresses experienced by plants throughout their life. To survive repeated stresses, plants provide responses that may be different from their response during the first encounter with the stress. A different response to a similar stress represents the concept of 'stress memory'. A coordinated reaction at the organismal, cellular and gene/genome levels is thought to increase survival chances by improving the plant's tolerance/avoidance abilities. Ultimately, stress memory may provide a mechanism for acclimation and adaptation. At the molecular level, the concept of stress memory indicates that the mechanisms responsible for memory-type transcription during repeated stresses are not based on repetitive activation of the same response pathways activated by the first stress. Some recent advances in the search for transcription 'memory factors' are discussed with an emphasis on super-induced dehydration stress memory response genes in Arabidopsis. © 2015 The Author The Plant Journal © 2015 John Wiley & Sons Ltd.
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Directory of Open Access Journals (Sweden)
Haghdadi Mina
2015-01-01
Full Text Available A DFT study of the reactivity, regio- and stereoselectivity of Diels-Alder reaction between 3-bromo, 5-bromo, and 3,5-dibromo-2(H-pyran-2-ones and some weakly activated and unactivated alkenes has been carried out using density functional theory (DFT. Four possible reaction channels, which are related to the formation of meta- and para- and endo- and exo-cycloadducts have been explored and characterized. The energy and natural bond orbital analysis shows that the meta-regioselectivity on the exo pathway is preferred and follows an asynchronous concerted mechanism with a polar nature in all Diels-Alder cycloadditions. Moreover, the activation free energies of Diels-Alder cycloadditions of 3,5-dibromo-2(H-pyran-2one are lower than 3- bromo-2(H-pyran-2one and 5-bromo-2(H-pyran-2one, which are in line with experimental observation. DFT-based reactivity indices clearly predict the regiochemistry of the isolated cycloadducts.
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Directory of Open Access Journals (Sweden)
Su Zhen
2011-07-01
Full Text Available Abstract Background Salt stress hinders the growth of plants and reduces crop production worldwide. However, different plant species might possess different adaptive mechanisms to mitigate salt stress. We conducted a detailed pathway analysis of transcriptional dynamics in the roots of Medicago truncatula seedlings under salt stress and selected a transcription factor gene, MtCBF4, for experimental validation. Results A microarray experiment was conducted using root samples collected 6, 24, and 48 h after application of 180 mM NaCl. Analysis of 11 statistically significant expression profiles revealed different behaviors between primary and secondary metabolism pathways in response to external stress. Secondary metabolism that helps to maintain osmotic balance was induced. One of the highly induced transcription factor genes was successfully cloned, and was named MtCBF4. Phylogenetic analysis revealed that MtCBF4, which belongs to the AP2-EREBP transcription factor family, is a novel member of the CBF transcription factor in M. truncatula. MtCBF4 is shown to be a nuclear-localized protein. Expression of MtCBF4 in M. truncatula was induced by most of the abiotic stresses, including salt, drought, cold, and abscisic acid, suggesting crosstalk between these abiotic stresses. Transgenic Arabidopsis over-expressing MtCBF4 enhanced tolerance to drought and salt stress, and activated expression of downstream genes that contain DRE elements. Over-expression of MtCBF4 in M. truncatula also enhanced salt tolerance and induced expression level of corresponding downstream genes. Conclusion Comprehensive transcriptomic analysis revealed complex mechanisms exist in plants in response to salt stress. The novel transcription factor gene MtCBF4 identified here played an important role in response to abiotic stresses, indicating that it might be a good candidate gene for genetic improvement to produce stress-tolerant plants.
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2011-01-01
Background Salt stress hinders the growth of plants and reduces crop production worldwide. However, different plant species might possess different adaptive mechanisms to mitigate salt stress. We conducted a detailed pathway analysis of transcriptional dynamics in the roots of Medicago truncatula seedlings under salt stress and selected a transcription factor gene, MtCBF4, for experimental validation. Results A microarray experiment was conducted using root samples collected 6, 24, and 48 h after application of 180 mM NaCl. Analysis of 11 statistically significant expression profiles revealed different behaviors between primary and secondary metabolism pathways in response to external stress. Secondary metabolism that helps to maintain osmotic balance was induced. One of the highly induced transcription factor genes was successfully cloned, and was named MtCBF4. Phylogenetic analysis revealed that MtCBF4, which belongs to the AP2-EREBP transcription factor family, is a novel member of the CBF transcription factor in M. truncatula. MtCBF4 is shown to be a nuclear-localized protein. Expression of MtCBF4 in M. truncatula was induced by most of the abiotic stresses, including salt, drought, cold, and abscisic acid, suggesting crosstalk between these abiotic stresses. Transgenic Arabidopsis over-expressing MtCBF4 enhanced tolerance to drought and salt stress, and activated expression of downstream genes that contain DRE elements. Over-expression of MtCBF4 in M. truncatula also enhanced salt tolerance and induced expression level of corresponding downstream genes. Conclusion Comprehensive transcriptomic analysis revealed complex mechanisms exist in plants in response to salt stress. The novel transcription factor gene MtCBF4 identified here played an important role in response to abiotic stresses, indicating that it might be a good candidate gene for genetic improvement to produce stress-tolerant plants. PMID:21718548
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Directory of Open Access Journals (Sweden)
Francesco Iorio
Full Text Available We present a novel strategy to identify drug-repositioning opportunities. The starting point of our method is the generation of a signature summarising the consensual transcriptional response of multiple human cell lines to a compound of interest (namely the seed compound. This signature can be derived from data in existing databases, such as the connectivity-map, and it is used at first instance to query a network interlinking all the connectivity-map compounds, based on the similarity of their transcriptional responses. This provides a drug neighbourhood, composed of compounds predicted to share some effects with the seed one. The original signature is then refined by systematically reducing its overlap with the transcriptional responses induced by drugs in this neighbourhood that are known to share a secondary effect with the seed compound. Finally, the drug network is queried again with the resulting refined signatures and the whole process is carried on for a number of iterations. Drugs in the final refined neighbourhood are then predicted to exert the principal mode of action of the seed compound. We illustrate our approach using paclitaxel (a microtubule stabilising agent as seed compound. Our method predicts that glipizide and splitomicin perturb microtubule function in human cells: a result that could not be obtained through standard signature matching methods. In agreement, we find that glipizide and splitomicin reduce interphase microtubule growth rates and transiently increase the percentage of mitotic cells-consistent with our prediction. Finally, we validated the refined signatures of paclitaxel response by mining a large drug screening dataset, showing that human cancer cell lines whose basal transcriptional profile is anti-correlated to them are significantly more sensitive to paclitaxel and docetaxel.
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International Nuclear Information System (INIS)
Piret, Jean-Pascal; Vankoningsloo, Sebastien; Noel, Florence; Saout, Christelle; Toussaint, Olivier; Mendoza, Jorge Mejia; Lucas, Stephane
2011-01-01
Poor information are currently available about the biological effects of multi-walled carbon nanotubes (MWCNT) on the liver. In this study, we evaluated the effects of MWCNT at the transcriptional level on the classical in vitro model of HepG2 hepatocarcinoma cells. The expression levels of 96 transcript species implicated in the inflammatory and immune responses was studied after a 24h incubation of HepG2 cells in presence of raw MWCNT dispersed in water by stirring. Among the 46 transcript species detected, only a few transcripts including mRNA coding for interleukine-7, chemokines receptor of the C-C families CCR7, as well as Endothelin-1, were statistically more abundant after treatment with MWCNT. Altogether, these data indicate that MWCNT can only induce a weak inflammatory response in HepG2 cells.
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Piret, Jean-Pascal; Vankoningsloo, Sébastien; Noël, Florence; Mejia Mendoza, Jorge; Lucas, Stéphane; Saout, Christelle; Toussaint, Olivier
2011-07-01
Poor information are currently available about the biological effects of multi-walled carbon nanotubes (MWCNT) on the liver. In this study, we evaluated the effects of MWCNT at the transcriptional level on the classical in vitro model of HepG2 hepatocarcinoma cells. The expression levels of 96 transcript species implicated in the inflammatory and immune responses was studied after a 24h incubation of HepG2 cells in presence of raw MWCNT dispersed in water by stirring. Among the 46 transcript species detected, only a few transcripts including mRNA coding for interleukine-7, chemokines receptor of the C-C families CCR7, as well as Endothelin-1, were statistically more abundant after treatment with MWCNT. Altogether, these data indicate that MWCNT can only induce a weak inflammatory response in HepG2 cells.
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Intramolecular and Transannular Diels-Alder Reactions
DEFF Research Database (Denmark)
Tanner, David Ackland; Ascic, Erhad
2014-01-01
Few reactions can compete with the Diels-Alder (DA) [4+2] cycloaddition for the rapid and efficient generation of molecular complexity. The DA reaction is atom-economic and stereospecific, as well as diastereo- and regioselective. The intramolecular version (IMDA) of the DA cycloaddition and its...... and dienophile, methods for acceleration of IMDA reactions (such as use of high pressure) and catalysis (using oxophilic or carbophilic metal complexes, Brønsted acids, and enzymes). The use of furans as diene components (IMDAF), intramolecular hetero-DA (IMHDA) and IMDA reactions with inverse electron demand...... are also covered. Applications of IMDA to asymmetric synthesis (from substrate control through to enantioselective catalysis, including organocatalysis) are presented, along with tandem sequences involving IMDA cycloaddition. A theme pervading the whole chapter is the use of IMDA reactions for the total...
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Diel infection of cyanobacteria by cyanophages
Directory of Open Access Journals (Sweden)
Tianchi eNi
2016-01-01
Full Text Available Cyanobacteria exhibit biological rhythms as an adaptation to the daily light-dark (diel cycle. Light is also crucial for bacteriophages (cyanophages that infect cyanobacteria. As the first step of infection, the adsorption of some cyanophages to their host cells is light-dependent. Moreover, cyanophage replication is affected by light intensity and possibly the host cell cycle. Photosynthesis and carbon metabolism genes have been found in cyanophage genomes. With these genes, cyanophages may affect the host metabolic rhythm. Field studies suggest that cyanophage infection of cyanobacteria in aquatic environments is synchronized directly or indirectly to the light-dark cycle. These discoveries are beginning to reveal how the daily light-dark cycle shapes the interaction of cyanophages and cyanobacteria, which eventually influences matter and energy transformation in aquatic environments.
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Diels-Alder reactions onto fluorinated and hydrogenated graphene
Denis, Pablo A.
2017-09-01
We studied Diels-Alder (DA) reactions onto functionalized graphene. When fluorine, hydrogen or oxygen functional groups are present on one side of the sheet, the DA cycloadditions become significantly more exergonic when performed on the opposite side. Hydrogen is more effective than fluorine and oxygen to promote these cycloadditions. In contrast with the results obtained for perfect graphene, the functionalization with H, F or O turns the DA reactions exergonic, with ΔG°298 = -127.2 kcal/mol. The reaction barriers are expected to be considerably lowered with respect to perfect graphene because the functional groups significantly reduce the distortion energy.
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Boswell, William T; Boswell, Mikki; Walter, Dylan J; Navarro, Kaela L; Chang, Jordan; Lu, Yuan; Savage, Markita G; Shen, Jianjun; Walter, Ronald B
2018-06-01
It has been reported that exposure to artificial light may affect oxygen intake, heart rate, absorption of vitamins and minerals, and behavioral responses in humans. We have reported specific gene expression responses in the skin of Xiphophorus fish after exposure to ultraviolet light (UV), as well as, both broad spectrum and narrow waveband visible light. In regard to fluorescent light (FL), we have shown that male X. maculatus exposed to 4100K FL (i.e. "cool white") rapidly suppress transcription of many genes involved with DNA replication and repair, chromosomal segregation, and cell cycle progression in skin. We have also detailed sex specific transcriptional responses of Xiphophorus skin after exposure to UVB. However, investigation of gender differences in global gene expression response after exposure to 4100K FL has not been reported, despite common use of this FL source for residential, commercial, and animal facility illumination. Here, we compare RNA-Seq results analyzed to assess changes in the global transcription profiles of female and male X. maculatus skin in response to 4100K FL exposure. Our results suggest 4100K FL exposure incites a sex-biased genetic response including up-modulation of inflammation in females and down modulation of DNA repair/replication in males. In addition, we identify clusters of genes that become oppositely modulated in males and females after FL exposure that are principally involved in cell death and cell proliferation. Copyright © 2017 Elsevier Inc. All rights reserved.
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Estimating dew formation in rice, using seasonally averaged diel patterns of weather variables
Luo, W.; Goudriaan, J.
2004-01-01
If dew formation cannot be measured it has to be estimated. Available simulation models for estimating dew formation require hourly weather data as input. However, such data are not available for places without an automatic weather station. In such cases the diel pattern of weather variables might
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Hadjichristidis, Nikolaos; Alkayal, Nazeeha
2015-01-01
A novel strategy towards well-defined polymethylene-based co/terpolymers, by combining anthracene/maleimide Diels-Alder reaction with polyhomologation, is presented. For the synthesis of diblock copolymers the following approach was applied: a
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Directory of Open Access Journals (Sweden)
Arainga Mariluz
2012-03-01
Full Text Available Abstract Background Bovine leukemia virus (BLV is associated with enzootic bovine leukosis and is closely related to human T-cell leukemia virus type I. The Tax protein of BLV is a transcriptional activator of viral replication and a key contributor to oncogenic potential. We previously identified interesting mutant forms of Tax with elevated (TaxD247G or reduced (TaxS240P transactivation effects on BLV replication and propagation. However, the effects of these mutations on functions other than transcriptional activation are unknown. In this study, to identify genes that play a role in the cascade of signal events regulated by wild-type and mutant Tax proteins, we used a large-scale host cell gene-profiling approach. Results Using a microarray containing approximately 18,400 human mRNA transcripts, we found several alterations after the expression of Tax proteins in genes involved in many cellular functions such as transcription, signal transduction, cell growth, apoptosis, stress response, and immune response, indicating that Tax protein has multiple biological effects on various cellular environments. We also found that TaxD247G strongly regulated more genes involved in transcription, signal transduction, and cell growth functions, contrary to TaxS240P, which regulated fewer genes. In addition, the expression of genes related to stress response significantly increased in the presence of TaxS240P as compared to wild-type Tax and TaxD247G. By contrast, the largest group of downregulated genes was related to immune response, and the majority of these genes belonged to the interferon family. However, no significant difference in the expression level of downregulated genes was observed among the Tax proteins. Finally, the expression of important cellular factors obtained from the human microarray results were validated at the RNA and protein levels by real-time quantitative reverse transcription-polymerase chain reaction and western blotting
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Kang, Byung Young; Lee, Ki-Hwan; Lee, Yong Sung; Hong, Il; Lee, Mi-Ock; Min, Daejin; Chang, Ihseop; Hwang, Jae Sung; Park, Jun Seong; Kim, Duck Hee
2008-01-01
Kaempferol is the major flavonol in green tea and exhibits many biomedically useful properties such as antioxidative, cytoprotective and anti-apoptotic activities. To elucidate its effects on the skin, we investigated the transcriptional profiles of kaempferol-treated HaCaT cells using cDNA microarray analysis and identified 147 transcripts that exhibited significant changes in expression. Of these, 18 were up-regulated and 129 were down-regulated. These transcripts were then classified into 12 categories according to their functional roles: cell adhesion/cytoskeleton, cell cycle, redox homeostasis, immune/defense responses, metabolism, protein biosynthesis/modification, intracellular transport, RNA processing, DNA modification/ replication, regulation of transcription, signal transduction and transport. We then analyzed the promoter sequences of differentially-regulated genes and identified over-represented regulatory sites and candidate transcription factors (TFs) for gene regulation by kaempferol. These included c-REL, SAP-1, Ahr-ARNT, Nrf-2, Elk-1, SPI-B, NF-κB and p65. In addition, we validated the microarray results and promoter analyses using conventional methods such as real-time PCR and ELISA-based transcription factor assay. Our microarray analysis has provided useful information for determining the genetic regulatory network affected by kaempferol, and this approach will be useful for elucidating gene-phytochemical interactions. PMID:18446059
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Origin of Exo/Endo Selectivity in the Intramolecular Diels-Alder Reaction
International Nuclear Information System (INIS)
Yan, Shihai; Ryu, Do Hyun; Lee, Jin Yong
2010-01-01
The stereoselectivity of the intramolecular Diels-Alder reactions of 1 and its derivatives were investigated by ab initio calculations. The stereoselectivity mainly originates from the steric repulsion and the orbital interactions. The additional s-cis and s-trans conformations by introducing the carbonyl group at the neighbor of diene or dienophile may change the stereoselectivity, hence this kind of substitution can be utilized for stereoselective asymmetric synthesis
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The CWI Pathway: Regulation of the Transcriptional Adaptive Response to Cell Wall Stress in Yeast
Directory of Open Access Journals (Sweden)
Ana Belén Sanz
2017-12-01
Full Text Available Fungi are surrounded by an essential structure, the cell wall, which not only confers cell shape but also protects cells from environmental stress. As a consequence, yeast cells growing under cell wall damage conditions elicit rescue mechanisms to provide maintenance of cellular integrity and fungal survival. Through transcriptional reprogramming, yeast modulate the expression of genes important for cell wall biogenesis and remodeling, metabolism and energy generation, morphogenesis, signal transduction and stress. The yeast cell wall integrity (CWI pathway, which is very well conserved in other fungi, is the key pathway for the regulation of this adaptive response. In this review, we summarize the current knowledge of the yeast transcriptional program elicited to counterbalance cell wall stress situations, the role of the CWI pathway in the regulation of this program and the importance of the transcriptional input received by other pathways. Modulation of this adaptive response through the CWI pathway by positive and negative transcriptional feedbacks is also discussed. Since all these regulatory mechanisms are well conserved in pathogenic fungi, improving our knowledge about them will have an impact in the developing of new antifungal therapies.
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Kay, R.T.; Groschen, G.E.; Cygan, G.; Dupre, David H.
2011-01-01
Diel variations in the concentrations of a number of constituents have the potential to substantially affect the appropriate sampling regimen in acidic streams. Samples taken once during the course of the day cannot adequately reflect diel variations in water quality and may result in an inaccurate understanding of biogeochemical processes, ecological conditions, and of the threat posed by the water to human health and the associated wildlife. Surface water and groundwater affected by acid drainage were sampled every 60 to 90. min over a 48-hour period at a former zinc smelter known as the Hegeler Zinc Superfund Site, near Hegeler, Illinois. Diel variations related to water quality in the aquifer were not observed in groundwater. Diel variations were observed in the temperature, pH, and concentration of dissolved oxygen, nitrite, barium, iron, lead, vanadium, and possibly uranium in surface water. Temperature, dissolved oxygen, nitrite, barium, lead, and uranium generally attained maximum values during the afternoon and minimum values during the night. Iron, vanadium, and pH generally attained minimum values during the afternoon and maximum values during the night. Concentrations of dissolved oxygen were affected by the intensity of photosynthetic activity and respiration, which are dependent upon insolation. Nitrite, an intermediary in many nitrogen reactions, may have been formed by the oxidation of ammonium by dissolved oxygen and converted to other nitrogen species as part of the decomposition of organic matter. The timing of the pH cycles was distinctly different from the cycles found in Midwestern alkaline streams and likely was the result of the photoreduction of Fe3+ to Fe 2+ and variations in the intensity of precipitation of hydrous ferric oxide minerals. Diel cycles of iron and vanadium also were primarily the result of variations in the intensity of precipitation of hydrous ferric oxide minerals. The diel variation in the concentrations of lead, uranium
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Stefańska, Karolina; Jędrzejewska, Hanna; Wierzbicki, Michał; Szumna, Agnieszka; Iwanek, Waldemar
2016-07-15
The Diels-Alder reaction enables introduction of new functionalities onto the resorcinarene skeleton with simultaneous generation of new stereogenic centers and expansion of the internal cavity. We present highly regio- and diastereoselective inverse electron demand oxa-Diels-Alder reactions of resorcinarene ortho-quinone methide with benzofuran and indene, each generating 12 new stereogenic centers. The mechanism and reasons for regioselectivity and diastereoselectivity were analyzed using theoretical calculations (NBO charges, Fukui functions, transition state energies, and thermodynamic stability of the products). Enantiomers were separated, and their configurations were determined by comparison of experimental and theoretical electronic circular dichroism spectra.
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Sleep is not just for the brain: transcriptional responses to sleep in peripheral tissues
2013-01-01
Background Many have assumed that the primary function of sleep is for the brain. We evaluated the molecular consequences of sleep and sleep deprivation outside the brain, in heart and lung. Using microarrays we compared gene expression in tissue from sleeping and sleep deprived mice euthanized at the same diurnal times. Results In each tissue, nearly two thousand genes demonstrated statistically significant differential expression as a function of sleep/wake behavioral state. To mitigate the influence of an artificial deprivation protocol, we identified a subset of these transcripts as specifically sleep-enhanced or sleep-repressed by requiring that their expression also change over the course of unperturbed sleep. 3% and 6% of the assayed transcripts showed “sleep specific” changes in the lung and heart respectively. Sleep specific transcripts in these tissues demonstrated highly significant overlap and shared temporal dynamics. Markers of cellular stress and the unfolded protein response were reduced during sleep in both tissues. These results mirror previous findings in brain. Sleep-enhanced pathways reflected the unique metabolic functions of each tissue. Transcripts related to carbohydrate and sulfur metabolic processes were enhanced by sleep in the lung, and collectively favor buffering from oxidative stress. DNA repair and protein metabolism annotations were significantly enriched among the sleep-enhanced transcripts in the heart. Our results also suggest that sleep may provide a Zeitgeber, or synchronizing cue, in the lung as a large cluster of transcripts demonstrated systematic changes in inter-animal variability as a function of both sleep duration and circadian time. Conclusion Our data support the notion that the molecular consequences of sleep/wake behavioral state extend beyond the brain to include peripheral tissues. Sleep state induces a highly overlapping response in both heart and lung. We conclude that sleep enhances organ specific
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Sleep is not just for the brain: transcriptional responses to sleep in peripheral tissues.
Anafi, Ron C; Pellegrino, Renata; Shockley, Keith R; Romer, Micah; Tufik, Sergio; Pack, Allan I
2013-05-30
Many have assumed that the primary function of sleep is for the brain. We evaluated the molecular consequences of sleep and sleep deprivation outside the brain, in heart and lung. Using microarrays we compared gene expression in tissue from sleeping and sleep deprived mice euthanized at the same diurnal times. In each tissue, nearly two thousand genes demonstrated statistically significant differential expression as a function of sleep/wake behavioral state. To mitigate the influence of an artificial deprivation protocol, we identified a subset of these transcripts as specifically sleep-enhanced or sleep-repressed by requiring that their expression also change over the course of unperturbed sleep. 3% and 6% of the assayed transcripts showed "sleep specific" changes in the lung and heart respectively. Sleep specific transcripts in these tissues demonstrated highly significant overlap and shared temporal dynamics. Markers of cellular stress and the unfolded protein response were reduced during sleep in both tissues. These results mirror previous findings in brain. Sleep-enhanced pathways reflected the unique metabolic functions of each tissue. Transcripts related to carbohydrate and sulfur metabolic processes were enhanced by sleep in the lung, and collectively favor buffering from oxidative stress. DNA repair and protein metabolism annotations were significantly enriched among the sleep-enhanced transcripts in the heart. Our results also suggest that sleep may provide a Zeitgeber, or synchronizing cue, in the lung as a large cluster of transcripts demonstrated systematic changes in inter-animal variability as a function of both sleep duration and circadian time. Our data support the notion that the molecular consequences of sleep/wake behavioral state extend beyond the brain to include peripheral tissues. Sleep state induces a highly overlapping response in both heart and lung. We conclude that sleep enhances organ specific molecular functions and that it has a
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Lee, Jihoon; Panek, James S
2014-06-20
A sequential Diels-Alder reaction/silicon-directed [4 + 2]-annulation was developed to assemble hydroisochromene-type ring systems from menadione 2. In the first step, a Diels-Alder of the 1-silyl-substituted butadiene 1 with 2 furnished an intermediate cyclic allylsilane. Subsequently, TMSOTf promoted a [4 + 2]-annulation through trapping of an oxonium, generated by condensation between an aldehyde and the TBS protected alcohol resulted in the formation of a cis-fused hydroisochromene 13.
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Effects of the Hydrophobicity of the Reactants on Diels-Alder Reactions in Water
Meijer, Ale; Otto, Sijbren; Engberts, Jan B.F.N.
1998-01-01
To assess the importance of the hydrophobicity of different parts of diene and dienophile on the aqueous acceleration of Diels-Alder reactions, second-order rate constants have been determined for the reactions of cyclopentadiene (1), 2,3-dimethyl-1,3-butadiene (4), and 1,3-cyclohexadiene (6) with
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Transcriptional profiles of Treponema denticola in response to environmental conditions.
Directory of Open Access Journals (Sweden)
Ian McHardy
Full Text Available The periodontal pathogen T. denticola resides in a stressful environment rife with challenges, the human oral cavity. Knowledge of the stress response capabilities of this invasive spirochete is currently very limited. Whole genome expression profiles in response to different suspected stresses including heat shock, osmotic downshift, oxygen and blood exposure were examined. Most of the genes predicted to encode conserved heat shock proteins (HSPs were found to be induced under heat and oxygen stress. Several of these HSPs also seem to be important for survival in hypotonic solutions and blood. In addition to HSPs, differential regulation of many genes encoding metabolic proteins, hypothetical proteins, transcriptional regulators and transporters was observed in patterns that could betoken functional associations. In summary, stress responses in T. denticola exhibit many similarities to the corresponding stress responses in other organisms but also employ unique components including the induction of hypothetical proteins.
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Diel and tidal variations in larval fish exchange in the mouth region ...
African Journals Online (AJOL)
Diel and tidal variations in density of larval fishes were monitored over one neap and one spring tidal cycle in the mouth region of the warm temperate Gamtoos Estuary, South Africa. Data were collected over two 24h periods, using mixed method sampling with WP2 nets and a pushnet to sample both channel and margin ...
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Transcription factor assisted loading and enhancer dynamics dictate the hepatic fasting response
Goldstein, Ido; Baek, Songjoon; Presman, Diego M.; Paakinaho, Ville; Swinstead, Erin E.; Hager, Gordon L.
2017-01-01
Fasting elicits transcriptional programs in hepatocytes leading to glucose and ketone production. This transcriptional program is regulated by many transcription factors (TFs). To understand how this complex network regulates the metabolic response to fasting, we aimed at isolating the enhancers and TFs dictating it. Measuring chromatin accessibility revealed that fasting massively reorganizes liver chromatin, exposing numerous fasting-induced enhancers. By utilizing computational methods in combination with dissecting enhancer features and TF cistromes, we implicated four key TFs regulating the fasting response: glucocorticoid receptor (GR), cAMP responsive element binding protein 1 (CREB1), peroxisome proliferator activated receptor alpha (PPARA), and CCAAT/enhancer binding protein beta (CEBPB). These TFs regulate fuel production by two distinctly operating modules, each controlling a separate metabolic pathway. The gluconeogenic module operates through assisted loading, whereby GR doubles the number of sites occupied by CREB1 as well as enhances CREB1 binding intensity and increases accessibility of CREB1 binding sites. Importantly, this GR-assisted CREB1 binding was enhancer-selective and did not affect all CREB1-bound enhancers. Single-molecule tracking revealed that GR increases the number and DNA residence time of a portion of chromatin-bound CREB1 molecules. These events collectively result in rapid synergistic gene expression and higher hepatic glucose production. Conversely, the ketogenic module operates via a GR-induced TF cascade, whereby PPARA levels are increased following GR activation, facilitating gradual enhancer maturation next to PPARA target genes and delayed ketogenic gene expression. Our findings reveal a complex network of enhancers and TFs that dynamically cooperate to restore homeostasis upon fasting. PMID:28031249
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Directory of Open Access Journals (Sweden)
Francesca D’Auria
2017-05-01
Full Text Available Cyclic AMP response element binding (CREB protein is a member of the CREB/activating transcription factor (ATF family of transcription factors that play an important role in the cell response to different environmental stimuli leading to proliferation, differentiation, apoptosis, and survival. A number of studies highlight the involvement of CREB in the resistance to ionizing radiation (IR therapy, demonstrating a relationship between IR-induced CREB family members’ activation and cell survival. Consistent with these observations, we have recently demonstrated that CREB and ATF-1 are expressed in leukemia cell lines and that low-dose radiation treatment can trigger CREB activation, leading to survival of erythro-leukemia cells (K562. On the other hand, a number of evidences highlight a proapoptotic role of CREB following IR treatment of cancer cells. Since the development of multiple mechanisms of resistance is one key problem of most malignancies, including those of hematological origin, it is highly desirable to identify biological markers of responsiveness/unresponsiveness useful to follow-up the individual response and to adjust anticancer treatments. Taking into account all these considerations, this mini-review will be focused on the involvement of CREB/ATF family members in response to IR therapy, to deepen our knowledge of this topic, and to pave the way to translation into a therapeutic context.
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Chen, Mao-Sheng; Pan, Bang-Zhen; Wang, Gui-Juan; Ni, Jun; Niu, Longjian; Xu, Zeng-Fu
2014-11-30
Jatropha curcas L. is a potential biofuel plant. Application of exogenous cytokinin (6-benzyladenine, BA) on its inflorescence buds can significantly increase the number of female flowers, thereby improving seed yield. To investigate which genes and signal pathways are involved in the response to cytokinin in J. curcas inflorescence buds, we monitored transcriptional activity in inflorescences at 0, 3, 12, 24, and 48 h after BA treatment using a microarray. We detected 5,555 differentially expressed transcripts over the course of the experiment, which could be grouped into 12 distinct temporal expression patterns. We also identified 31 and 131 transcripts in J. curcas whose homologs in model plants function in flowering and phytohormonal signaling pathways, respectively. According to the transcriptional analysis of genes involved in flower development, we hypothesized that BA treatment delays floral organ formation by inhibiting the transcription of the A, B and E classes of floral organ-identity genes, which would allow more time to generate more floral primordia in inflorescence meristems, thereby enhancing inflorescence branching and significantly increasing flower number per inflorescence. BA treatment might also play an important role in maintaining the flowering signals by activating the transcription of GIGANTEA (GI) and inactivating the transcription of CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) and TERMINAL FLOWER 1b (TFL1b). In addition, exogenous cytokinin treatment could regulate the expression of genes involved in the metabolism and signaling of other phytohormones, indicating that cytokinin and other phytohormones jointly regulate flower development in J. curcas inflorescence buds. Our study provides a framework to better understand the molecular mechanisms underlying changes in flowering traits in response to cytokinin treatment in J. curcas inflorescence buds. The results provide valuable information related to the mechanisms of cross-talk among
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DEFF Research Database (Denmark)
Pin, C.; Hansen, Trine; Munoz-Cuevas, M.
2012-01-01
We investigated if the transcriptional response of Salmonella Typhimurium to temperature and acid variations was hysteretic, i.e. whether the transcriptional regulation caused by environmental stimuli showed memory and remained after the stimuli ceased. The transcriptional activity of non......, implying that down-regulation was significantly less synchronized than upregulation. The hysteretic transcriptional response to heat shock was accompanied by higher resistance to inactivation at 50uC as well as cross-resistance to inactivation at pH 3; however, growth rates and lag times at 43uC and at p......H 4.5 were not affected. The exposure to pH 5 only caused up-regulation of 12 genes and this response was neither hysteretic nor accompanied of increased resistance to inactivation conditions. Cellular memory at the transcriptional level may represent a mechanism of adaptation to the environment...
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Digital Repository Service at National Institute of Oceanography (India)
Vineetha, G.; Jyothibabu, R.; Madhu, N.V.; Kusum, K.K.; Sooria, P.M.; Shivaprasad, A.; Reny, P.D.; Deepak, M.P.
habitats is often determined by their dominant behavioral patterns: diel vertical migration (DVM) and tidal vertical migration (TVM). The modes of these endogenous rhythms often vary among estuaries based on the river runoff and tidal characteristics...
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Li, Wei; Cui, Xiao; Meng, Zhaolu; Huang, Xiahe; Xie, Qi; Wu, Heng; Jin, Hailing; Zhang, Dabing; Liang, Wanqi
2012-03-01
The accumulation of a number of small RNAs in plants is affected by abscisic acid (ABA) and abiotic stresses, but the underlying mechanisms are poorly understood. The miR168-mediated feedback regulatory loop regulates ARGONAUTE1 (AGO1) homeostasis, which is crucial for gene expression modulation and plant development. Here, we reveal a transcriptional regulatory mechanism by which MIR168 controls AGO1 homeostasis during ABA treatment and abiotic stress responses in Arabidopsis (Arabidopsis thaliana). Plants overexpressing MIR168a and the AGO1 loss-of-function mutant ago1-27 display ABA hypersensitivity and drought tolerance, while the mir168a-2 mutant shows ABA hyposensitivity and drought hypersensitivity. Both the precursor and mature miR168 were induced under ABA and several abiotic stress treatments, but no obvious decrease for the target of miR168, AGO1, was shown under the same conditions. However, promoter activity analysis indicated that AGO1 transcription activity was increased under ABA and drought treatments, suggesting that transcriptional elevation of MIR168a is required for maintaining a stable AGO1 transcript level during the stress response. Furthermore, we showed both in vitro and in vivo that the transcription of MIR168a is directly regulated by four abscisic acid-responsive element (ABRE) binding factors, which bind to the ABRE cis-element within the MIR168a promoter. This ABRE motif is also found in the promoter of MIR168a homologs in diverse plant species. Our findings suggest that transcriptional regulation of miR168 and posttranscriptional control of AGO1 homeostasis may play an important and conserved role in stress response and signal transduction in plants.
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Reddi, Durga; Belibasakis, Georgios N.
2012-01-01
Periodontitis is an infectious inflammatory disease that destroys the tooth-supporting (periodontal) tissues. Porphyromonas gingivalis is an oral pathogen highly implicated in the pathogenesis of this disease. It can exert its effects to a number of cells, including osteogenic bone marrow stromal cells which are important for homeostastic capacity of the tissues. By employing gene microarray technology, this study aimed to describe the overall transcriptional events (>2-fold regulation) elicited by P. gingivalis secreted products in bone marrow stromal cells, and to dissect further the categories of genes involved in bone metabolism, inflammatory and immune responses. After 6 h of challenge with P. gingivalis, 271 genes were up-regulated whereas 209 genes were down-regulated, whereas after 24 h, these numbers were 259 and 109, respectively. The early (6 h) response was characterised by regulation of genes associated with inhibition of cell cycle, induction of apoptosis and loss of structural integrity, whereas the late (24 h) response was characterised by induction of chemokines, cytokines and their associated intracellular pathways (such as NF-κB), mediators of connective tissue and bone destruction, and suppression of regulators of osteogenic differentiation. The most strongly up-regulated genes were lipocalin 2 (LCN2) and serum amyloid A3 (SAA3), both encoding for proteins of the acute phase inflammatory response. Collectively, these transcriptional changes elicited by P. gingivalis denote that the fundamental cellular functions are hindered, and that the cells acquire a phenotype commensurate with propagated innate immune response and inflammatory-mediated tissue destruction. In conclusion, the global transcriptional profile of bone marrow stromal cells in response to P. gingivalis is marked by deregulated homeostatic functions, with implications in the pathogenesis of periodontitis. PMID:22937121
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Directory of Open Access Journals (Sweden)
Yamaguchi-Shinozaki Kazuko
2011-02-01
Full Text Available Abstract Background Phytohormones organize plant development and environmental adaptation through cell-to-cell signal transduction, and their action involves transcriptional activation. Recent international efforts to establish and maintain public databases of Arabidopsis microarray data have enabled the utilization of this data in the analysis of various phytohormone responses, providing genome-wide identification of promoters targeted by phytohormones. Results We utilized such microarray data for prediction of cis-regulatory elements with an octamer-based approach. Our test prediction of a drought-responsive RD29A promoter with the aid of microarray data for response to drought, ABA and overexpression of DREB1A, a key regulator of cold and drought response, provided reasonable results that fit with the experimentally identified regulatory elements. With this succession, we expanded the prediction to various phytohormone responses, including those for abscisic acid, auxin, cytokinin, ethylene, brassinosteroid, jasmonic acid, and salicylic acid, as well as for hydrogen peroxide, drought and DREB1A overexpression. Totally 622 promoters that are activated by phytohormones were subjected to the prediction. In addition, we have assigned putative functions to 53 octamers of the Regulatory Element Group (REG that have been extracted as position-dependent cis-regulatory elements with the aid of their feature of preferential appearance in the promoter region. Conclusions Our prediction of Arabidopsis cis-regulatory elements for phytohormone responses provides guidance for experimental analysis of promoters to reveal the basis of the transcriptional network of phytohormone responses.
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Digital Repository Service at National Institute of Oceanography (India)
Patre, R.E.; Gawas, S.; Sen, S.; Parameswaran, P.S.; Tilve, S.G.
A domino Wittig Diels - Alder reaction has been employed in delineating a short and flexible synthetic stratagem for ready access to the AB ring system and the tricyclic framework of furanosesquiterpenes, such as the bioactive natural products...
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Otani, Takashi; Tamai, Yumiko; Seki, Kazunori; Kikuchi, Tomohiro; Miyazawa, Taiichiro; Saito, Takao
2015-06-07
We describe the stereoselective synthesis of polyring-fused heterocyclic compounds based on diene-transmissive hetero-Diels-Alder reactions utilizing β,γ-unsaturated α-keto esters. This protocol involves the initial endo- or exo-selective Diels-Alder (DA) reactions with electron-rich dienophiles, methylenation of the ester carbonyl groups with the Tebbe reagent, and a stereoselective second DA reaction with electron-deficient dienophiles. The use of enantioselective DA reactions in the initial reaction enables access to chiral polyring-fused heterocyclic compounds with multiple chiral centres.
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Diel turbidity cycles in a headwater stream: evidence of nocturnal bioturbation?
Cooper, Richard J.; Outram, Faye; Hiscock, Kevin M.
2016-01-01
Purpose: A small number of recent studies have linked daily cycles in stream turbidity to nocturnal bioturbation by aquatic fauna, principally crayfish, and demonstrated this process can significantly impact upon water quality under baseflow conditions. Adding to this limited body of research, we use high-resolution water quality monitoring data to investigate evidence of diel turbidity cycles in a lowland, headwater stream with a known signal crayfish (Pacifastacus leniusculus) population an...
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Khan, Ahamed; Shrestha, Ankita; Bhuyan, Kashyap; Maiti, Indu B; Dey, Nrisingha
2018-01-01
The promoter fragment described in this study can be employed for strong transgene expression under both biotic and abiotic stress conditions. Plant-infecting Caulimoviruses have evolved multiple regulatory mechanisms to address various environmental stimuli during the course of evolution. One such mechanism involves the retention of discrete stress responsive cis-elements which are required for their survival and host-specificity. Here we describe the characterization of a novel Caulimoviral promoter isolated from Horseradish Latent Virus (HRLV) and its regulation by multiple stress responsive Transcription factors (TFs) namely DREB1, AREB1 and TGA1a. The activity of full length transcript (Flt-) promoter from HRLV (- 677 to + 283) was investigated in both transient and transgenic assays where we identified H12 (- 427 to + 73) as the highest expressing fragment having ~ 2.5-fold stronger activity than the CaMV35S promoter. The H12 promoter was highly active and near-constitutive in the vegetative and reproductive parts of both Tobacco and Arabidopsis transgenic plants. Interestingly, H12 contains a distinct cluster of cis-elements like dehydration-responsive element (DRE-core; GCCGAC), an ABA-responsive element (ABRE; ACGTGTC) and as-1 element (TGACG) which are known to be induced by cold, drought and pathogen/SA respectively. The specific binding of DREB1, AREB1 and TGA1a to DRE, ABRE and as-1 elements respectively were confirmed by the gel-binding assays using H12 promoter-specific probes. Detailed mutational analysis of the H12 promoter suggested that the presence of DRE-core and as-1 element was indispensable for its activity which was further confirmed by the transactivation assays. Our studies imply that H12 could be a valuable genetic tool for regulated transgene expression under diverse environmental conditions.
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The Preparation and Properties of Thermo-reversibly Cross-linked Rubber Via Diels-Alder Chemistry
Polgar, Lorenzo Massimo; van Duin, Martin; Picchioni, Francesco
2016-01-01
A method for using Diels Alder thermo-reversible chemistry as cross-linking tool for rubber products is demonstrated. In this work, a commercial ethylene-propylene rubber, grafted with maleic anhydride, is thermo-reversibly cross-linked in two steps. The pending anhydride moieties are first modified
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Reduction in cab and psb A RNA transcripts in response to supplementary ultraviolet-B radiation.
Jordan, B R; Chow, W S; Strid, A; Anderson, J M
1991-06-17
The cab and psb A RNA transcript levels have been determined in Pisum sativum leaves exposed to supplementary ultraviolet-B radiation. The nuclear-encoded cab transcripts are reduced to low levels after only 4 h of UV-B treatment and are undetectable after 3 days exposure. In contrast, the chloroplast-encoded psb A transcript levels, although reduced, are present for at least 3 days. After short periods of UV-B exposure (4 h or 8 h), followed by recovery under control conditions, cab RNA transcript levels had not recovered after 1 day, but were re-established to ca. 60% of control levels after 2 more days. Increased irradiance during exposure to UV-B reduced the effect upon cab transcripts, although the decrease was still substantial. These results indicate rapid changes in the cellular regulation of gene expression in response to supplementary UV-B and suggest increased UV-B radiation may have profound consequences for future productivity of sensitive crop species.
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Reinthaler, David; Roy, Jacques; Landais, Damien; Piel, Clement; Resco de Dios, Victor; Bahn, Michael
2015-04-01
Soil respiration (Rs) is the biggest source of CO2 emitted from terrestrial ecosystems to the atmosphere. Therefore the understanding of its drivers is of major importance for models of carbon cycling. Next to temperature as a major abiotic factor, photosynthesis has been suggested as an important driver influencing diel patterns in Rs. Under natural conditions it is difficult to disentangle abiotic and biotic effects on soil CO2 production, as fluctuating light intensity affects both photosynthetic activity and soil temperature. To analyse individual and combined effects of soil temperature and light on the dynamics of soil CO2 production and efflux, we performed a controlled environment study at the ECOTRON facility in Montpellier. The study manipulated temperature and photosynthetically active radiation independently and was carried out in large macrocosms, hosting canopies of either a woody (cotton) or a herbaceous (bean) crop. In each macrocosm membrane tubes had been installed across the soil profile for continuous measurement of soil CO2 concentrations. In addition, an automated soil respiration system was installed in each macrocosm, whose data were also used for validating a model of soil CO2 production and transport based on the concentration profiles. Both for cotton and for bean canopies, under conditions of naturally fluctuating temperature and light conditions, soil CO2 production and efflux followed a clear diel pattern. Under constantly dark conditions (excluding immediate effects of photosynthesis) and constant temperature, no significant diel changes in Rs could be observed. Furthermore, soil CO2 production and efflux did not increase significantly upon exposure of previously darkened macrocosms to light. Under constant temperature and fluctuating light conditions, we observed a dampened diel pattern of Rs, which did not match diurnal solar cycles. A detailed residual analysis accounting for temporal trends in soil moisture suggested a significant
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Bentley, Kale T; Schindler, Daniel E; Cline, Timothy J; Armstrong, Jonathan B; Macias, Daniel; Ciepiela, Lindsy R; Hilborn, Ray
2014-11-01
Daily movements of mobile organisms between habitats in response to changing trade-offs between predation risk and foraging gains are well established; however, less in known about whether similar tactics are used during reproduction, a time period when many organisms are particularly vulnerable to predators. We investigated the reproductive behaviour of adult sockeye salmon (Oncorhynchus nerka) and the activity of their principal predator, brown bears (Ursus arctos), on streams in south-western Alaska. Specifically, we continuously monitored movements of salmon between lake habitat, where salmon are invulnerable to bears, and three small streams, where salmon spawn and are highly vulnerable to bears. We conducted our study across 2 years that offered a distinct contrast in bear activity and predation rates. Diel movements by adult sockeye salmon between stream and lake habitat were observed in 51.3% ± 17.7% (mean ± SD) of individuals among years and sites. Fish that moved tended to hold in the lake for most of the day and then migrated into spawning streams during the night, coincident with when bear activity on streams tended to be lowest. Additionally, cyclic movements between lakes and spawning streams were concentrated earlier in the spawning season. Individuals that exhibited diel movements had longer average reproductive life spans than those who made only one directed movement into a stream. However, the relative effect was dependent on the timing of bear predation, which varied between years. When predation pressure primarily occurred early in the spawning run (i.e., during the height of the diel movements), movers lived 120-310% longer than non-movers. If predation pressure was concentrated later in the spawning run (i.e. when most movements had ceased), movers only lived 10-60% longer. Our results suggest a dynamic trade-off in reproductive strategies of sockeye salmon; adults must be in the stream to reproduce, but must also avoid predation long
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Transcriptional repression of BODENLOS by HD-ZIP transcription factor HB5 in Arabidopsis thaliana.
Smet, De I.; Lau, S.; Ehrismann, J.S.; Axiotis, I.; Kolb, M.; Kientz, M.; Weijers, D.; Jürgens, G.
2013-01-01
In Arabidopsis thaliana, the phytohormone auxin is an important patterning agent during embryogenesis and post-embryonic development, exerting effects through transcriptional regulation. The main determinants of the transcriptional auxin response machinery are AUXIN RESPONSE FACTOR (ARF)
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Hydrogen-Bonding Catalysis of Tetraalkylammonium Salts in an Aza-Diels-Alder Reaction.
Kumatabara, Yusuke; Kaneko, Shiho; Nakata, Satoshi; Shirakawa, Seiji; Maruoka, Keiji
2016-08-05
A piperidine-derived tetraalkylammonium salt with a non-coordinating counteranion worked as an effective hydrogen-bonding catalyst in an aza-Diels-Alder reaction of imines and a Danishefsky diene. The hydrogen-bonding interaction between the ammonium salt and an imine was observed as part of a (1) H NMR titration study. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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International Nuclear Information System (INIS)
Goodale, Britton C.; Tilton, Susan C.; Corvi, Margaret M.; Wilson, Glenn R.; Janszen, Derek B.; Anderson, Kim A.; Waters, Katrina M.; Tanguay, Robert L.
2013-01-01
Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous in the environment as components of fossil fuels and by-products of combustion. These multi-ring chemicals differentially activate the aryl hydrocarbon receptor (AHR) in a structurally dependent manner, and induce toxicity via both AHR-dependent and -independent mechanisms. PAH exposure is known to induce developmental malformations in zebrafish embryos, and recent studies have shown cardiac toxicity induced by compounds with low AHR affinity. Unraveling the potentially diverse molecular mechanisms of PAH toxicity is essential for understanding the hazard posed by complex PAH mixtures present in the environment. We analyzed transcriptional responses to PAH exposure in zebrafish embryos exposed to benz(a)anthracene (BAA), dibenzothiophene (DBT) and pyrene (PYR) at concentrations that induced developmental malformations by 120 h post-fertilization (hpf). Whole genome microarray analysis of mRNA expression at 24 and 48 hpf identified genes that were differentially regulated over time and in response to the three PAH structures. PAH body burdens were analyzed at both time points using GC–MS, and demonstrated differences in PAH uptake into the embryos. This was important for discerning dose-related differences from those that represented unique molecular mechanisms. While BAA misregulated the least number of transcripts, it caused strong induction of cyp1a and other genes known to be downstream of the AHR, which were not induced by the other two PAHs. Analysis of functional roles of misregulated genes and their predicted regulatory transcription factors also distinguished the BAA response from regulatory networks disrupted by DBT and PYR exposure. These results indicate that systems approaches can be used to classify the toxicity of PAHs based on the networks perturbed following exposure, and may provide a path for unraveling the toxicity of complex PAH mixtures. - Highlights: • Defined global mRNA expression
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Diel foraging and shelter use of large juvenile brown trout (Salmo trutta) under food satiation
DEFF Research Database (Denmark)
Conallin, J.; Jyde, M.; Filrup, K.
2012-01-01
The diel partitioning of juvenile brown trout Salmo trutta foraging behaviour is controlled by a number of factors including predation risk, competition, temperature and food availability. The present study uses PIT-tagging and visual observation to asses the use of shelter and foraging behaviour...... of Danish wild juvenile brown trout (13.5-15.6 cm). The experiment was conducted in a fluvarium and the fish were fed to satiation. It was hypothesised that food satiation would promote nocturnal foraging and increase daytime shelter use. Our results showed a significant difference in diel shelter use...... between day and night with a significant increase in shelter use during daytime conditions. Visual observations showed a significant preference for nocturnal feeding. Together with the significantly reduced shelter use during the night, our results support the hypothesis that young stream living trout...
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Rivero, Uxía; Meuwly, Markus; Willitsch, Stefan
2017-09-01
The neutral and cationic Diels-Alder-type reactions between 2,3-dibromo-1,3-butadiene and maleic anhydride have been computationally explored as the first step of a combined experimental and theoretical study. Density functional theory calculations show that the neutral reaction is concerted while the cationic reaction can be either concerted or stepwise. Further isomerizations of the Diels-Alder products have been studied in order to predict possible fragmentation pathways in gas-phase experiments. Rice-Ramsperger-Kassel-Marcus (RRKM) calculations suggest that under single-collision experimental conditions the neutral product may reform the reactants and the cationic product will most likely eliminate CO2.
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Roles of Arabidopsis WRKY3 and WRKY4 Transcription Factors in Plant Responses to Pathogens
Directory of Open Access Journals (Sweden)
Fan Baofang
2008-06-01
Full Text Available Abstract Background Plant WRKY DNA-binding transcription factors are involved in plant responses to biotic and abiotic responses. It has been previously shown that Arabidopsis WRKY3 and WRKY4, which encode two structurally similar WRKY transcription factors, are induced by pathogen infection and salicylic acid (SA. However, the role of the two WRKY transcription factors in plant disease resistance has not been directly analyzed. Results Both WRKY3 and WRKY4 are nuclear-localized and specifically recognize the TTGACC W-box sequences in vitro. Expression of WRKY3 and WRKY4 was induced rapidly by stress conditions generated by liquid infiltration or spraying. Stress-induced expression of WRKY4 was further elevated by pathogen infection and SA treatment. To determine directly their role in plant disease resistance, we have isolated T-DNA insertion mutants and generated transgenic overexpression lines for WRKY3 and WRKY4. Both the loss-of-function mutants and transgenic overexpression lines were examined for responses to the biotrophic bacterial pathogen Pseudomonas syringae and the necrotrophic fungal pathogen Botrytis cinerea. The wrky3 and wrky4 single and double mutants exhibited more severe disease symptoms and support higher fungal growth than wild-type plants after Botrytis infection. Although disruption of WRKY3 and WRKY4 did not have a major effect on plant response to P. syringae, overexpression of WRKY4 greatly enhanced plant susceptibility to the bacterial pathogen and suppressed pathogen-induced PR1 gene expression. Conclusion The nuclear localization and sequence-specific DNA-binding activity support that WRKY3 and WRKY4 function as transcription factors. Functional analysis based on T-DNA insertion mutants and transgenic overexpression lines indicates that WRKY3 and WRKY4 have a positive role in plant resistance to necrotrophic pathogens and WRKY4 has a negative effect on plant resistance to biotrophic pathogens.
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Vibrio elicits targeted transcriptional responses from copepod hosts.
Almada, Amalia A; Tarrant, Ann M
2016-06-01
Copepods are abundant crustaceans that harbor diverse bacterial communities, yet the nature of their interactions with microbiota are poorly understood. Here, we report that Vibrio elicits targeted transcriptional responses in the estuarine copepod Eurytemora affinis We pre-treated E. affinis with an antibiotic cocktail and exposed them to either a zooplankton specialist (Vibrio sp. F10 9ZB36) or a free-living species (Vibrio ordalii 12B09) for 24 h. We then identified via RNA-Seq a total of 78 genes that were differentially expressed following Vibrio exposure, including homologs of C-type lectins, chitin-binding proteins and saposins. The response differed between the two Vibrio treatments, with the greatest changes elicited upon inoculation with V. sp. F10 We suggest that these differentially regulated genes play important roles in cuticle integrity, the innate immune response, and general stress response, and that their expression may enable E. affinis to recognize and regulate symbiotic vibrios. We further report that V. sp. F10 culturability is specifically altered upon colonization of E. affinis These findings suggest that rather than acting as passive environmental vectors, copepods discriminately interact with vibrios, which may ultimately impact the abundance and activity of copepod-associated bacteria. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
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Younger, Andrew K D; Su, Peter Y; Shepard, Andrea J; Udani, Shreya V; Cybulski, Thaddeus R; Tyo, Keith E J; Leonard, Joshua N
2018-02-01
Naturally evolved metabolite-responsive biosensors enable applications in metabolic engineering, ranging from screening large genetic libraries to dynamically regulating biosynthetic pathways. However, there are many metabolites for which a natural biosensor does not exist. To address this need, we developed a general method for converting metabolite-binding proteins into metabolite-responsive transcription factors-Biosensor Engineering by Random Domain Insertion (BERDI). This approach takes advantage of an in vitro transposon insertion reaction to generate all possible insertions of a DNA-binding domain into a metabolite-binding protein, followed by fluorescence activated cell sorting to isolate functional biosensors. To develop and evaluate the BERDI method, we generated a library of candidate biosensors in which a zinc finger DNA-binding domain was inserted into maltose binding protein, which served as a model well-studied metabolite-binding protein. Library diversity was characterized by several methods, a selection scheme was deployed, and ultimately several distinct and functional maltose-responsive transcriptional biosensors were identified. We hypothesize that the BERDI method comprises a generalizable strategy that may ultimately be applied to convert a wide range of metabolite-binding proteins into novel biosensors for applications in metabolic engineering and synthetic biology. © The Author(s) 2018. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
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Unconventional exo selectivity in thermal normal-electron-demand Diels-Alder reactions
Ho, Guo-Ming; Huang, Ci-Jhang; Li, Elise Yu-Tzu; Hsu, Sheng-Kai; Wu, Ti; Zulueta, Medel Manuel L.; Wu, Kevin Binchia; Hung, Shang-Cheng
2016-10-01
The Diels-Alder reaction is a useful tool for generating functionalized chiral molecules through the concerted cycloaddition of dienes and dienophiles leading to six-membered rings. Traditionally, the selective predictions of the products rely heavily on consideration of the secondary orbital interactions that stabilize the endo pathway. However, there remain some basic examples defying this notion and produce the exo-isomer as major product. Here we systematically evaluated of the structural features driving exo selectivity in thermal normal-electron-demand Diels-Alder reactions. Substitution at the Cβ position and the size and electronegativity of the electron-withdrawing group of the dienophile are contributing factors. Experimental and computational studies both point toward the steric and electrostatic forces between the substituents in both the diene and the dienophile that increase the likelihood of the exo pathway. For these substrates, the dominance of the endo pathway is reduced by transition state distortions and poor structural alignments of the reacting partners. We also noted the tilt of the dienophile with respect to the diene causing steric strain on the functionalities at the more advanced bond forming carbon-carbon position of the endo transition state. Insights into such factors may benefit synthetic planning and asserting control over this important named reaction.
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Liu, Ning; Ding, Yong; Fromm, Michael; Avramova, Zoya
2014-05-01
Plants that have experienced several exposures to dehydration stress show increased resistance to future exposures by producing faster and/or stronger reactions, while many dehydration stress responding genes in Arabidopsis thaliana super-induce their transcription as a 'memory' from the previous encounter. A previously unknown, rather unusual, memory response pattern is displayed by a subset of the dehydration stress response genes. Despite robustly responding to a first stress, these genes return to their initial, pre-stressed, transcript levels during the watered recovery; surprisingly, they do not respond further to subsequent stresses of similar magnitude and duration. This transcriptional behavior defines the 'revised-response' memory genes. Here, we investigate the molecular mechanisms regulating this transcription memory behavior. Potential roles of abscisic acid (ABA), of transcription factors (TFs) from the ABA signaling pathways (ABF2/3/4 and MYC2), and of histone modifications (H3K4me3 and H3K27me3) as factors in the revised-response transcription memory patterns are elucidated. We identify the TF MYC2 as the critical component for the memory behavior of a specific subset of MYC2-dependent genes. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.
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The metal-responsive transcription factor-1 contributes to HIF-1 activation during hypoxic stress
International Nuclear Information System (INIS)
Murphy, Brian J.; Sato, Barbara G.; Dalton, Timothy P.; Laderoute, Keith R.
2005-01-01
Hypoxia-inducible factor-1 (HIF-1), the major transcriptional regulator of the mammalian cellular response to low oxygen (hypoxia), is embedded within a complex network of signaling pathways. We have been investigating the importance of another stress-responsive transcription factor, MTF-1, for the adaptation of cells to hypoxia. This article reports that MTF-1 plays a central role in hypoxic cells by contributing to HIF-1 activity. Loss of MTF-1 in transformed Mtf1 null mouse embryonic fibroblasts (MEFs) results in an attenuation of nuclear HIF-1α protein accumulation, HIF-1 transcriptional activity, and expression of an established HIF-1 target gene, glucose transporter-1 (Glut1). Mtf1 null (Mtf1 KO) MEFs also have constitutively higher levels of both glutathione (GSH) and the rate-limiting enzyme involved in GSH synthesis-glutamate cysteine ligase catalytic subunit-than wild type cells. The altered cellular redox state arising from increased GSH may perturb oxygen-sensing mechanisms in hypoxic Mtf1 KO cells and decrease the accumulation of HIF-1α protein. Together, these novel findings define a role for MTF-1 in the regulation of HIF-1 activity
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Haze, K; Okada, T; Yoshida, H; Yanagi, H; Yura, T; Negishi, M; Mori, K
2001-04-01
Eukaryotic cells control the levels of molecular chaperones and folding enzymes in the endoplasmic reticulum (ER) by a transcriptional induction process termed the unfolded protein response (UPR). The mammalian UPR is mediated by the cis-acting ER stress response element consisting of 19 nt (CCAATN(9)CCACG), the CCACG part of which is considered to provide specificity. We recently identified the basic leucine zipper (bZIP) protein ATF6 as a mammalian UPR-specific transcription factor; ATF6 is activated by ER stress-induced proteolysis and binds directly to CCACG. Here we report that eukaryotic cells express another bZIP protein closely related to ATF6 in both structure and function. This protein encoded by the G13 (cAMP response element binding protein-related protein) gene is constitutively synthesized as a type II transmembrane glycoprotein anchored in the ER membrane and processed into a soluble form upon ER stress as occurs with ATF6. The proteolytic processing of ATF6 and the G13 gene product is accompanied by their relocation from the ER to the nucleus; their basic regions seem to function as a nuclear localization signal. Overexpression of the soluble form of the G13 product constitutively activates the UPR, whereas overexpression of a mutant lacking the activation domain exhibits a strong dominant-negative effect. Furthermore, the soluble forms of ATF6 and the G13 gene product are unable to bind to several point mutants of the cis-acting ER stress response element in vitro that hardly respond to ER stress in vivo. We thus concluded that the two related bZIP proteins are crucial transcriptional regulators of the mammalian UPR, and propose calling the ATF6 gene product ATF6alpha and the G13 gene product ATF6beta.
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Microbial phylogeny determines transcriptional response of resistome to dynamic composting processes
Wang, Cheng; Dong, Da; Strong, P. J.; Zhu, Weijing; Ma, Zhuang; Qin, Yong; Wu, Weixiang
2017-01-01
Background Animal manure is a reservoir of antibiotic resistance genes (ARGs) that pose a potential health risk globally, especially for resistance to the antibiotics commonly used in livestock production (such as tetracycline, sulfonamide, and fluoroquinolone). Currently, the effects of biological treatment (composting) on the transcriptional response of manure ARGs and their microbial hosts are not well characterized. Composting is a dynamic process that consists of four distinct phases tha...
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Using whole genome Affymetrix ATH1 GeneChips we characterized the transcriptional response of Arabidopsis thaliana Columbia 24 hours after treatment with five different herbicides. Four of them (chloransulam, imazapyr, primisulfuron, sulfometuron) inhibit acetolactate synthase (A...
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Transcriptional and Proteomic Profiling of Aspergillus flavipes in Response to Sulfur Starvation.
El-Sayed, Ashraf S A; Yassin, Marwa A; Ali, Gul Shad
2015-01-01
Aspergillus flavipes has received considerable interest due to its potential to produce therapeutic enzymes involved in sulfur amino acid metabolism. In natural habitats, A. flavipes survives under sulfur limitations by mobilizing endogenous and exogenous sulfur to operate diverse cellular processes. Sulfur limitation affects virulence and pathogenicity, and modulates proteome of sulfur assimilating enzymes of several fungi. However, there are no previous reports aimed at exploring effects of sulfur limitation on the regulation of A. flavipes sulfur metabolism enzymes at the transcriptional, post-transcriptional and proteomic levels. In this report, we show that sulfur limitation affects morphological and physiological responses of A. flavipes. Transcription and enzymatic activities of several key sulfur metabolism genes, ATP-sulfurylase, sulfite reductase, methionine permease, cysteine synthase, cystathionine β- and γ-lyase, glutathione reductase and glutathione peroxidase were increased under sulfur starvation conditions. A 50 kDa protein band was strongly induced by sulfur starvation, and the proteomic analyses of this protein band using LC-MS/MS revealed similarity to many proteins involved in the sulfur metabolism pathway.
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Vandeputte, Patrick; Pradervand, Sylvain; Ischer, Françoise; Coste, Alix T; Ferrari, Sélène; Harshman, Keith; Sanglard, Dominique
2012-07-01
The identification of novel transcription factors associated with antifungal response may allow the discovery of fungus-specific targets for new therapeutic strategies. A collection of 241 Candida albicans transcriptional regulator mutants was screened for altered susceptibility to fluconazole, caspofungin, amphotericin B, and 5-fluorocytosine. Thirteen of these mutants not yet identified in terms of their role in antifungal response were further investigated, and the function of one of them, a mutant of orf19.6102 (RCA1), was characterized by transcriptome analysis. Strand-specific RNA sequencing and phenotypic tests assigned Rca1 as the regulator of hyphal formation through the cyclic AMP/protein kinase A (cAMP/PKA) signaling pathway and the transcription factor Efg1, but also probably through its interaction with a transcriptional repressor, most likely Tup1. The mechanisms responsible for the high level of resistance to caspofungin and fluconazole observed resulting from RCA1 deletion were investigated. From our observations, we propose that caspofungin resistance was the consequence of the deregulation of cell wall gene expression and that fluconazole resistance was linked to the modulation of the cAMP/PKA signaling pathway activity. In conclusion, our large-scale screening of a C. albicans transcription factor mutant collection allowed the identification of new effectors of the response to antifungals. The functional characterization of Rca1 assigned this transcription factor and its downstream targets as promising candidates for the development of new therapeutic strategies, as Rca1 influences host sensing, hyphal development, and antifungal response.
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Assessment of possible diel and sex-related differences in round goby (Neogobius melanostomus) diet
Czech Academy of Sciences Publication Activity Database
Všetičková, Lucie; Janáč, Michal; Roche, Kevin Francis; Jurajda, Pavel
2015-01-01
Roč. 64, č. 2 (2015), s. 104-111 ISSN 0139-7893 R&D Projects: GA ČR(CZ) GAP505/11/1768 Institutional support: RVO:68081766 Keywords : invasive species * diel feeding * inter-sex differences * nest-guarding * breeding season Subject RIV: EG - Zoology Impact factor: 0.592, year: 2015
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Martel, C.; Zhurov, V.; Navarro, M.; Martinez, M.; Cazaux, M.; Auger, P.; Migeon, A.; Santamaria, M.E.; Wybouw, N.; Diaz, I.; Van Leeuwen, T.; Navajas, M.; Grbic, M.; Grbic, V.
2015-01-01
The two-spotted spider mite Tetranychus urticae is one of the most significant mite pests in agriculture, feeding on more than 1,100 plant hosts, including model plants Arabidopsis thaliana and tomato, Solanum lycopersicum. Here, we describe timecourse tomato transcriptional responses to spider mite
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Nucleocytoplasmic shuttling of transcription factors
DEFF Research Database (Denmark)
Cartwright, P; Helin, K
2000-01-01
To elicit the transcriptional response following intra- or extracellular stimuli, the signals need to be transmitted to their site of action within the nucleus. The nucleocytoplasmic shuttling of transcription factors is a mechanism mediating this process. The activation and inactivation...... of the transcriptional response is essential for cells to progress through the cell cycle in a normal manner. The involvement of cytoplasmic and nuclear accessory molecules, and the general nuclear membrane transport components, are essential for this process. Although nuclear import and export for different...... transcription factor families are regulated by similar mechanisms, there are several differences that allow for the specific activation of each transcription factor. This review discusses the general import and export pathways found to be common amongst many different transcription factors, and highlights...
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Directory of Open Access Journals (Sweden)
Kazuo eNakashima
2014-05-01
Full Text Available Drought negatively impacts plant growth and the productivity of crops around the world. Understanding the molecular mechanisms in the drought response is important for improvement of drought tolerance using molecular techniques. In plants, abscisic acid (ABA is accumulated under osmotic stress conditions caused by drought, and has a key role in stress responses and tolerance. Comprehensive molecular analyses have shown that ABA regulates the expression of many genes under osmotic stress conditions, and the ABA-responsive element (ABRE is the major cis-element for ABA-responsive gene expression. Transcription factors (TFs are master regulators of gene expression. ABRE-binding protein (AREB and ABRE-binding factor (ABF TFs control gene expression in an ABA-dependent manner. SNF1-related protein kinases 2, group A 2C-type protein phosphatases, and ABA receptors were shown to control the ABA signaling pathway. ABA-independent signaling pathways such as dehydration-responsive element-binding protein (DREB TFs and NAC TFs are also involved in stress responses including drought, heat and cold. Recent studies have suggested that there are interactions between the major ABA signaling pathway and other signaling factors in stress responses. The important roles of these transcription factors in crosstalk among abiotic stress responses will be discussed. Control of ABA or stress signaling factor expression can improve tolerance to environmental stresses. Recent studies using crops have shown that stress-specific overexpression of TFs improves drought tolerance and grain yield compared with controls in the field.
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Czech Academy of Sciences Publication Activity Database
Koehler, K. C.; Ďuračková, Andrea; Kloxin, C. J.; Bowman, C. N.
2012-01-01
Roč. 58, č. 11 (2012), s. 3545-3552 ISSN 0001-1541 Institutional research plan: CEZ:AV0Z40500505 Keywords : Diels - Alder reaction s * self-healing polymer networks * thermoreversible reaction s Subject RIV: CD - Macromolecular Chemistry Impact factor: 2.493, year: 2012
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The velocity of light intensity increase modulates the photoprotective response in coastal diatoms.
Directory of Open Access Journals (Sweden)
Vasco Giovagnetti
Full Text Available In aquatic ecosystems, the superimposition of mixing events to the light diel cycle exposes phytoplankton to changes in the velocity of light intensity increase, from diurnal variations to faster mixing-related ones. This is particularly true in coastal waters, where diatoms are dominant. This study aims to investigate if coastal diatoms differently activate the photoprotective responses, xanthophyll cycle (XC and non-photochemical fluorescence quenching (NPQ, to cope with predictable light diel cycle and unpredictable mixing-related light variations. We compared the effect of two fast light intensity increases (simulating mixing events with that of a slower increase (corresponding to the light diel cycle on the modulation of XC and NPQ in the planktonic coastal diatom Pseudo-nitzschia multistriata. During each light treatment, the photon flux density (PFD progressively increased from darkness to five peaks, ranging from 100 to 650 µmol photons m-2 s-1. Our results show that the diel cycle-related PFD increase strongly activates XC through the enhancement of the carotenoid biosynthesis and induces a moderate and gradual NPQ formation over the light gradient. In contrast, during mixing-related PFD increases, XC is less activated, while higher NPQ rapidly develops at moderate PFD. We observe that together with the light intensity and its increase velocity, the saturation light for photosynthesis (Ek is a key parameter in modulating photoprotection. We propose that the capacity to adequately regulate and actuate alternative photoprotective 'safety valves' in response to changing velocity of light intensity increase further enhances the photophysiological flexibility of diatoms. This might be an evolutionary outcome of diatom adaptation to turbulent marine ecosystems characterized by unpredictable mixing-related light changes over the light diel cycle.
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Dimer formation and transcription activation in the sporulation response regulator Spo0A.
Lewis, Richard J; Scott, David J; Brannigan, James A; Ladds, Joanne C; Cervin, Marguerite A; Spiegelman, George B; Hoggett, James G; Barák, Imrich; Wilkinson, Anthony J
2002-02-15
The response regulator Spo0A is the master control element in the initiation of sporulation in Bacillus subtilis. Like many other multi-domain response regulators, the latent activity of the effector, C-terminal domain is stimulated by phosphorylation on a conserved aspartic acid residue in the regulatory, N-terminal domain. If a threshold concentration of phosphorylated Spo0A is achieved, the transcription of genes required for sporulation is activated, whereas the genes encoding stationary phase sentinels are repressed, and sporulation proceeds. Despite detailed genetic, biochemical and structural characterisation, it is not understood how the phosphorylation signal in the receiver domain is transduced into DNA binding and transcription activation in the distal effector domain. An obstacle to our understanding of Spo0A function is the uncertainty concerning changes in quaternary structure that accompany phosphorylation. Here we have revisited this question and shown unequivocally that Spo0A forms dimers upon phosphorylation and that the subunit interactions in the dimer are mediated principally by the receiver domain. Purified dimers of two mutants of Spo0A, in which the phosphorylatable aspartic acid residue has been substituted, activate transcription from the spoIIG promoter in vitro, whereas monomers do not. This suggests that dimers represent the activated form of Spo0A. Copyright 2002 Elsevier Science Ltd.
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Chen Zhixiang; Xiao Yong; Shi Junwei; Lai Zhibing; Chen Han; Xu Xinping
2010-01-01
Abstract Background WRKY transcription factors are involved in plant responses to both biotic and abiotic stresses. Arabidopsis WRKY18, WRKY40, and WRKY60 transcription factors interact both physically and functionally in plant defense responses. However, their role in plant abiotic stress response has not been directly analyzed. Results We report that the three WRKYs are involved in plant responses to abscisic acid (ABA) and abiotic stress. Through analysis of single, double, and triple muta...
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ATM-mediated transcriptional and developmental responses to gamma-rays in Arabidopsis.
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Lilian Ricaud
Full Text Available ATM (Ataxia Telangiectasia Mutated is an essential checkpoint kinase that signals DNA double-strand breaks in eukaryotes. Its depletion causes meiotic and somatic defects in Arabidopsis and progressive motor impairment accompanied by several cell deficiencies in patients with ataxia telangiectasia (AT. To obtain a comprehensive view of the ATM pathway in plants, we performed a time-course analysis of seedling responses by combining confocal laser scanning microscopy studies of root development and genome-wide expression profiling of wild-type (WT and homozygous ATM-deficient mutants challenged with a dose of gamma-rays (IR that is sublethal for WT plants. Early morphologic defects in meristematic stem cells indicated that AtATM, an Arabidopsis homolog of the human ATM gene, is essential for maintaining the quiescent center and controlling the differentiation of initial cells after exposure to IR. Results of several microarray experiments performed with whole seedlings and roots up to 5 h post-IR were compiled in a single table, which was used to import gene information and extract gene sets. Sequence and function homology searches; import of spatio-temporal, cell cycling, and mutant-constitutive expression characteristics; and a simplified functional classification system were used to identify novel genes in all functional classes. The hundreds of radiomodulated genes identified were not a random collection, but belonged to functional pathways such as those of the cell cycle; cell death and repair; DNA replication, repair, and recombination; and transcription; translation; and signaling, indicating the strong cell reprogramming and double-strand break abrogation functions of ATM checkpoints. Accordingly, genes in all functional classes were either down or up-regulated concomitantly with downregulation of chromatin deacetylases or upregulation of acetylases and methylases, respectively. Determining the early transcriptional indicators of
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Huh, Sung Un; Choi, La Mee; Lee, Gil-Je; Kim, Young Jin; Paek, Kyung-Hee
2012-12-01
WRKY transcription factors regulate biotic, abiotic, and developmental processes. In terms of plant defense, WRKY factors have important roles as positive and negative regulators via transcriptional regulation or protein-protein interaction. Here, we report the characterization of the gene encoding Capsicum annuum WRKY transcription factor d (CaWRKYd) isolated from microarray analysis in the Tobacco mosaic virus (TMV)-P(0)-inoculated hot pepper plants. CaWRKYd belongs to the WRKY IIa group, a very small clade in the WRKY subfamily, and WRKY IIa group has positive/negative regulatory roles in Arabidopsis and rice. CaWRKYd transcripts were induced by various plant defense-related hormone treatments and TMV-P(0) inoculation. Silencing of CaWRKYd affected TMV-P(0)-mediated hypersensitive response (HR) cell death and accumulation of TMV-P(0) coat protein in local and systemic leaves. Furthermore, expression of some pathogenesis-related (PR) genes and HR-related genes was reduced in the CaWRKYd-silenced plants compared with TRV2 vector control plants upon TMV-P(0) inoculation. CaWRKYd was confirmed to bind to the W-box. Thus CaWRKYd is a newly identified Capsicum annuum WRKY transcription factor that appears to be involved in TMV-P(0)-mediated HR cell death by regulating downstream gene expression. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.
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Ueno, Hiroshi; Kawakami, Hiroki; Nakagawa, Koji; Okada, Hiroshi; Ikuma, Naohiko; Aoyagi, Shinobu; Kokubo, Ken; Matsuo, Yutaka; Oshima, Takumi
2014-08-06
We studied the kinetics of the Diels-Alder reaction of Li(+)-encapsulated [60]fullerene with 1,3-cyclohexadiene and characterized the obtained product, [Li(+)@C60(C6H8)](PF6(-)). Compared with empty C60, Li(+)@C60 reacted 2400-fold faster at 303 K, a rate enhancement that corresponds to lowering the activation energy by 24.2 kJ mol(-1). The enhanced Diels-Alder reaction rate was well explained by DFT calculation at the M06-2X/6-31G(d) level of theory considering the reactant complex with dispersion corrections. The calculated activation energies for empty C60 and Li(+)@C60 (65.2 and 43.6 kJ mol(-1), respectively) agreed fairly well with the experimentally obtained values (67.4 and 44.0 kJ mol(-1), respectively). According to the calculation, the lowering of the transition state energy by Li(+) encapsulation was associated with stabilization of the reactant complex (by 14.1 kJ mol(-1)) and the [4 + 2] product (by 5.9 kJ mol(-1)) through favorable frontier molecular orbital interactions. The encapsulated Li(+) ion catalyzed the Diels-Alder reaction by lowering the LUMO of Li(+)@C60. This is the first detailed report on the kinetics of a Diels-Alder reaction catalyzed by an encapsulated Lewis acid catalyst rather than one coordinated to a heteroatom in the dienophile.
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Silwal-Pandit, Laxmi; Nord, Silje; von der Lippe Gythfeldt, Hedda; Møller, Elen K; Fleischer, Thomas; Rødland, Einar; Krohn, Marit; Borgen, Elin; Garred, Øystein; Olsen, Tone; Vu, Phuong; Skjerven, Helle; Fangberget, Anne; Holmen, Marit M; Schlitchting, Ellen; Wille, Elisabeth; Nordberg Stokke, Mette; Moen Vollan, Hans Kristian; Kristensen, Vessela; Langerød, Anita; Lundgren, Steinar; Wist, Erik; Naume, Bjørn; Lingjærde, Ole Christian; Børresen-Dale, Anne-Lise; Engebraaten, Olav
2017-08-15
Purpose: Chemotherapy-induced alterations to gene expression are due to transcriptional reprogramming of tumor cells or subclonal adaptations to treatment. The effect on whole-transcriptome mRNA expression was investigated in a randomized phase II clinical trial to assess the effect of neoadjuvant chemotherapy with the addition of bevacizumab. Experimental Design: Tumor biopsies and whole-transcriptome mRNA profiles were obtained at three fixed time points with 66 patients in each arm. Altogether, 358 specimens from 132 patients were available, representing the transcriptional state before treatment start, at 12 weeks and after treatment (25 weeks). Pathologic complete response (pCR) in breast and axillary nodes was the primary endpoint. Results: pCR was observed in 15 patients (23%) receiving bevacizumab and chemotherapy and 8 patients (12%) receiving only chemotherapy. In the estrogen receptor-positive patients, 11 of 54 (20%) treated with bevacizumab and chemotherapy achieved pCR, while only 3 of 57 (5%) treated with chemotherapy reached pCR. In patients with estrogen receptor-positive tumors treated with combination therapy, an elevated immune activity was associated with good response. Proliferation was reduced after treatment in both treatment arms and most pronounced in the combination therapy arm, where the reduction in proliferation accelerated during treatment. Transcriptional alterations during therapy were subtype specific, and the effect of adding bevacizumab was most evident for luminal-B tumors. Conclusions: Clinical response and gene expression response differed between patients receiving combination therapy and chemotherapy alone. The results may guide identification of patients likely to benefit from antiangiogenic therapy. Clin Cancer Res; 23(16); 4662-70. ©2017 AACR . ©2017 American Association for Cancer Research.
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The Complex Transcriptional Response of Acaryochloris marina to Different Oxygen Levels
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Miguel A. Hernández-Prieto
2017-02-01
Full Text Available Ancient oxygenic photosynthetic prokaryotes produced oxygen as a waste product, but existed for a long time under an oxygen-free (anoxic atmosphere, before an oxic atmosphere emerged. The change in oxygen levels in the atmosphere influenced the chemistry and structure of many enzymes that contained prosthetic groups that were inactivated by oxygen. In the genome of Acaryochloris marina, multiple gene copies exist for proteins that are normally encoded by a single gene copy in other cyanobacteria. Using high throughput RNA sequencing to profile transcriptome responses from cells grown under microoxic and hyperoxic conditions, we detected 8446 transcripts out of the 8462 annotated genes in the Cyanobase database. Two-thirds of the 50 most abundant transcripts are key proteins in photosynthesis. Microoxic conditions negatively affected the levels of expression of genes encoding photosynthetic complexes, with the exception of some subunits. In addition to the known regulation of the multiple copies of psbA, we detected a similar transcriptional pattern for psbJ and psbU, which might play a key role in the altered components of photosystem II. Furthermore, regulation of genes encoding proteins important for reactive oxygen species-scavenging is discussed at genome level, including, for the first time, specific small RNAs having possible regulatory roles under varying oxygen levels.
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The Complex Transcriptional Response of Acaryochloris marina to Different Oxygen Levels
Hernández-Prieto, Miguel A.; Lin, Yuankui; Chen, Min
2016-01-01
Ancient oxygenic photosynthetic prokaryotes produced oxygen as a waste product, but existed for a long time under an oxygen-free (anoxic) atmosphere, before an oxic atmosphere emerged. The change in oxygen levels in the atmosphere influenced the chemistry and structure of many enzymes that contained prosthetic groups that were inactivated by oxygen. In the genome of Acaryochloris marina, multiple gene copies exist for proteins that are normally encoded by a single gene copy in other cyanobacteria. Using high throughput RNA sequencing to profile transcriptome responses from cells grown under microoxic and hyperoxic conditions, we detected 8446 transcripts out of the 8462 annotated genes in the Cyanobase database. Two-thirds of the 50 most abundant transcripts are key proteins in photosynthesis. Microoxic conditions negatively affected the levels of expression of genes encoding photosynthetic complexes, with the exception of some subunits. In addition to the known regulation of the multiple copies of psbA, we detected a similar transcriptional pattern for psbJ and psbU, which might play a key role in the altered components of photosystem II. Furthermore, regulation of genes encoding proteins important for reactive oxygen species-scavenging is discussed at genome level, including, for the first time, specific small RNAs having possible regulatory roles under varying oxygen levels. PMID:27974439
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Digital Repository Service at National Institute of Oceanography (India)
Goswami, S.C.; KrishnaKumari, L.; Shrivastava, Y.
Diel variations in zooplankton biomass, common groups and proximate composition zooplankton at stations between Vengurla to Ratnagiri, along west coast of India were studied. Higher biomass values were obtained for the night samples (av = 80 ml/100...
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A Computational Experiment of the Endo versus Exo Preference in a Diels-Alder Reaction
Rowley, Christopher N.; Woo, Tom K.
2009-01-01
We have developed and tested a computational laboratory that investigates an endo versus exo Diels-Alder cycloaddition. This laboratory employed density functional theory (DFT) calculations to study the cycloaddition of N-phenylmaleimide to furan. The endo and exo stereoisomers of the product were distinguished by building the two isomers in a…
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Directory of Open Access Journals (Sweden)
Su Yang
Full Text Available The cyclic AMP receptor protein family of transcription factors regulates various metabolic pathways in bacteria, and also play roles in response to environmental changes. Here, we identify four homologs of the CRP family in Deinococcus radiodurans, one of which tolerates extremely high levels of oxidative stress and DNA-damaging reagents. Transcriptional levels of CRP were increased under hydrogen peroxide (H2O2 treatment during the stationary growth phase, indicating that CRPs function in response to oxidative stress. By constructing all CRP single knockout mutants, we found that the dr0997 mutant showed the lowest tolerance toward H2O2, ultraviolet radiation, ionizing radiation, and mitomycin C, while the phenotypes of the dr2362, dr0834, and dr1646 mutants showed slight or no significant differences from those of the wild-type strain. Taking advantage of the conservation of the CRP-binding site in many bacteria, we found that transcription of 18 genes, including genes encoding chromosome-partitioning protein (dr0998, Lon proteases (dr0349 and dr1974, NADH-quinone oxidoreductase (dr1506, thiosulfate sulfurtransferase (dr2531, the DNA repair protein UvsE (dr1819, PprA (dra0346, and RecN (dr1447, are directly regulated by DR0997. Quantitative real-time polymerase chain reaction (qRT-PCR analyses showed that certain genes involved in anti-oxidative responses, DNA repair, and various cellular pathways are transcriptionally attenuated in the dr0997 mutant. Interestingly, DR0997 also regulate the transcriptional levels of all CRP genes in this bacterium. These data suggest that DR0997 contributes to the extreme stress resistance of D. radiodurans via its regulatory role in multiple cellular pathways, such as anti-oxidation and DNA repair pathways.
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The unexpected product of Diels-Alder reaction between "indanocyclon" and maleimide
Dobrowolski, Michał A.; Roszkowski, Piotr; Struga, Marta; Szulczyk, Daniel
2017-02-01
A heterocyclic compound commonly known as "indanocyclon" undergoes an unexpected Diels-Alder addition with maleimide. The resulting product has been isolated and characterized in order to get an information about its structure and possible mechanism of the reaction. Extensive comparison of single crystal properties of 3-(2,8-dioxo-1,3-diphenyl-2,8-dihydrocyclopenta[a]inden-8a(1H)-yl)pyrrolidine-2,5-dione and favorable product of the reaction has been also performed.
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New L-Serine Derivative Ligands as Cocatalysts for Diels-Alder Reaction
Sousa, Carlos A. D.; Rodríguez-Borges, José E.; Freire, Cristina
2013-01-01
New L-serine derivative ligands were prepared and tested as cocatalyst in the Diels-Alder reactions between cyclopentadiene (CPD) and methyl acrylate, in the presence of several Lewis acids. The catalytic potential of the in situ formed complexes was evaluated based on the reaction yield. Bidentate serine ligands showed good ability to coordinate medium strength Lewis acids, thus boosting their catalytic activity. The synthesis of the L-serine ligands proved to be highly efficient and straightforward. PMID:24383009
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Dose-specific transcriptional responses in thyroid tissue in mice after 131I administration
International Nuclear Information System (INIS)
Rudqvist, Nils; Schüler, Emil; Parris, Toshima Z.; Langen, Britta; Helou, Khalil; Forssell-Aronsson, Eva
2015-01-01
Introduction: In the present investigation, microarray analysis was used to monitor transcriptional activity in thyroids in mice 24 h after 131 I exposure. The aims of this study were to 1) assess the transcriptional patterns associated with 131 I exposure in normal mouse thyroid tissue and 2) propose biomarkers for 131 I exposure of the thyroid. Methods: Adult BALB/c nude mice were i.v. injected with 13, 130 or 260 kBq of 131 I and killed 24 h after injection (absorbed dose to thyroid: 0.85, 8.5, or 17 Gy). Mock-treated mice were used as controls. Total RNA was extracted from thyroids and processed using the Illumina platform. Results: In total, 497, 546, and 90 transcripts were regulated (fold change ≥ 1.5) in the thyroid after 0.85, 8.5, and 17 Gy, respectively. These were involved in several biological functions, e.g. oxygen access, inflammation and immune response, and apoptosis/anti-apoptosis. Approximately 50% of the involved transcripts at each absorbed dose level were dose-specific, and 18 transcripts were commonly detected at all absorbed dose levels. The Agpat9, Plau, Prf1, and S100a8 gene expression displayed a monotone decrease in regulation with absorbed dose, and further studies need to be performed to evaluate if they may be useful as dose-related biomarkers for 131I exposure. Conclusion: Distinct and substantial differences in gene expression and affected biological functions were detected at the different absorbed dose levels. The transcriptional profiles were specific for the different absorbed dose levels. We propose that the Agpat9, Plau, Prf1, and S100a8 genes might be novel potential absorbed dose-related biomarkers to 131 I exposure of thyroid. Advances in knowledge: During the recent years, genomic techniques have been developed; however, they have not been fully utilized in nuclear medicine and radiation biology. We have used RNA microarrays to investigate genome-wide transcriptional regulations in thyroid tissue in mice after low
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Anderson, Samantha R; Wiens, John J
2017-08-01
Many animals are active only during a particular time (e.g., day vs. night), a partitioning that may have important consequences for species coexistence. An open question is the extent to which this diel activity niche is evolutionarily conserved or labile. Here, we analyze diel activity data across a phylogeny of 1914 tetrapod species. We find strong phylogenetic signal, showing that closely related species tend to share similar activity patterns. Ancestral reconstructions show that nocturnality was the most likely ancestral diel activity pattern for tetrapods and many major clades within it (e.g., amphibians, mammals). Remarkably, nocturnal activity appears to have been maintained continuously in some lineages for ∼350 million years. Thus, we show that traits involved in local-scale resource partitioning can be conserved over strikingly deep evolutionary time scales. We also demonstrate a potentially important (but often overlooked) metric of niche conservatism. Finally, we show that diurnal lineages appear to have faster speciation and diversification rates than nocturnal lineages, which may explain why there are presently more diurnal tetrapod species even though diurnality appears to have evolved more recently. Overall, our results may have implications for studies of community ecology, species richness, and the evolution of diet and communication systems. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.
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Directory of Open Access Journals (Sweden)
Ronald N. Warrener
2000-12-01
Full Text Available Ab initio and DFT quantum chemical calculations have been applied to a study of the Diels-Alder reaction of o-benzoquinone as diene and norbornadiene as dienophile. Transition states for the different reactions are located and activation energies estimated. The prefered exo-À-facial selectivity and exo,endo-stereoselectivity exhibited in this cycloaddition are readily predicted using RHF/3-21G or higher levels of calculations. Differences between experimentally observed results and calculations may be explained by the postulation of a second, nonconcerted biradical mechanism leading to formation of hetero Diels-Alder products.
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Variation in the transcriptional response of threatened coral larvae to elevated temperatures.
Polato, Nicholas R; Altman, Naomi S; Baums, Iliana B
2013-03-01
Coral populations have declined worldwide largely due to increased sea surface temperatures. Recovery of coral populations depends in part upon larval recruitment. Many corals reproduce during the warmest time of year when further increases in temperature can lead to low fertilization rates of eggs and high larval mortality. Microarray experiments were designed to capture and assess variability in the thermal stress responses of Acropora palmata larvae from Puerto Rico. Transcription profiles showed a striking acceleration of normal developmental gene expression patterns with increased temperature. The transcriptional response to heat suggested rapid depletion of larval energy stores via peroxisomal lipid oxidation and included key enzymes that indicated the activation of the glyoxylate cycle. High temperature also resulted in expression differences in key developmental signalling genes including the conserved WNT pathway that is critical for pattern formation and tissue differentiation in developing embryos. Expression of these and other important developmental and thermal stress genes such as ferritin, heat shock proteins, cytoskeletal components, cell adhesion and autophagy proteins also varied among larvae derived from different parent colonies. Disruption of normal developmental and metabolic processes will have negative impacts on larval survival and dispersal as temperatures rise. However, it appears that variation in larval response to high temperature remains despite the dramatic population declines. Further research is needed to determine whether this variation is heritable or attributable to maternal effects. © 2013 Blackwell Publishing Ltd.
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Diels-Alder cyclo-addition as an efficient tool for linking π-donors onto fullerene C60
International Nuclear Information System (INIS)
Hudhomme, P.
2006-01-01
Diels-Alder reaction of endo-cyclic, acyclic 1,3-dienes or (hetero) o-quinodimethanes with the dienophilic fullerene C 60 is presented as an efficient tool for linking electro-active units giving rise to systems where both the donor and C 60 partners take up well defined volumes and orientations with respect to one another. While porphyrin is the most frequently used electron donor in artificial photosynthetic models, C 60 -based tetrathiafulvalene (TTF) or p-conjugated oligomer adducts remain interesting candidates for the preparation of photovoltaic devices. In this account, we focus on the use of the Diels-Alder cyclo-addition and its use in the synthesis of TTF-C 60 dyads, (TTF) n -C 60 polyads and C 60 -TTF-C 60 dumbbells as part of ongoing research into materials which display efficient photo-induced electron transfer. (author)
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Jha, Sanjiv; Brown, Katie; Subramanian, Gopinath
We apply a recent formulation for searching minimum energy reaction path (MERP) and saddle point to atomic systems subjected to an external force. We demonstrate the effect of a loading modality resembling hydrostatic pressure on the trans to cis conformational change of 1,3-butadiene, and the simplest Diels-Alder reaction between ethylene and 1,3-butadiene. The calculated MERP and saddle points on the generalized force modified potential energy surface (G-FMPES) are compared with the corresponding quantities on an unmodified potential energy surface. Our study is performed using electronic structure calculations at the HF/6-31G** level as implemented in the AIMS-MOLPRO code. Our calculations suggest that the added compressive pressure lowers the energy of cis butadiene. The activation energy barrier for the concerted Diels-Alder reaction is found to decrease progressively with increasing compressive pressure.
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Responses of human cells to ZnO nanoparticles: a gene transcription study†
Moos, Philip J.; Olszewski, Kyle; Honeggar, Matthew; Cassidy, Pamela; Leachman, Sancy; Woessner, David; Cutler, N. Shane; Veranth, John M.
2013-01-01
The gene transcript profile responses to metal oxide nanoparticles was studied using human cell lines derived from the colon and skin tumors. Much of the research on nanoparticle toxicology has focused on models of inhalation and intact skin exposure, and effects of ingestion exposure and application to diseased skin are relatively unknown. Powders of nominally nanosized SiO2, TiO2, ZnO and Fe2O3 were chosen because these substances are widely used in consumer products. The four oxides were evaluated using colon-derived cell lines, RKO and CaCo-2, and ZnO and TiO2 were evaluated further using skin-derived cell lines HaCaT and SK Mel-28. ZnO induced the most notable gene transcription changes, even though this material was applied at the lowest concentration. Nano-sized and conventional ZnO induced similar responses suggesting common mechanisms of action. The results showed neither a non-specific response pattern common to all substances nor synergy of the particles with TNF-α cotreatment. The response to ZnO was not consistent with a pronounced proinflammatory signature, but involved changes in metal metabolism, chaperonin proteins, and protein folding genes. This response was observed in all cell lines when ZnO was in contact with the human cells. When the cells were exposed to soluble Zn, the genes involved in metal metabolism were induced but the genes involved in protein refoldling were unaffected. This provides some of the first data on the effects of commercial metal oxide nanoparticles on human colon-derived and skin-derived cells. PMID:21769377
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Transcriptional Responses in the Hemiparasitic Plant Triphysaria versicolor to Host Plant Signals1[w
Matvienko, Marta; Torres, Manuel J.; Yoder, John I.
2001-01-01
Parasitic plants in the Scrophulariaceae use chemicals released by host plant roots to signal developmental processes critical for heterotrophy. Haustoria, parasitic plant structures that attach to and invade host roots, develop on roots of the hemiparasitic plant Triphysaria versicolor within a few hours of exposure to either maize (Zea mays) root exudate or purified haustoria-inducing factors. We prepared a normalized, subtractive cDNA library enriched for transcripts differentially abundant in T. versicolor root tips treated with the allelopathic quinone 2,6-dimethoxybenzoquinone (DMBQ). Northern analyses estimated that about 10% of the cDNAs represent transcripts strongly up-regulated in roots exposed to DMBQ. Northern and reverse northern analyses demonstrated that most DMBQ-responsive messages were similarly up-regulated in T. versicolor roots exposed to maize root exudates. From the cDNA sequences we assembled a unigene set of 137 distinct transcripts and assigned functions by homology comparisons. Many of the proteins encoded by the transcripts are predicted to function in quinone detoxification, whereas others are more likely associated with haustorium development. The identification of genes transcriptionally regulated by haustorium-inducing factors provides a framework for dissecting genetic pathways recruited by parasitic plants during the transition to heterotrophic growth. PMID:11553755
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Silvestri, Michael G.; Dills, Charles E.
1989-01-01
Describes an organic chemistry experiment for teaching the basic concepts of chemical kinetics. Provides background information about first- and second-order reactions, experimental procedures of the Diels-Alder reaction between cyclopentadiene and dimethyl fumarate, and the experimental results. (YP)
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Danisman, Selahattin
2016-01-01
Plants are sessile and as such their reactions to environmental challenges differ from those of mobile organisms. Many adaptions involve growth responses and hence, growth regulation is one of the most crucial biological processes for plant survival and fitness. The plant-specific TEOSINTE BRANCHED 1, CYCLOIDEA, PCF1 (TCP) transcription factor family is involved in plant development from cradle to grave, i.e., from seed germination throughout vegetative development until the formation of flowers and fruits. TCP transcription factors have an evolutionary conserved role as regulators in a variety of plant species, including orchids, tomatoes, peas, poplar, cotton, rice and the model plant Arabidopsis. Early TCP research focused on the regulatory functions of TCPs in the development of diverse organs via the cell cycle. Later research uncovered that TCP transcription factors are not static developmental regulators but crucial growth regulators that translate diverse endogenous and environmental signals into growth responses best fitted to ensure plant fitness and health. I will recapitulate the research on TCPs in this review focusing on two topics: the discovery of TCPs and the elucidation of their evolutionarily conserved roles across the plant kingdom, and the variety of signals, both endogenous (circadian clock, plant hormones) and environmental (pathogens, light, nutrients), TCPs respond to in the course of their developmental roles.
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Castellanos-Galindo, G. A.; Krumme, U.
2014-08-01
Intertidal fish assemblages are thought to respond to tidal and diel rhythms although the assumption that these patterns are stable over long time scales (>1 year) is largely untested. Testing the validity of this assumption is necessary to assess whether short-term temporal patterns, once established, can be extrapolated over time and give a better understanding of the temporal dynamics of fish assemblages in coastal habitats. Here, we compare the fish assemblage structure from two intertidal mangrove creeks in North Brazil (Bragança Peninsula, Caeté estuary) sampled with the same sampling methodology (block nets), effort (two lunar cycles) and design (accounting for the combination of tidal and diel cycle) in the rainy seasons of 1999 and 2012 to evaluate the persistence, stability and recurrence of short-term patterns in the fish community organization. The interaction of tidal and diel cycles (inundations at spring tide-night, spring tide-day, neap tide-night, neap tide-day), found to be stable after 13 years, resulted in recurrent and stable intertidal mangrove fish assemblage compositions. The intertidal mangrove creek fish assemblage consisted of a persistent number of dominant species (seven). However, there were notable changes in fish catch mass, abundance and species dominance between 1999 and 2012. The most severe drought in North Brazil in 30 years, linked to lower precipitation and river runoff in the rainy season of 2012, may have resulted in (1) lower abundance of small juveniles of several dominant species in this assemblage (especially Ariidae - Cathorops agassizii and Sciades herzbergii) and (2) increased dominance of large-sized specimens of the tetraodontid Colomesus psittacus. Our findings highlight: (1) the overriding importance and stability of the interactive pulse of the tidal and diel cycles in determining short-term temporal patterns in intertidal mangrove fish assemblages in neotropical macrotidal estuaries despite the occurrence of
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Directory of Open Access Journals (Sweden)
Walker M Andrew
2010-07-01
Full Text Available Abstract Background Plant cytochrome P450 monooxygenases (CYP mediate synthesis and metabolism of many physiologically important primary and secondary compounds that are related to plant defense against a range of pathogenic microbes and insects. To determine if cytochrome P450 monooxygenases are involved in defense response to Xylella fastidiosa (Xf infection, we investigated expression and regulatory mechanisms of the cytochrome P450 monooxygenase CYP736B gene in both disease resistant and susceptible grapevines. Results Cloning of genomic DNA and cDNA revealed that the CYP736B gene was composed of two exons and one intron with GT as a donor site and AG as an acceptor site. CYP736B transcript was up-regulated in PD-resistant plants and down-regulated in PD-susceptible plants 6 weeks after Xf inoculation. However, CYP736B expression was very low in stem tissues at all evaluated time points. 5'RACE and 3'RACE sequence analyses revealed that there were three candidate transcription start sites (TSS in the upstream region and three candidate polyadenylation (PolyA sites in the downstream region of CYP736B. Usage frequencies of each transcription initiation site and each polyadenylation site varied depending on plant genotype, developmental stage, tissue, and treatment. These results demonstrate that expression of CYP736B is regulated developmentally and in response to Xf infection at both transcriptional and post-transcriptional levels. Multiple transcription start and polyadenylation sites contribute to regulation of CYP736B expression. Conclusions This report provides evidence that the cytochrome P450 monooxygenase CYP736B gene is involved in defense response at a specific stage of Xf infection in grapevines; multiple transcription initiation and polyadenylation sites exist for CYP736B in grapevine; and coordinative and selective use of transcription initiation and polyadenylation sites play an important role in regulation of CYP736B expression
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Pascual, Ma Belén; Cánovas, Francisco M; Ávila, Concepción
2015-10-24
NAC transcription factors comprise a large plant-specific gene family involved in the regulation of diverse biological processes. Despite the growing number of studies on NAC transcription factors in various species, little information is available about this family in conifers. The goal of this study was to identify the NAC transcription family in maritime pine (Pinus pinaster), to characterize ATAF-like genes in response to various stresses and to study their molecular regulation. We have isolated two maritime pine NAC genes and using a transient expression assay in N. benthamiana leaves estudied the promoter jasmonate response. In this study, we identified 37 NAC genes from maritime pine and classified them into six main subfamilies. The largest group includes 12 sequences corresponding to stress-related genes. Two of these NAC genes, PpNAC2 and PpNAC3, were isolated and their expression profiles were examined at various developmental stages and in response to various types of stress. The expression of both genes was strongly induced by methyl jasmonate (MeJA), mechanical wounding, and high salinity. The promoter regions of these genes were shown to contain cis-elements involved in the stress response and plant hormonal regulation, including E-boxes, which are commonly found in the promoters of genes that respond to jasmonate, and binding sites for bHLH proteins. Using a transient expression assay in N. benthamiana leaves, we found that the promoter of PpNAC3 was rapidly induced upon MeJA treatment, while this response disappeared in plants in which the transcription factor NbbHLH2 was silenced. Our results suggest that PpNAC2 and PpNAC3 encode stress-responsive NAC transcription factors involved in the jasmonate response in pine. Furthermore, these data also suggest that the jasmonate signaling pathway is conserved between angiosperms and gymnosperms. These findings may be useful for engineering stress tolerance in pine via biotechnological approaches.
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Okay, Sezer; Derelli, Ebru; Unver, Turgay
2014-10-01
The WRKY superfamily of transcription factors was shown to be involved in biotic and abiotic stress responses in plants such as wheat (Triticum aestivum L.), one of the major crops largely cultivated and consumed all over the world. Drought is an important abiotic stress resulting in a considerable amount of loss in agronomical yield. Therefore, identification of drought responsive WRKY members in wheat has a profound significance. Here, a total of 160 TaWRKY proteins were characterized according to sequence similarity, motif varieties, and their phylogenetic relationships. The conserved sequences of the TaWRKYs were aligned and classified into three main groups and five subgroups. A novel motif in wheat, WRKYGQR, was identified. To putatively determine the drought responsive TaWRKY members, publicly available RNA-Seq data were analyzed for the first time in this study. Through in silico searches, 35 transcripts were detected having an identity to ten known TaWRKY genes. Furthermore, relative expression levels of TaWRKY16/TaWRKY16-A, TaWRKY17, TaWRKY19-C, TaWRKY24, TaWRKY59, TaWRKY61, and TaWRKY82 were measured in root and leaf tissues of drought-tolerant Sivas 111/33 and susceptible Atay 85 cultivars. All of the quantified TaWRKY transcripts were found to be up-regulated in root tissue of Sivas 111/33. Differential expression of TaWRKY16, TaWRKY24, TaWRKY59, TaWRKY61 and TaWRKY82 genes was discovered for the first time upon drought stress in wheat. These comprehensive analyses bestow a better understanding about the WRKY TFs in bread wheat under water deficit, and increased number of drought responsive WRKYs would contribute to the molecular breeding of tolerant wheat cultivars.
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Foyer, Christine H; Verrall, Susan R; Hancock, Robert D
2015-02-01
Phloem-feeding insects (PFIs), of which aphids are the largest group, are major agricultural pests causing extensive damage to crop plants. In contrast to chewing insects, the nature of the plant response to PFIs remains poorly characterized. Scrutiny of the literature concerning transcriptional responses of model and crop plant species to PFIs reveals surprisingly little consensus with respect to the transcripts showing altered abundance following infestation. Nevertheless, core features of the transcriptional response to PFIs can be defined in Arabidopsis thaliana. This comparison of the PFI-associated transcriptional response observed in A. thaliana infested by the generalists Myzus persicae and Bemisia tabaci with the specialist Brevicoryne brassicae highlights the importance of calcium-dependent and receptor kinase-associated signalling. We discuss these findings within the context of the complex cross-talk between the different hormones regulating basal immune response mechanisms in plants. We identify PFI-responsive genes, highlighting the importance of cell wall-associated kinases in plant-PFI interactions, as well as the significant role of kinases containing the domain of unknown function 26. A common feature of plant-PFI interaction is enhanced abundance of transcripts encoding WRKY transcription factors. However, significant divergence was observed with respect to secondary metabolism dependent upon the insect attacker. Transcripts encoding enzymes and proteins associated with glucosinolate metabolism were decreased following attack by the generalist M. persicae but not by the specialist B. brassicae. This analysis provides a comprehensive overview of the molecular patterns associated with the plant response to PFIs and suggests that plants recognize and respond to perturbations in the cell wall occurring during PFI infestation. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights
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Naphthalene Diels-Alder in a self-assembled molecular flask.
Murase, Takashi; Horiuchi, Shinnosuke; Fujita, Makoto
2010-03-10
Despite its inertness toward pericyclic reactions under common conditions, naphthalenes readily undergo Diels-Alder reactions when coencapsulated with a suitable dienophile within the cavity of a self-assembled host. Localization of the reactant pair significantly reduces the entropic cost of the reaction, and preorganization within the host cavity controls both the regio- and stereoselectivity of the reaction: electronically disfavored exo adducts were obtained, and with substituted naphthalenes, the reaction takes place on the less electron-rich, unsubstituted ring. Our findings highlight the fact that judicious tuning of substrate size and shape within molecular flasks can unveil new and unusual reactivities for otherwise unreactive molecules.
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Sulfate Reduction and Thiosulfate Transformations in a Cyanobacterial Mat during a Diel Oxygen Cycle
DEFF Research Database (Denmark)
JØRGENSEN, BB
1994-01-01
Bacterial sulfate reduction and transformations of thiosulfate were studied with radiotracers in a Microcoleus chthono-plastes-dominated microbial mat growing in a hypersaline pond at the Red Sea. The study showed how a diel cycle of oxygen evolution affected respiration by sulfate-reducing bacte......Bacterial sulfate reduction and transformations of thiosulfate were studied with radiotracers in a Microcoleus chthono-plastes-dominated microbial mat growing in a hypersaline pond at the Red Sea. The study showed how a diel cycle of oxygen evolution affected respiration by sulfate......-reducing bacteria and the metabolism of thiosulfate through oxidative and reductive pathways. Sulfate reduction occurred in both oxic and anoxic layers of the mat and varied diurnally, apparently according to temperature rather than to oxygen. Time course experiments showed that the radiotracer method...... underestimated sulfate reduction in the oxic zone due to rapid reoxidation of the produced sulfide. Extremely high reduction rates of up to 10 mu mol cm(-3) d(-1) were measured just below the euphotic zone. Although thiosulfate was simultaneously oxidized, reduced and disproportionated by bacteria in all layers...
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Vertical nitrogen flux from the oceanic photic zone by diel migrant zooplankton and nekton
Longhurst, Alan R.; Glen Harrison, W.
1988-06-01
Where the photic zone is a biological steady-state, the downward flux of organic material across the pycnocline to the interior of the ocean is thought to be balanced by upward turbulent flux of inorganic nitrogen across the nutricline. This model ignores a significant downward dissolved nitrogen flux caused by the diel vertical migration of interzonal zooplankton and nekton that feed in the photic zone at night and excrete nitrogenous compounds at depth by day. In the oligotrophic ocean this flux can be equivalent to the flux of particulate organic nitrogen from the photic zone in the form of faecal pellets and organic flocculates. Where nitrogen is the limiting plant nutrient, and the flux by diel migration of interzonal plankton is significant compared to other nitrogen exports from the photic zone, there must be an upward revision of previous estimates for the ratio of new to total primary production in the photic zone if a nutrient balance is to be maintained. This upward revision is of the order 5-100% depending on the oceanographic regime.
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Pérez-Sayas, Consuelo; Aguilar-Fenollosa, Ernestina; Hurtado, Mónica A; Jaques, Josep A; Pina, Tatiana
2017-06-16
Predatory mites of the Phytoseiidae family are considered one of the most important groups of natural enemies used in biological control. The behavioral patterns of arthropods can differ greatly daily and seasonally; however, there is a lack of literature related to Phytoseiidae diel and seasonal predation patterns. The predatory activity of three phytoseiid species (two Tetranychidae-specialists, Phytoseiulus persimilis and Neoseiulus californicus, and one omnivore, Euseius stipulatus) that occur naturally in Spanish citrus orchards was observed under laboratory conditions in winter and summer. The temperature and photoperiod of the climatic chamber where the mites were reared did not change during the experiment. Our study demonstrates that phytoseiids can exhibit diel and seasonal predatory patterns when feeding on Tetranychus urticae (Acari: Tetranychidae). Neoseiulus californicus was revealed to be a nocturnal predator in summer but diurnal in winter. In contrast, P. persimilis activity was maximal during the daytime, and E. stipulatus showed no clear daily predation patterns. The predatory patterns described in this study should be taken into account when designing laboratory studies and also in field samplings, especially when applying molecular techniques to unveil trophic relationships. © 2017 Institute of Zoology, Chinese Academy of Sciences.
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Energy Technology Data Exchange (ETDEWEB)
Looman, Arún, E-mail: arun.looman@scu.edu.au [National Marine Science Centre, Southern Cross University, Coffs Harbour, New South Wales (Australia); School of Environment, Science, and Engineering, Southern Cross University, Lismore, New South Wales (Australia); Santos, Isaac R.; Tait, Douglas R.; Webb, Jackie R. [National Marine Science Centre, Southern Cross University, Coffs Harbour, New South Wales (Australia); School of Environment, Science, and Engineering, Southern Cross University, Lismore, New South Wales (Australia); Sullivan, Caroline A.; Maher, Damien T. [School of Environment, Science, and Engineering, Southern Cross University, Lismore, New South Wales (Australia)
2016-04-15
Catchment headwaters comprise the majority of all stream length globally, however, carbon (C) dynamics in these systems remains poorly understood. We combined continuous measurements of pCO{sub 2} and radon ({sup 222}Rn, a natural groundwater tracer) with discrete sampling for particulate organic, dissolved organic and inorganic carbon (POC, DOC, and DIC) to assess the short-term carbon dynamics of a pristine subtropical headwater stream in Australia, over contrasting hydrologic regimes of drought, flash-flooding and recovery. Observations over 23 days revealed a shift from carbon losses dominated by CO{sub 2} outgassing under conditions of low flow (66.4 ± 0.4% of carbon export) to downstream exports of carbon during the flood (87.8 ± 9.7% of carbon export). DOC was the dominant form of downstream exports throughout the study (DOC:DIC:POC = 0.82:0.05:0.13). The broadest diel variability among variables occurred during the drought phase, with diel variability up to 662 μatm d{sup −1} (or 27 μM [CO{sub 2}*] d{sup −1}), 17 μM d{sup −1} and 268 Bq m{sup −3} d{sup −1} for pCO{sub 2}, dissolved oxygen and {sup 222}Rn, respectively. Diel dynamics indicated multiple interrelated drivers of stream water chemistry including groundwater seepage and in-stream metabolism. The catchment exported terrestrial carbon throughout the field campaign, with a mean net stream flux of 4.7 ± 7.8 mmol C m{sup −2} (catchment area) d{sup −1} which is equivalent to 1.4 ± 2.3% of the estimated local terrestrial net primary production. Our observations highlight the importance of accounting for hydrological extremes when assessing the carbon budgets and ecosystem metabolism of headwater streams, and provide a first estimate of aquatic carbon exports from a pristine Australian subtropical rainforest. - Highlights: • First carbon export estimates of a pristine Australian subtropical headwater catchment. • Metabolism and hydrology were drivers of aquatic carbon flux.
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International Nuclear Information System (INIS)
Looman, Arún; Santos, Isaac R.; Tait, Douglas R.; Webb, Jackie R.; Sullivan, Caroline A.; Maher, Damien T.
2016-01-01
Catchment headwaters comprise the majority of all stream length globally, however, carbon (C) dynamics in these systems remains poorly understood. We combined continuous measurements of pCO_2 and radon ("2"2"2Rn, a natural groundwater tracer) with discrete sampling for particulate organic, dissolved organic and inorganic carbon (POC, DOC, and DIC) to assess the short-term carbon dynamics of a pristine subtropical headwater stream in Australia, over contrasting hydrologic regimes of drought, flash-flooding and recovery. Observations over 23 days revealed a shift from carbon losses dominated by CO_2 outgassing under conditions of low flow (66.4 ± 0.4% of carbon export) to downstream exports of carbon during the flood (87.8 ± 9.7% of carbon export). DOC was the dominant form of downstream exports throughout the study (DOC:DIC:POC = 0.82:0.05:0.13). The broadest diel variability among variables occurred during the drought phase, with diel variability up to 662 μatm d"−"1 (or 27 μM [CO_2*] d"−"1), 17 μM d"−"1 and 268 Bq m"−"3 d"−"1 for pCO_2, dissolved oxygen and "2"2"2Rn, respectively. Diel dynamics indicated multiple interrelated drivers of stream water chemistry including groundwater seepage and in-stream metabolism. The catchment exported terrestrial carbon throughout the field campaign, with a mean net stream flux of 4.7 ± 7.8 mmol C m"−"2 (catchment area) d"−"1 which is equivalent to 1.4 ± 2.3% of the estimated local terrestrial net primary production. Our observations highlight the importance of accounting for hydrological extremes when assessing the carbon budgets and ecosystem metabolism of headwater streams, and provide a first estimate of aquatic carbon exports from a pristine Australian subtropical rainforest. - Highlights: • First carbon export estimates of a pristine Australian subtropical headwater catchment. • Metabolism and hydrology were drivers of aquatic carbon flux. • Catchment exports ranged between 1.1 and 18.6 mmol C m
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Karunakaran, Jayachandran; Mohanakrishnan, Arasambattu K
2018-02-16
Diels-Alder reaction of 1,3-diarylbenzo[c]furan/cyclopentadienone with TTF followed by triflic acid mediated cleavage of the resulting adducts led to the formation of the respective 1,4-diaryl substituted naphthalenes, fluoranthenes, and fluorenones. The photophysical properties of representative diaryl-substituted hydrocarbons are also reported.
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Czech Academy of Sciences Publication Activity Database
Drahota, P.; Nováková, B.; Matoušek, Tomáš; Mihaljevič, M.; Rohovec, Jan; Filippi, Michal
2013-01-01
Roč. 31, APR (2013), s. 84-93 ISSN 0883-2927 Institutional research plan: CEZ:AV0Z30130516 Institutional support: RVO:68081715 ; RVO:67985831 Keywords : arsenic * molybdenum * antimony * trace elements * diel cycle Subject RIV: CB - Analytical Chemistry, Separation; DD - Geochemistry (GLU-S) Impact factor: 2.021, year: 2013
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VLDL hydrolysis by hepatic lipase regulates PPARδ transcriptional responses.
Directory of Open Access Journals (Sweden)
Jonathan D Brown
Full Text Available PPARs (α,γ,δ are a family of ligand-activated transcription factors that regulate energy balance, including lipid metabolism. Despite these critical functions, the integration between specific pathways of lipid metabolism and distinct PPAR responses remains obscure. Previous work has revealed that lipolytic pathways can activate PPARs. Whether hepatic lipase (HL, an enzyme that regulates VLDL and HDL catabolism, participates in PPAR responses is unknown.Using PPAR ligand binding domain transactivation assays, we found that HL interacted with triglyceride-rich VLDL (>HDL≫LDL, IDL to activate PPARδ preferentially over PPARα or PPARγ, an effect dependent on HL catalytic activity. In cell free ligand displacement assays, VLDL hydrolysis by HL activated PPARδ in a VLDL-concentration dependent manner. Extended further, VLDL stimulation of HL-expressing HUVECs and FAO hepatoma cells increased mRNA expression of canonical PPARδ target genes, including adipocyte differentiation related protein (ADRP, angiopoietin like protein 4 and pyruvate dehydrogenase kinase-4. HL/VLDL regulated ADRP through a PPRE in the promoter region of this gene. In vivo, adenoviral-mediated hepatic HL expression in C57BL/6 mice increased hepatic ADRP mRNA levels by 30%. In ob/ob mice, a model with higher triglycerides than C57BL/6 mice, HL overexpression increased ADRP expression by 70%, demonstrating the importance of triglyceride substrate for HL-mediated PPARδ activation. Global metabolite profiling identified HL/VLDL released fatty acids including oleic acid and palmitoleic acid that were capable of recapitulating PPARδ activation and ADRP gene regulation in vitro.These data define a novel pathway involving HL hydrolysis of VLDL that activates PPARδ through generation of specific monounsaturated fatty acids. These data also demonstrate how integrating cell biology with metabolomic approaches provides insight into specific lipid mediators and pathways of lipid
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Wijnen, J.W.; Engberts, Jan B.F.N.
1997-01-01
The retro-Diels-Alder (RDA) reaction of anthracenedione 1a proceeds considerably faster in aqueous solutions than in organic solvents. Addition of organic solvents to water retards the reaction, whereas glucose induces a modest acceleration. SDS micelles induce a considerable retardation, but even
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Li, Wei; Cui, Xiao; Meng, Zhaolu; Huang, Xiahe; Xie, Qi; Wu, Heng; Jin, Hailing; Zhang, Dabing; Liang, Wanqi
2012-01-01
The accumulation of a number of small RNAs in plants is affected by abscisic acid (ABA) and abiotic stresses, but the underlying mechanisms are poorly understood. The miR168-mediated feedback regulatory loop regulates ARGONAUTE1 (AGO1) homeostasis, which is crucial for gene expression modulation and plant development. Here, we reveal a transcriptional regulatory mechanism by which MIR168 controls AGO1 homeostasis during ABA treatment and abiotic stress responses in Arabidopsis (Arabidopsis thaliana). Plants overexpressing MIR168a and the AGO1 loss-of-function mutant ago1-27 display ABA hypersensitivity and drought tolerance, while the mir168a-2 mutant shows ABA hyposensitivity and drought hypersensitivity. Both the precursor and mature miR168 were induced under ABA and several abiotic stress treatments, but no obvious decrease for the target of miR168, AGO1, was shown under the same conditions. However, promoter activity analysis indicated that AGO1 transcription activity was increased under ABA and drought treatments, suggesting that transcriptional elevation of MIR168a is required for maintaining a stable AGO1 transcript level during the stress response. Furthermore, we showed both in vitro and in vivo that the transcription of MIR168a is directly regulated by four abscisic acid-responsive element (ABRE) binding factors, which bind to the ABRE cis-element within the MIR168a promoter. This ABRE motif is also found in the promoter of MIR168a homologs in diverse plant species. Our findings suggest that transcriptional regulation of miR168 and posttranscriptional control of AGO1 homeostasis may play an important and conserved role in stress response and signal transduction in plants. PMID:22247272
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Energy Technology Data Exchange (ETDEWEB)
Park, Serk In, E-mail: serkin@korea.edu [Department of Biochemistry and Molecular Biology, Korea University College of Medicine, Seoul (Korea, Republic of); The BK21 Plus Program for Biomedical Sciences, Korea University College of Medicine, Seoul (Korea, Republic of); Department of Medicine and Center for Bone Biology, Vanderbilt University School of Medicine, Nashville, TN (United States); Park, Sung-Jun [Department of Biochemistry and Molecular Biology, Korea University College of Medicine, Seoul (Korea, Republic of); Laboratory of Obesity and Aging Research, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD (United States); Lee, Junghan; Kim, Hye Eun; Park, Su Jin; Sohn, Jeong-Won [Department of Biochemistry and Molecular Biology, Korea University College of Medicine, Seoul (Korea, Republic of); Park, Yun Gyu, E-mail: parkyg@korea.ac.kr [Department of Biochemistry and Molecular Biology, Korea University College of Medicine, Seoul (Korea, Republic of)
2016-01-15
The radiation stress induces cytotoxic responses of cell death as well as cytoprotective responses of cell survival. Understanding exact cellular mechanism and signal transduction pathways is important in improving cancer radiotherapy. Increasing evidence suggests that cyclic AMP response element binding protein (CREB)/activating transcription factor (ATF) family proteins act as a survival factor and a signaling molecule in response to stress. We postulated that CREB inhibition via CRE decoy oligonucleotide increases tumor cell sensitization to γ-irradiation-induced cytotoxic stress. In the present study, we demonstrate that CREB phosphorylation and CREB DNA-protein complex formation increased in time- and radiation dose-dependent manners, while there was no significant change in total protein level of CREB. In addition, CREB was phosphorylated in response to γ-irradiation through p38 MAPK pathway. Further investigation revealed that CREB blockade by decoy oligonucleotides functionally inhibited transactivation of CREB, and significantly increased radiosensitivity of multiple human cancer cell lines including TP53- and/or RB-mutated cells with minimal effects on normal cells. We also demonstrate that tumor cells ectopically expressing dominant negative mutant CREB (KCREB) and the cells treated with p38 MAPK inhibitors were more sensitive to γ-irradiation than wild type parental cells or control-treated cells. Taken together, we conclude that CREB protects tumor cells from γ-irradiation, and combination of CREB inhibition plus ionizing radiation will be a promising radiotherapeutic approach. - Highlights: • γ-Irradiation induced CREB phosphorylation and CRE-directed transcription in tumor. • γ-Irradiation-induced transcriptional activation of CREB was via p38 MAPK pathway. • CRE blockade increased radiosensitivity of tumor cells but not of normal cells. • CRE decoy oligonucleotides or p38 MAPK inhibitors can be used as radiosensitizers.
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International Nuclear Information System (INIS)
Park, Serk In; Park, Sung-Jun; Lee, Junghan; Kim, Hye Eun; Park, Su Jin; Sohn, Jeong-Won; Park, Yun Gyu
2016-01-01
The radiation stress induces cytotoxic responses of cell death as well as cytoprotective responses of cell survival. Understanding exact cellular mechanism and signal transduction pathways is important in improving cancer radiotherapy. Increasing evidence suggests that cyclic AMP response element binding protein (CREB)/activating transcription factor (ATF) family proteins act as a survival factor and a signaling molecule in response to stress. We postulated that CREB inhibition via CRE decoy oligonucleotide increases tumor cell sensitization to γ-irradiation-induced cytotoxic stress. In the present study, we demonstrate that CREB phosphorylation and CREB DNA-protein complex formation increased in time- and radiation dose-dependent manners, while there was no significant change in total protein level of CREB. In addition, CREB was phosphorylated in response to γ-irradiation through p38 MAPK pathway. Further investigation revealed that CREB blockade by decoy oligonucleotides functionally inhibited transactivation of CREB, and significantly increased radiosensitivity of multiple human cancer cell lines including TP53- and/or RB-mutated cells with minimal effects on normal cells. We also demonstrate that tumor cells ectopically expressing dominant negative mutant CREB (KCREB) and the cells treated with p38 MAPK inhibitors were more sensitive to γ-irradiation than wild type parental cells or control-treated cells. Taken together, we conclude that CREB protects tumor cells from γ-irradiation, and combination of CREB inhibition plus ionizing radiation will be a promising radiotherapeutic approach. - Highlights: • γ-Irradiation induced CREB phosphorylation and CRE-directed transcription in tumor. • γ-Irradiation-induced transcriptional activation of CREB was via p38 MAPK pathway. • CRE blockade increased radiosensitivity of tumor cells but not of normal cells. • CRE decoy oligonucleotides or p38 MAPK inhibitors can be used as radiosensitizers.
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Bakshi, Madhunita; Oelmüller, Ralf
2014-01-01
WRKY transcription factors are one of the largest families of transcriptional regulators found exclusively in plants. They have diverse biological functions in plant disease resistance, abiotic stress responses, nutrient deprivation, senescence, seed and trichome development, embryogenesis, as well as additional developmental and hormone-controlled processes. WRKYs can act as transcriptional activators or repressors, in various homo- and heterodimer combinations. Here we review recent progress on the function of WRKY transcription factors in Arabidopsis and other plant species such as rice, potato, and parsley, with a special focus on abiotic, developmental, and hormone-regulated processes. PMID:24492469
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The influence of diel period on fish assemblage in the unstructured littoral of reservoirs
Czech Academy of Sciences Publication Activity Database
Říha, Milan; Kubečka, Jan; Prchalová, Marie; Mrkvička, Tomáš; Čech, Martin; Draštík, Vladislav; Frouzová, Jaroslava; Hohausová, Eva; Jůza, Tomáš; Kratochvíl, Michal; Peterka, Jiří; Tušer, Michal; Vašek, Mojmír
2011-01-01
Roč. 18, č. 4 (2011), s. 339-347 ISSN 0969-997X R&D Projects: GA ČR(CZ) GA206/07/1392; GA MZe(CZ) QH81046 Institutional research plan: CEZ:AV0Z60170517 Keywords : beach seining * diel migration * sampling * species composition * Římov Reservoir Subject RIV: EG - Zoology Impact factor: 1.294, year: 2011
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Directory of Open Access Journals (Sweden)
Jawad eMerhej
2016-05-01
Full Text Available The yeast Candida glabrata has become the second cause of systemic candidemia in humans. However, relatively few genome-wide studies have been conducted in this organism and our knowledge of its transcriptional regulatory network is quite limited. In the present work, we combined genome-wide chromatin immunoprecipitation (ChIP-seq, transcriptome analyses and DNA binding motif predictions to describe the regulatory interactions of the seven Yap (Yeast AP1 transcription factors of C. glabrata. We described a transcriptional network containing 255 regulatory interactions and 309 potential target genes. We predicted with high confidence the preferred DNA binding sites for 5 of the 7 CgYaps and showed a strong conservation of the Yap DNA binding properties between S. cerevisiae and C. glabrata. We provided reliable functional annotation for 3 of the 7 Yaps and identified for Yap1 and Yap5 a core regulon which is conserved in S. cerevisiae, C. glabrata and C. albicans. We uncovered new roles for CgYap7 in the regulation of iron-sulfur cluster biogenesis, for CgYap1 in the regulation of heme biosynthesis and for CgYap5 in the repression of GRX4 in response to iron starvation. These transcription factors define an interconnected transcriptional network at the cross-roads between redox homeostasis, oxygen consumption and iron metabolism.
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Stepwise or concerted? DFT study on the mechanism of ionic Diels-Alder reaction of chromanes
Directory of Open Access Journals (Sweden)
Haghdadi Mina
2016-01-01
Full Text Available The stepwise and concerted Ionic Diels-Alder reaction between phenyl (pyridin-2-ylmethylene oxonium and styrene derivatives are explored using theoretical method. The results support using computational method via persistent intermediates. The DFT method was essential to reproduce a reasonable potential energy surface for these challenging systems.
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Ghattas, Wadih; Cotchico-Alonso, Lur; Maréchal, Jean-Didier; Urvoas, Agathe; Rousseau, Maëva; Mahy, Jean-Pierre; Ricoux, Rémy
2016-03-02
A copper(II) cofactor coupled to a testosterone anchor, copper(II)-(5-(Piperazin-1-yl)-1,10-phenanthroline)testosterone-17-hemisuccinamide (10) was synthesized and associated with a neocarzinostatin variant, NCS-3.24 (KD =3 μm), thus generating a new artificial metalloenzyme by following a "Trojan horse" strategy. Interestingly, the artificial enzyme was able to efficiently catalyze the Diels-Alder cyclization reaction of cyclopentadiene (1) with 2-azachalcone (2). In comparison with what was observed with cofactor 10 alone, the artificial enzymes favored formation of the exo products (endo/exo ratios of 84:16 and 62:38, respectively, after 12 h). Molecular modeling studies assigned the synergy between the copper complex and the testosterone (KD =13 μm) moieties in the binding of 10 to good van der Waals complementarity. Moreover, by pushing the modeling exercise to its limits, we hypothesize on the molecular grounds that are responsible for the observed selectivity. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Breeding response of transcript profiling in developing seeds of Brassica napus
Directory of Open Access Journals (Sweden)
Li Xiaodan
2009-05-01
Full Text Available Abstract Background The upgrading of rapeseed cultivars has resulted in a substantial improvement in yield and quality in China over the past 30 years. With the selective pressure against fatty acid composition and oil content, high erucic acid- and low oil-content cultivars have been replaced by low erucic acid- and high oil-content cultivars. The high erucic acid cultivar Zhongyou 821 and its descendent, low erucic acid cultivar Zhongshuang 9, are representatives of two generations of the most outstanding Chinese rapeseed cultivars (B. napus developed the past 2 decades. This paper compares the transcriptional profiles of Zhongshuang 9 and Zhongyou 821 for 32 genes that are principally involved in lipid biosynthesis during seed development in order to elucidate how the transcriptional profiles of these genes responded to quality improvement over the past 20 years. Results Comparison of the cultivar Zhongyou 821 with its descendent, Zhongshuang 9, shows that the transcriptional levels of seven of the 32 genes were upregulated by 30% to 109%, including FAD3, ACCase, FAE1, GKTP, Caleosin, GAPDH, and PEPC. Of the 32 genes, 10 (KAS3, β-CT, BcRK6, P450, FatA, Oleosin, FAD6, FatB, α-CT and SUC1 were downregulated by at least 20% and most by 50%. The Napin gene alone accounted for over 75% of total transcription from all 32 genes assessed in both cultivars. Most of the genes showed significant correlation with fatty acid accumulation, but the correlation in ZS9 was significantly different from that in ZY821. Higher KCR2 activity is associated with higher C16:0, C18:0, and C18:2 in both cultivars, lower C22:1 and total fatty acid content in ZY821, and lower 18:1 in ZS9. Conclusion This paper illustrates the response of the transcription levels of 32 genes to breeding in developing rapeseed seeds. Both cultivars showed similar transcription profiles, with the Napin gene predominantly transcribed. Selective pressure for zero erucic acid, low
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Lee, Jong-Hyuk; Kang, Byung-Hee; Jang, Hyonchol; Kim, Tae Wan; Choi, Jinmi; Kwak, Sojung; Han, Jungwon; Cho, Eun-Jung; Youn, Hong-Duk
2015-01-01
Post-translational modifications of core histones affect various cellular processes, primarily through transcription. However, their relationship with the termination of transcription has remained largely unknown. In this study, we show that DNA damage-activated AKT phosphorylates threonine 45 of core histone H3 (H3-T45). By genome-wide chromatin immunoprecipitation sequencing (ChIP-seq) analysis, H3-T45 phosphorylation was distributed throughout DNA damage-responsive gene loci, particularly ...
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Hamperl, Stephan; Bocek, Michael J; Saldivar, Joshua C; Swigut, Tomek; Cimprich, Karlene A
2017-08-10
Conflicts between transcription and replication are a potent source of DNA damage. Co-transcriptional R-loops could aggravate such conflicts by creating an additional barrier to replication fork progression. Here, we use a defined episomal system to investigate how conflict orientation and R-loop formation influence genome stability in human cells. R-loops, but not normal transcription complexes, induce DNA breaks and orientation-specific DNA damage responses during conflicts with replication forks. Unexpectedly, the replisome acts as an orientation-dependent regulator of R-loop levels, reducing R-loops in the co-directional (CD) orientation but promoting their formation in the head-on (HO) orientation. Replication stress and deregulated origin firing increase the number of HO collisions leading to genome-destabilizing R-loops. Our findings connect DNA replication to R-loop homeostasis and suggest a mechanistic basis for genome instability resulting from deregulated DNA replication, observed in cancer and other disease states. Copyright © 2017 Elsevier Inc. All rights reserved.
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Islam, Afsana; Mercer, Chris F; Leung, Susanna; Dijkwel, Paul P; McManus, Michael T
2015-01-01
The transcription of four members of the Kunitz proteinase inhibitor (KPI) gene family of white clover (Trifolium repens L.), designated as Tr-KPI1, Tr-KPI2, Tr-KPI4 and Tr-KPI5, was investigated at both local infection (roots) and systemic (leaf tissue) sites in white clover in response to infection with the clover root knot nematode (CRKN) Meloidogyne trifoliophila and the clover cyst nematode (CCN) Heterodera trifolii. Invasion by the CRKN resulted in a significant decrease in transcript abundance of Tr-KPI4 locally at both 4 days post-infection (dpi) and at 8 dpi, and an increase in transcription of Tr-KPI1 systemically at 8 dpi. In contrast, an increase in transcript abundance of all four Tr-KPI genes locally at 4 and 8 dpi, and an increase of Tr-KPI1, Tr-KPI2, and Tr-KPI5 at 8 dpi systemically was observed in response to infection with the CCN. Challenge of a resistant (R) genotype and a susceptible (S) genotype of white clover with the CCN revealed a significant increase in transcript abundance of all four Tr-KPI genes locally in the R genotype, while an increase in abundance of only Tr-KPI1, Tr-KPI2, and Tr-KPI5 was observed in the S genotype, and only at 4 dpi. The transcript abundance of a member of the1-AMINOCYCLOPROPANE-1-CARBOXYLATE (ACC) SYNTHASE gene family from white clover (Tr-ACS1) was significantly down-regulated locally in response to CRKN infection at 4 and 8 dpi and at 4 dpi, systemically, while abundance increased locally and systemically at 8 dpi in response to CCN challenge. Conversely, the abundance of the jasmonic acid (JA) signalling gene, CORONATINE-INSENSITIVE PROTEIN 1 from white clover (Tr-COI1) increased significantly at 8 dpi locally in response to CRKN infection, but decreased at 8 dpi in response to CCN infection. The significance of this differential regulation of transcription is discussed with respect to differences in infection strategy of the two nematode species.
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Yang, Limin; Wang, Fei; Lee, Richmond; Lv, Yunbo; Huang, Kuo-Wei; Zhong, Guofu
2014-01-01
A facile N-heterocyclic carbene catalytic enantioselective aza-Diels-Alder reaction of oxodiazenes with α-chloroaldehydes as dienophile precursors is reported, with excellent enantioselectivity (ee > 99%) and excellent yield (up to 93%). DFT study
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Plett, Darren
2015-06-02
Elucidation of the gene networks underlying the response to N supply and demand will facilitate the improvement of the N uptake efficiency of plants. We undertook a transcriptomic analysis of maize to identify genes responding to both a non-growth-limiting decrease in NO3- provision and to development-based N demand changes at seven representative points across the life cycle. Gene co-expression networks were derived by cluster analysis of the transcript profiles. The majority of NO3--responsive transcription occurred at 11 (D11), 18 (D18) and 29 (D29) days after emergence, with differential expression predominating in the root at D11 and D29 and in the leaf at D18. A cluster of 98 probe sets was identified, the expression pattern of which is similar to that of the high-affinity NO3- transporter (NRT2) genes across the life cycle. The cluster is enriched with genes encoding enzymes and proteins of lipid metabolism and transport, respectively. These are candidate genes for the response of maize to N supply and demand. Only a few patterns of differential gene expression were observed over the entire life cycle; however, the composition of the classes of the genes differentially regulated at individual time points was unique, suggesting tightly controlled regulation of NO3--responsive gene expression. © 2015 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.
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Plett, Darren; Baumann, Ute; Schreiber, Andreas W.; Holtham, Luke; Kalashyan, Elena; Toubia, John; Nau, John; Beatty, Mary; Rafalski, Antoni; Dhugga, Kanwarpal S.; Tester, Mark A.; Garnett, Trevor; Kaiser, Brent N.
2015-01-01
Elucidation of the gene networks underlying the response to N supply and demand will facilitate the improvement of the N uptake efficiency of plants. We undertook a transcriptomic analysis of maize to identify genes responding to both a non-growth-limiting decrease in NO3- provision and to development-based N demand changes at seven representative points across the life cycle. Gene co-expression networks were derived by cluster analysis of the transcript profiles. The majority of NO3--responsive transcription occurred at 11 (D11), 18 (D18) and 29 (D29) days after emergence, with differential expression predominating in the root at D11 and D29 and in the leaf at D18. A cluster of 98 probe sets was identified, the expression pattern of which is similar to that of the high-affinity NO3- transporter (NRT2) genes across the life cycle. The cluster is enriched with genes encoding enzymes and proteins of lipid metabolism and transport, respectively. These are candidate genes for the response of maize to N supply and demand. Only a few patterns of differential gene expression were observed over the entire life cycle; however, the composition of the classes of the genes differentially regulated at individual time points was unique, suggesting tightly controlled regulation of NO3--responsive gene expression. © 2015 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.
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Kowalczyk, Marcin; Lupton, David W
2014-05-19
The addition of an N-heterocyclic carbene to the carbonyl group of an α,β,γ,δ-unsaturated enol ester affords a hemiacetal azolium intermediate that enables a cascade olefin isomerization/Diels-Alder reaction, for which mechanistic studies implicate Lewis base catalysis. Preliminary studies into the utility of the products have been undertaken with reductive and oxidative cleavage, giving materials for potential use in complex-target synthesis. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Lou, Yonggen; Baldwin, Ian T.
2004-01-01
Although nitrogen (N) availability is known to alter constitutive resistance against herbivores, its influence on herbivore-induced responses, including signaling pathways, transcriptional signatures, and the subsequently elicited chemical defenses is poorly understood. We used the native tobacco, Nicotiana attenuata, which germinates in the postfire environment and copes with large changes in soil N during postfire succession, to compare a suite of Manduca sexta- and elicitor-induced responses in plants grown under high- and low-N (LN) supply rates. LN supply decreased relative growth rates and biomass by 35% at 40 d compared to high-N plants; furthermore, it also attenuated (by 39 and 60%) the elicitor-induced jasmonate and salicylate bursts, two N-intensive direct defenses (nicotine and trypsin proteinase inhibitors, albeit by different mechanisms), and carbon-containing nonvolatile defenses (rutin, chlorogenic acid, and diterpene glycosides), but did not affect the induced release of volatiles (cis-α-bergamotene and germacrene A), which function as indirect defenses. M. sexta and methyl jasmonate-induced transcriptional responses measured with a microarray enriched in herbivore-induced genes were also substantially reduced in plants grown under LN supply rates. In M. sexta-attacked LN plants, only 36 (45%) up-regulated and 46 (58%) down-regulated genes showed the same regulation as those in attacked high-N plants. However, transcriptional responses frequently directly countered the observed metabolic changes. Changes in a leaf's sensitivity to elicitation, an attacked leaf's waning ability to export oxylipin wound signals, and/or resource limitations in LN plants can account for the observed results, underscoring the conclusion that defense activation is a resource-intensive response. PMID:15133153
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A facile avenue to conductive polymer brushes via cyclopentadiene-maleimide Diels-Alder ligation
Czech Academy of Sciences Publication Activity Database
Yameen, B.; Rodriguez-Emmenegger, C.; Preuss, C. M.; Pop-Georgievski, Ognen; Verveniotis, Elisseos; Trouillet, V.; Rezek, Bohuslav; Barner-Kowollik, C.
2013-01-01
Roč. 49, č. 77 (2013), s. 8623-8625 ISSN 1359-7345 R&D Projects: GA ČR GBP205/12/G118; GA ČR GAP108/11/1857; GA ČR(CZ) GBP108/12/G108 Institutional support: RVO:61389013 ; RVO:68378271 Keywords : conductive poly(3-hexylthiophen) brushes * Diels-Alder ligation * Kelvin Probe Force Microscopy (KFM) Subject RIV: CD - Macromolecular Chemistry Impact factor: 6.718, year: 2013
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Transcriptional Response to Lactic Acid Stress in the Hybrid Yeast Zygosaccharomyces parabailii.
Ortiz-Merino, Raúl A; Kuanyshev, Nurzhan; Byrne, Kevin P; Varela, Javier A; Morrissey, John P; Porro, Danilo; Wolfe, Kenneth H; Branduardi, Paola
2018-03-01
Lactic acid has a wide range of applications starting from its undissociated form, and its production using cell factories requires stress-tolerant microbial hosts. The interspecies hybrid yeast Zygosaccharomyces parabailii has great potential to be exploited as a novel host for lactic acid production, due to high organic acid tolerance at low pH and a fermentative metabolism with a high growth rate. Here we used mRNA sequencing (RNA-seq) to analyze Z. parabailii 's transcriptional response to lactic acid added exogenously, and we explore the biological mechanisms involved in tolerance. Z. parabailii contains two homeologous copies of most genes. Under lactic acid stress, the two genes in each homeolog pair tend to diverge in expression to a significantly greater extent than under control conditions, indicating that stress tolerance is facilitated by interactions between the two gene sets in the hybrid. Lactic acid induces downregulation of genes related to cell wall and plasma membrane functions, possibly altering the rate of diffusion of lactic acid into cells. Genes related to iron transport and redox processes were upregulated, suggesting an important role for respiratory functions and oxidative stress defense. We found differences in the expression profiles of genes putatively regulated by Haa1 and Aft1/Aft2, previously described as lactic acid responsive in Saccharomyces cerevisiae Furthermore, formate dehydrogenase ( FDH ) genes form a lactic acid-responsive gene family that has been specifically amplified in Z. parabailii in comparison to other closely related species. Our study provides a useful starting point for the engineering of Z. parabailii as a host for lactic acid production. IMPORTANCE Hybrid yeasts are important in biotechnology because of their tolerance to harsh industrial conditions. The molecular mechanisms of tolerance can be studied by analyzing differential gene expression under conditions of interest and relating gene expression patterns
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LENUS (Irish Health Repository)
Guida, Alessandro
2011-12-22
Abstract Background Candida parapsilosis is one of the most common causes of Candida infection worldwide. However, the genome sequence annotation was made without experimental validation and little is known about the transcriptional landscape. The transcriptional response of C. parapsilosis to hypoxic (low oxygen) conditions, such as those encountered in the host, is also relatively unexplored. Results We used next generation sequencing (RNA-seq) to determine the transcriptional profile of C. parapsilosis growing in several conditions including different media, temperatures and oxygen concentrations. We identified 395 novel protein-coding sequences that had not previously been annotated. We removed > 300 unsupported gene models, and corrected approximately 900. We mapped the 5\\' and 3\\' UTR for thousands of genes. We also identified 422 introns, including two introns in the 3\\' UTR of one gene. This is the first report of 3\\' UTR introns in the Saccharomycotina. Comparing the introns in coding sequences with other species shows that small numbers have been gained and lost throughout evolution. Our analysis also identified a number of novel transcriptional active regions (nTARs). We used both RNA-seq and microarray analysis to determine the transcriptional profile of cells grown in normoxic and hypoxic conditions in rich media, and we showed that there was a high correlation between the approaches. We also generated a knockout of the UPC2 transcriptional regulator, and we found that similar to C. albicans, Upc2 is required for conferring resistance to azole drugs, and for regulation of expression of the ergosterol pathway in hypoxia. Conclusion We provide the first detailed annotation of the C. parapsilosis genome, based on gene predictions and transcriptional analysis. We identified a number of novel ORFs and other transcribed regions, and detected transcripts from approximately 90% of the annotated protein coding genes. We found that the transcription factor
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Intramolecular anionic diels-alder reactions of 1-aryl-4-oxahepta-1,6-diyne systems in DMSO.
Kudoh, Takayuki; Mori, Tomoko; Shirahama, Mitsuhito; Yamada, Masashi; Ishikawa, Teruhiko; Saito, Seiki; Kobayashi, Hisayoshi
2007-04-25
Base-promoted cycloaddition reactions of 1-aryl- or 1-aryl-7-substituted-4-oxahepta-1,6-diyne systems in DMSO have proven to involve an anionic intramolecular Diels-Alder process taking place even at room temperature in spite of the reaction suffering from temporary disruption of aromaticity. Although initially formed alpha-arylallenide anion can be protonated by DMSO, it can be back to the allenide anion probably because of a small acidity difference between alpha-arylallene and DMSO. The alpha-arylallenide anion in combination with the alpha-aryl substituent can constitute an anionic diene structure that undergoes the intramolecular Diels-Alder reaction involving the C(6)-yne part, a very fast process probably because of the increased HOMO-1 level of the anionic diene, as shown by DFT calculations. Diversified substituted naphthalenes, benzofurans, phenanthrenes, and quinolines, including biaryl architectures, are available from 4-oxahepta-1,6-diynes in a highly expeditious way.
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Yu, Feng; Cao, Xiaodong; Zeng, Lei; Zhang, Qing; Chen, Xiaofeng
2013-08-14
In order to mimic the natural cartilage extracellular matrix, a novel biological degradable interpenetrating network hydrogel was synthesized from the gelatin (G), hyaluronic acid (HA) and chondroitin sulfate (CS) by Diels-Alder "click" chemistry. HA was modified with furylamine and G was modified with furancarboxylic acid respectively. (1)H NMR spectra and elemental analysis showed that the substitution degrees of HA-furan and G-furan were 71.5% and 44.5%. Then the hydrogels were finally synthesized by cross-linking furan-modified HA and G derivatives with dimaleimide poly(ethylene glycol) (MAL-PEG-MAL). The mechanical and degradation properties of the hydrogels could be tuned simply through varying the molar ratio between furan and maleimide. Rheological, mechanical and degradation studies demonstrated that the Diels-Alder "click" chemistry is an efficient method for preparing high performance biological interpenetrating hydrogels. This biomimic hydrogel with improved mechanical properties could have great potential applications in cartilage tissue engineering. Copyright © 2013 Elsevier Ltd. All rights reserved.
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Structure, function and networks of transcription factors involved in abiotic stress responses
DEFF Research Database (Denmark)
Lindemose, Søren; O'Shea, Charlotte; Jensen, Michael Krogh
2013-01-01
Transcription factors (TFs) are master regulators of abiotic stress responses in plants. This review focuses on TFs from seven major TF families, known to play functional roles in response to abiotic stresses, including drought, high salinity, high osmolarity, temperature extremes...... and the phytohormone ABA. Although ectopic expression of several TFs has improved abiotic stress tolerance in plants, fine-tuning of TF expression and protein levels remains a challenge to avoid crop yield loss. To further our understanding of TFs in abiotic stress responses, emerging gene regulatory networks based...... on TFs and their direct targets genes are presented. These revealed components shared between ABA-dependent and independent signaling as well as abiotic and biotic stress signaling. Protein structure analysis suggested that TFs hubs of large interactomes have extended regions with protein intrinsic...
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Jasiński, Radomir
2017-08-01
DFT computational study shows that Diels-Alder (DA) reactions of 1-chloro-1-nitroethene with cyclopentadiene and furan have polar nature. However, their mechanism is substantially different. In particular, 1-chloro-1-nitroethene react with cyclopentadiene according to one-step mechanism. In the same time, more favourable channel associated with the P-DA reaction between furan and 1-chloro-1-nitroethene is a domino process, that comprises an initial hetero-Diels-Alder reaction yielding a [2+4] cycloadduct, which experiences a subsequent [3,3] sigmatropic shift to yield the expected formal [4+2] cycloadduct. This is a consequence of more polar nature of reaction, due to higher nucleophilicity of furan in comparison to cyclopentadiene. Copyright © 2017 Elsevier Inc. All rights reserved.
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Directory of Open Access Journals (Sweden)
Deyholos Michael K
2009-06-01
Full Text Available Abstract Background Members of plant WRKY transcription factor families are widely implicated in defense responses and various other physiological processes. For canola (Brassica napus L., no WRKY genes have been described in detail. Because of the economic importance of this crop, and its evolutionary relationship to Arabidopsis thaliana, we sought to characterize a subset of canola WRKY genes in the context of pathogen and hormone responses. Results In this study, we identified 46 WRKY genes from canola by mining the expressed sequence tag (EST database and cloned cDNA sequences of 38 BnWRKYs. A phylogenetic tree was constructed using the conserved WRKY domain amino acid sequences, which demonstrated that BnWRKYs can be divided into three major groups. We further compared BnWRKYs to the 72 WRKY genes from Arabidopsis and 91 WRKY from rice, and we identified 46 presumptive orthologs of AtWRKY genes. We examined the subcellular localization of four BnWRKY proteins using green fluorescent protein (GFP and we observed the fluorescent green signals in the nucleus only. The responses of 16 selected BnWRKY genes to two fungal pathogens, Sclerotinia sclerotiorum and Alternaria brassicae, were analyzed by quantitative real time-PCR (qRT-PCR. Transcript abundance of 13 BnWRKY genes changed significantly following pathogen challenge: transcripts of 10 WRKYs increased in abundance, two WRKY transcripts decreased after infection, and one decreased at 12 h post-infection but increased later on (72 h. We also observed that transcript abundance of 13/16 BnWRKY genes was responsive to one or more hormones, including abscisic acid (ABA, and cytokinin (6-benzylaminopurine, BAP and the defense signaling molecules jasmonic acid (JA, salicylic acid (SA, and ethylene (ET. We compared these transcript expression patterns to those previously described for presumptive orthologs of these genes in Arabidopsis and rice, and observed both similarities and differences in
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Wen, Bi-Qing; Xing, Mei-Qing; Zhang, Hua; Dai, Cheng; Xue, Hong-Wei
2011-11-01
Homeobox transcription factors are involved in various aspects of plant development, including maintenance of the biosynthesis and signaling pathways of different hormones. However, few direct targets of homeobox proteins have been identified. We here show that overexpression of rice homeobox gene HOX1a resulted in enhanced gibberellin (GA) response, indicating a positive effect of HOX1a in GA signaling. HOX1a is induced by GA and encodes a homeobox transcription factor with transcription repression activity. In addition, HOX1a suppresses the transcription of early flowering1 (EL1), a negative regulator of GA signaling, and further electrophoretic mobility shift assay and chromatin immunoprecipitation analysis revealed that HOX1a directly bound to the promoter region of EL1 to suppress its expression and stimulate GA signaling. These results demonstrate that HOX1a functions as a positive regulator of GA signaling by suppressing EL1, providing informative hints on the study of GA signaling. © 2011 Institute of Botany, Chinese Academy of Sciences.
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Directory of Open Access Journals (Sweden)
Young-Jin Kim
2018-05-01
Full Text Available The dry root of Angelica sinensis (Oliv. Diels, also known as “female ginseng”, is a popular herbal drug amongst women, used to treat a variety of health issues and cardiovascular diseases. The aim of this study is to evaluate the detailed molecular mechanism for anti-inflammatory effects of Angelica sinensis root water extract (ASW. The anti-inflammatory effect of ASW on lipopolysaccharide (LPS-induced RAW 264.7 mouse macrophages was evaluated by the tetrazolium-based colorimetric assay (MTT, Griess reagent assay, multiplex cytokine assay, real time reverse transcription polymerase chain reaction (RT-PCR, and Fluo-4 calcium assay. ASW restored cell viability in RAW 264.7 at concentrations of up to 200 µg/mL. ASW showed notable anti-inflammatory effects. ASW exhibited IC50 = 954.3, 387.3, 191.7, 317.8, 1267.0, 347.0, 110.1, 573.6, 1171.0, 732.6, 980.8, 125.0, and 257.0 µg/mL for interleukin (IL-6, tumor necrosis factor (TNF-α, monocyte chemotactic activating factor (MCP-1, regulated on activation, normal T cell expressed and secreted (RANTES, granulocyte colony-stimulating factor (G-CSF, granulocyte macrophage colony-stimulating factor (GM-CSF, vascular endothelial growth factor (VEGF, lipopolysaccharide-induced CXC chemokine (LIX, macrophage inflammatory protein (MIP-1α, MIP-1β, MIP-2, IL-10, and intracellular calcium, respectively. Additionally, ASW inhibited the LPS-induced production of nitric oxide and the LPS-induced mRNA expression of CHOP (GADD153, Janus kinase 2 (JAK2, signal transducers and activators of transcription 1 (STAT1, first apoptosis signal receptor (FAS, and c-Fos, NOS2, and PTGS2 (COX2 in RAW 264.7 significantly (p < 0.05. Data suggest that ASW exerts an anti-inflammatory effect on LPS-induced RAW 264.7 via NO-bursting/calcium-mediated JAK-STAT pathway.
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Genome-wide transcription responses to synchrotron microbeam radiotherapy.
Sprung, Carl N; Yang, Yuqing; Forrester, Helen B; Li, Jason; Zaitseva, Marina; Cann, Leonie; Restall, Tina; Anderson, Robin L; Crosbie, Jeffrey C; Rogers, Peter A W
2012-10-01
The majority of cancer patients achieve benefit from radiotherapy. A significant limitation of radiotherapy is its relatively low therapeutic index, defined as the maximum radiation dose that causes acceptable normal tissue damage to the minimum dose required to achieve tumor control. Recently, a new radiotherapy modality using synchrotron-generated X-ray microbeam radiotherapy has been demonstrated in animal models to ablate tumors with concurrent sparing of normal tissue. Very little work has been undertaken into the cellular and molecular mechanisms that differentiate microbeam radiotherapy from broad beam. The purpose of this study was to investigate and compare the whole genome transcriptional response of in vivo microbeam radiotherapy versus broad beam irradiated tumors. We hypothesized that gene expression changes after microbeam radiotherapy are different from those seen after broad beam. We found that in EMT6.5 tumors at 4-48 h postirradiation, microbeam radiotherapy differentially regulates a number of genes, including major histocompatibility complex (MHC) class II antigen gene family members, and other immunity-related genes including Ciita, Ifng, Cxcl1, Cxcl9, Indo and Ubd when compared to broad beam. Our findings demonstrate molecular differences in the tumor response to microbeam versus broad beam irradiation and these differences provide insight into the underlying mechanisms of microbeam radiotherapy and broad beam.
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Luisier, Raphaëlle; Lempiäinen, Harri; Scherbichler, Nina; Braeuning, Albert; Geissler, Miriam; Dubost, Valerie; Müller, Arne; Scheer, Nico; Chibout, Salah-Dine; Hara, Hisanori; Picard, Frank; Theil, Diethilde; Couttet, Philippe; Vitobello, Antonio; Grenet, Olivier; Grasl-Kraupp, Bettina; Ellinger-Ziegelbauer, Heidrun; Thomson, John P; Meehan, Richard R; Elcombe, Clifford R; Henderson, Colin J; Wolf, C Roland; Schwarz, Michael; Moulin, Pierre; Terranova, Rémi; Moggs, Jonathan G
2014-06-01
The constitutive androstane receptor (CAR) and the pregnane X receptor (PXR) are closely related nuclear receptors involved in drug metabolism and play important roles in the mechanism of phenobarbital (PB)-induced rodent nongenotoxic hepatocarcinogenesis. Here, we have used a humanized CAR/PXR mouse model to examine potential species differences in receptor-dependent mechanisms underlying liver tissue molecular responses to PB. Early and late transcriptomic responses to sustained PB exposure were investigated in liver tissue from double knock-out CAR and PXR (CAR(KO)-PXR(KO)), double humanized CAR and PXR (CAR(h)-PXR(h)), and wild-type C57BL/6 mice. Wild-type and CAR(h)-PXR(h) mouse livers exhibited temporally and quantitatively similar transcriptional responses during 91 days of PB exposure including the sustained induction of the xenobiotic response gene Cyp2b10, the Wnt signaling inhibitor Wisp1, and noncoding RNA biomarkers from the Dlk1-Dio3 locus. Transient induction of DNA replication (Hells, Mcm6, and Esco2) and mitotic genes (Ccnb2, Cdc20, and Cdk1) and the proliferation-related nuclear antigen Mki67 were observed with peak expression occurring between 1 and 7 days PB exposure. All these transcriptional responses were absent in CAR(KO)-PXR(KO) mouse livers and largely reversible in wild-type and CAR(h)-PXR(h) mouse livers following 91 days of PB exposure and a subsequent 4-week recovery period. Furthermore, PB-mediated upregulation of the noncoding RNA Meg3, which has recently been associated with cellular pluripotency, exhibited a similar dose response and perivenous hepatocyte-specific localization in both wild-type and CAR(h)-PXR(h) mice. Thus, mouse livers coexpressing human CAR and PXR support both the xenobiotic metabolizing and the proliferative transcriptional responses following exposure to PB.
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Johnson, James H.; McKenna, James E.
2015-01-01
Interspecific partitioning of food and habitat resources has been widely studied in stream salmonids. Most studies have examined resource partitioning between two native species or between a native species and one that has been introduced. In this study we examine the diel feeding ecology and habitat use of three species of juvenile salmonids (i.e., Atlantic Salmon Salmo salar, Brown Trout Salmo trutta, and Rainbow Trout Oncorhynchus mykiss) in a tributary of Skaneateles Lake, New York. Subyearling Brown Trout and Rainbow Trout fed more heavily from the drift than the benthos, whereas subyearling Atlantic Salmon fed more from the benthos than either species of trout. Feeding activity of Atlantic Salmon and Rainbow Trout was similar, with both species increasing feeding at dusk, whereas Brown Trout had no discernable feeding peak or trough. Habitat availability was important in determining site-specific habitat use by juvenile salmonids. Habitat selection was greater during the day than at night. The intrastream, diel, intraspecific, and interspecific variation we observed in salmonid habitat use in Grout Brook illustrates the difficulty of acquiring habitat use information for widespread management applications.
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DEFF Research Database (Denmark)
Ishøy, Mette; Petersen, Rico; Petersen, Michael Åxman
2017-01-01
A high-yielding, stereoselective and extraordinarily complexity generatingPetasis 3-component/intramolecular Diels-Alderreaction has been developed. In combination with ROM-RCM, rapid access to complex sp3-rich heterocyclic scaffolds amenableto subsequent functionalization and library synthesis...
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Moran, P.W.; Aluru, N.; Black, R.W.; Vijayan, M.M.
2007-01-01
The consistent cold temperatures and large amount of precipitation in the Olympic and Cascade ranges of Washington State are thought to enhance atmospheric deposition of contaminants. However, little is known about contaminant levels in organisms residing in these remote high elevation lakes. We measured total mercury and 28 organochlorine compounds in trout collected from 14 remote lakes in the Olympic, Mt. Rainer, and North Cascades National Parks. Mercury was detected in trout from all lakes sampled (15 to 262 ??g/kg ww), while two organochlorines, total polychlorinated biphenyls (tPCB) and dichlorodiphenyldichloroethylene (DDE), were also detected in these fish tissues (<25 ??g/kg ww). In sediments, organochlorine levels were below detection, while median total and methyl mercury were 30.4 and 0.34 ??g/ kg dry weight (ww), respectively. Using fish from two lakes, representing different contaminant loading levels (Wilcox lake: high; Skymo lake: low), we examined transcriptional response in the liver using a custom-made low-density targeted rainbow trout cDNA microarray. We detected significant differences in liver transcriptional response, including significant changes in metabolic, endocrine, and immune-related genes, in fish collected from Wilcox Lake compared to Skymo Lake. Overall, our results suggest that local urban areas contribute to the observed contaminant patterns in these high elevation lakes, while the transcriptional changes point to a biological response associated with exposure to these contaminants in fish. Specifically, the gene expression pattern leads us to hypothesize a role for mercury in disrupting the metabolic and reproductive pathways in fish from high elevation lakes in western Washington. ?? 2007 American Chemical Society.
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NAC Transcription Factors in Stress Responses and Senescence
DEFF Research Database (Denmark)
O'Shea, Charlotte
Plant-specific NAM/ATAF/CUC (NAC) transcription factors have recently received considerable attention due to their significant roles in plant development and stress signalling. This interest has resulted in a number of physiological, genetic and cell biological studies of their functions. Some...... of these studies have also revealed emerging gene regulatory networks and protein-protein interaction networks. However, structural studies relating structure to function are lagging behind. Structure-function analysis of the NAC transcription factors has therefore been the main focus of this PhD thesis...... not involve significant folding-upon-binding but fuzziness or an extended ANAC046 region. The ANAC046 regulatory domain functions as an entropic chain with a bait for interactions with for example RCD1. RCD1 interacts with transcription factors from several different families, and the large stress...
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Directory of Open Access Journals (Sweden)
Takashi Ikeda
Full Text Available The activity patterns of mammals are generally categorized as nocturnal, diurnal, crepuscular (active at twilight, and cathemeral (active throughout the day. These patterns are highly variable across regions and seasons even within the same species. However, quantitative data is still lacking, particularly for sympatric species. We monitored the seasonal and diel activity patterns of terrestrial mammals in Hokkaido, Japan. Through an intensive camera-trap survey a total of 13,279 capture events were recorded from eight mammals over 20,344 camera-trap days, i.e., two years. Diel activity patterns were clearly divided into four categories: diurnal (Eurasian red squirrels, nocturnal (raccoon dogs and raccoons, crepuscular (sika deer and mountain hares, and cathemeral (Japanese martens, red foxes, and brown bears. Some crepuscular and cathemeral mammals shifted activity peaks across seasons. Particularly, sika deer changed peaks from twilight during spring-autumn to day-time in winter, possibly because of thermal constraints. Japanese martens were cathemeral during winter-summer, but nocturnal in autumn. We found no clear indication of predator-prey and competitive interactions, suggesting that animal densities are not very high or temporal niche partitioning is absent among the target species. This long-term camera-trap survey was highly cost-effective and provided one of the most detailed seasonal and diel activity patterns in multiple sympatric mammals under natural conditions.
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Sood, Archit; Jaiswal, Varun; Chanumolu, Sree Krishna; Malhotra, Nikhil; Pal, Tarun; Chauhan, Rajinder Singh
2014-11-01
Jatropha (Jatropha curcas L.) and Castor bean (Ricinus communis) are oilseed crops of family Euphorbiaceae with the potential of producing high quality biodiesel and having industrial value. Both the bioenergy plants are becoming susceptible to various biotic stresses directly affecting the oil quality and content. No report exists as of today on analysis of Nucleotide Binding Site-Leucine Rich Repeat (NBS-LRR) gene repertoire and defense response transcription factors in both the plant species. In silico analysis of whole genomes and transcriptomes identified 47 new NBS-LRR genes in both the species and 122 and 318 defense response related transcription factors in Jatropha and Castor bean, respectively. The identified NBS-LRR genes and defense response transcription factors were mapped onto the respective genomes. Common and unique NBS-LRR genes and defense related transcription factors were identified in both the plant species. All NBS-LRR genes in both the species were characterized into Toll/interleukin-1 receptor NBS-LRRs (TNLs) and coiled-coil NBS-LRRs (CNLs), position on contigs, gene clusters and motifs and domains distribution. Transcript abundance or expression values were measured for all NBS-LRR genes and defense response transcription factors, suggesting their functional role. The current study provides a repertoire of NBS-LRR genes and transcription factors which can be used in not only dissecting the molecular basis of disease resistance phenotype but also in developing disease resistant genotypes in Jatropha and Castor bean through transgenic or molecular breeding approaches.
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Rahman, M.M.; Meyer, C.G.
2009-01-01
In order to better understand behaviour patterns of common carp Cyprinus carpio in aquaculture ponds, their diel grazing, swimming, resting and schooling behaviours were observed in six 1 m(2) tanks under simulated pond conditions. Each tank was fertilized to stimulate natural food production before
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Directory of Open Access Journals (Sweden)
Simon Blankley
Full Text Available The use of human whole blood for transcriptomic analysis has potential advantages over the use of isolated immune cells for studying the transcriptional response to pathogens and their products. Whole blood stimulation can be carried out in a laboratory without the expertise or equipment to isolate immune cells from blood, with the added advantage of being able to undertake experiments using very small volumes of blood. Toll like receptors (TLRs are a family of pattern recognition receptors which recognise highly conserved microbial products. Using the TLR2 ligand (Pam3CSK4 and the TLR4 ligand (LPS, human whole blood was stimulated for 0, 1, 3, 6, 12 or 24 hours at which times mRNA was isolated and a comparative microarray was undertaken. A common NFκB transcriptional programme was identified following both TLR2 and TLR4 ligation which peaked at between 3 to 6 hours including upregulation of many of the NFκB family members. In contrast an interferon transcriptional response was observed following TLR4 but not TLR2 ligation as early as 1 hour post stimulation and peaking at 6 hours. These results recapitulate the findings observed in previously published studies using isolated murine and human myeloid cells indicating that in vitro stimulated human whole blood can be used to interrogate the early transcriptional kinetic response of innate cells to TLR ligands. Our study demonstrates that a transcriptomic analysis of mRNA isolated from human whole blood can delineate both the temporal response and the key transcriptional differences following TLR2 and TLR4 ligation.
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Choi, Sunju; Xu, Lu; Sze, Ji Ying
2013-01-01
In Caenorhabditis elegans the Toll-interleukin receptor domain adaptor protein TIR-1 via a conserved mitogen-activated protein kinase (MAPK) signaling cascade induces innate immunity and upregulates serotonin (5-HT) biosynthesis gene tph-1 in a pair of ADF chemosensory neurons in response to infection. Here, we identify transcription factors downstream of the TIR-1 signaling pathway. We show that common transcription factors control the innate immunity and 5-HT biosynthesis. We demonstrate that a cysteine to tyrosine substitution in an ARM motif of the HEAT/Arm repeat region of the TIR-1 protein confers TIR-1 hyperactivation, leading to constitutive tph-1 upregulation in the ADF neurons, increased expression of intestinal antimicrobial genes, and enhanced resistance to killing by the human opportunistic pathogen Pseudomonas aeruginosa PA14. A forward genetic screen for suppressors of the hyperactive TIR-1 led to the identification of DAF-19, an ortholog of regulatory factor X (RFX) transcription factors that are required for human adaptive immunity. We show that DAF-19 concerts with ATF-7, a member of the activating transcription factor (ATF)/cAMP response element-binding B (CREB) family of transcription factors, to regulate tph-1 and antimicrobial genes, reminiscent of RFX-CREB interaction in human immune cells. daf-19 mutants display heightened susceptibility to killing by PA14. Remarkably, whereas the TIR-1-MAPK-DAF-19/ATF-7 pathway in the intestinal immunity is regulated by DKF-2/protein kinase D, we found that the regulation of tph-1 expression is independent of DKF-2 but requires UNC-43/Ca2+/calmodulin-dependent protein kinase (CaMK) II. Our results suggest that pathogenic cues trigger a common core-signaling pathway via tissue-specific mechanisms and demonstrate a novel role for RFX factors in neuronal and innate immune responses to infection. PMID:23505381
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Venkataramanan, Keerthi P; Min, Lie; Hou, Shuyu; Jones, Shawn W; Ralston, Matthew T; Lee, Kelvin H; Papoutsakis, E Terry
2015-01-01
Clostridium acetobutylicum is a model organism for both clostridial biology and solvent production. The organism is exposed to its own toxic metabolites butyrate and butanol, which trigger an adaptive stress response. Integrative analysis of proteomic and RNAseq data may provide novel insights into post-transcriptional regulation. The identified iTRAQ-based quantitative stress proteome is made up of 616 proteins with a 15 % genome coverage. The differentially expressed proteome correlated poorly with the corresponding differential RNAseq transcriptome. Up to 31 % of the differentially expressed proteins under stress displayed patterns opposite to those of the transcriptome, thus suggesting significant post-transcriptional regulation. The differential proteome of the translation machinery suggests that cells employ a different subset of ribosomal proteins under stress. Several highly upregulated proteins but with low mRNA levels possessed mRNAs with long 5'UTRs and strong RBS scores, thus supporting the argument that regulatory elements on the long 5'UTRs control their translation. For example, the oxidative stress response rubrerythrin was upregulated only at the protein level up to 40-fold without significant mRNA changes. We also identified many leaderless transcripts, several displaying different transcriptional start sites, thus suggesting mRNA-trimming mechanisms under stress. Downregulation of Rho and partner proteins pointed to changes in transcriptional elongation and termination under stress. The integrative proteomic-transcriptomic analysis demonstrated complex expression patterns of a large fraction of the proteome. Such patterns could not have been detected with one or the other omic analyses. Our analysis proposes the involvement of specific molecular mechanisms of post-transcriptional regulation to explain the observed complex stress response.
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Pokemon (FBI-1) interacts with Smad4 to repress TGF-β-induced transcriptional responses.
Yang, Yutao; Cui, Jiajun; Xue, Feng; Zhang, Chuanfu; Mei, Zhu; Wang, Yue; Bi, Mingjun; Shan, Dapeng; Meredith, Alex; Li, Hui; Xu, Zhi-Qing David
2015-03-01
Pokemon, an important proto-oncoprotein, is a transcriptional repressor that belongs to the POK (POZ and Krüppel) family. Smad4, a key component of TGF-β pathway, plays an essential role in TGF-β-induced transcriptional responses. In this study, we show that Pokemon can interact directly with Smad4 both in vitro and in vivo. Overexpression of Pokemon decreases TGF-β-induced transcriptional activities, whereas knockdown of Pokemon increases these activities. Interestingly, Pokemon does not affect activation of Smad2/3, formation of Smads complex, or DNA binding activity of Smad4. TGF-β1 treatment increases the interaction between Pokemon and Smad4, and also enhances the recruitment of Pokemon to Smad4-DNA complex. In addition, we also find that Pokemon recruits HDAC1 to Smad4 complex but decreases the interaction between Smad4 and p300/CBP. Taken together, all these data suggest that Pokemon is a new partner of Smad4 and plays a negative role in TGF-β pathway. Copyright © 2014. Published by Elsevier B.V.
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Directory of Open Access Journals (Sweden)
Kehua Wang
2017-06-01
Full Text Available Perennial ryegrass (Lolium perenne is one of the most widely used forage and turf grasses in the world due to its desirable agronomic qualities. However, as a cool-season perennial grass species, high temperature is a major factor limiting its performance in warmer and transition regions. In this study, a de novo transcriptome was generated using a cDNA library constructed from perennial ryegrass leaves subjected to short-term heat stress treatment. Then the expression profiling and identification of perennial ryegrass heat response genes by digital gene expression analyses was performed. The goal of this work was to produce expression profiles of high temperature stress responsive genes in perennial ryegrass leaves and further identify the potentially important candidate genes with altered levels of transcript, such as those genes involved in transcriptional regulation, antioxidant responses, plant hormones and signal transduction, and cellular metabolism. The de novo assembly of perennial ryegrass transcriptome in this study obtained more total and annotated unigenes compared to previously published ones. Many DEGs identified were genes that are known to respond to heat stress in plants, including HSFs, HSPs, and antioxidant related genes. In the meanwhile, we also identified four gene candidates mainly involved in C4 carbon fixation, and one TOR gene. Their exact roles in plant heat stress response need to dissect further. This study would be important by providing the gene resources for improving heat stress tolerance in both perennial ryegrass and other cool-season perennial grass plants.
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Türkmen, Yunus E; Montavon, Timothy J; Kozmin, Sergey A; Rawal, Viresh H
2012-06-06
A highly effective silver-catalyzed formal inverse electron-demand Diels-Alder reaction of 1,2-diazines and siloxy alkynes has been developed. The reactions provide ready access to a wide range of siloxy naphthalenes and anthracenes, which are formed in good to high yields, under mild reaction conditions, using low catalyst loadings.
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Dypvik, Eivind; Kaartvedt, Stein
2012-01-01
The vertical migration and diel feeding periodicity of the skinnycheek lanternfish (Benthosema pterotum) were studied by use of a hull-mounted 38 kHz echo sounder, ROV-deployments and net-sampling at two locations (∼24°48′N, ∼36°15′E and ∼21°27′N
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Moschen, Sebastián; Di Rienzo, Julio A; Higgins, Janet; Tohge, Takayuki; Watanabe, Mutsumi; González, Sergio; Rivarola, Máximo; García-García, Francisco; Dopazo, Joaquin; Hopp, H Esteban; Hoefgen, Rainer; Fernie, Alisdair R; Paniego, Norma; Fernández, Paula; Heinz, Ruth A
2017-07-01
By integration of transcriptional and metabolic profiles we identified pathways and hubs transcription factors regulated during drought conditions in sunflower, useful for applications in molecular and/or biotechnological breeding. Drought is one of the most important environmental stresses that effects crop productivity in many agricultural regions. Sunflower is tolerant to drought conditions but the mechanisms involved in this tolerance remain unclear at the molecular level. The aim of this study was to characterize and integrate transcriptional and metabolic pathways related to drought stress in sunflower plants, by using a system biology approach. Our results showed a delay in plant senescence with an increase in the expression level of photosynthesis related genes as well as higher levels of sugars, osmoprotectant amino acids and ionic nutrients under drought conditions. In addition, we identified transcription factors that were upregulated during drought conditions and that may act as hubs in the transcriptional network. Many of these transcription factors belong to families implicated in the drought response in model species. The integration of transcriptomic and metabolomic data in this study, together with physiological measurements, has improved our understanding of the biological responses during droughts and contributes to elucidate the molecular mechanisms involved under this environmental condition. These findings will provide useful biotechnological tools to improve stress tolerance while maintaining crop yield under restricted water availability.
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Li, Mao; Carreras, Virginie; Jalba, Angela; Ollevier, Thierry
2018-02-16
An asymmetric Fe III -bipyridine diol catalyzed Diels-Alder reaction of α,β-unsaturated oxazolidin-2-ones has been developed. Among various Fe II /Fe III salts, Fe(ClO 4 ) 3 ·6H 2 O was selected as the Lewis acid of choice. The use of a low catalyst loading (2 mol % of Fe(ClO 4 ) 3 ·6H 2 O and 2.4 mol % of Bolm's ligand) afforded high yields (up to 99%) and high enantiomeric excesses (up to 98%) of endo-cycloadducts for the Diels-Alder reaction between cyclopentadiene and substituted acryloyloxazolidin-2-ones. Other noncyclic dienes led to decreased enantioselectivities. A proposed model supports the observed stereoinduction.
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Fell, Jason S; Martin, Blanton N; Houk, K N
2017-02-17
The reactivities of butadiene, cyclopentadiene, furan, thiophene, pyrrole, and their 1-aza- and 2-aza-derivatives in Diels-Alder reactions with ethylene and fumaronitrile were investigated with density functional theory (M06-2X/6-311G(d,p)). The activation free energies for the Diels-Alder reactions of cyclic 1-azadienes are 10-14 kcal mol -1 higher than those of cyclic 2-azadienes, and the reaction free energies are 17-20 kcal mol -1 more endergonic. The distortion/interaction model shows that the increased activation energies of cyclic 1-azadienes originate from increased transition state distortion energies and unfavorable interaction energies, arising from addition to the nitrogen terminus of the C═N bond.
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The NBS1-Treacle complex controls ribosomal RNA transcription in response to DNA damage
DEFF Research Database (Denmark)
Larsen, Dorthe H; Hari, Flurina; Clapperton, Julie A
2014-01-01
Chromosome breakage elicits transient silencing of ribosomal RNA synthesis, but the mechanisms involved remained elusive. Here we discover an in trans signalling mechanism that triggers pan-nuclear silencing of rRNA transcription in response to DNA damage. This is associated with transient...... recruitment of the Nijmegen breakage syndrome protein 1 (NBS1), a central regulator of DNA damage responses, into the nucleoli. We further identify TCOF1 (also known as Treacle), a nucleolar factor implicated in ribosome biogenesis and mutated in Treacher Collins syndrome, as an interaction partner of NBS1...
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Asymmetric aza-Diels-Alder reaction of Danishefsky's diene with imines in a chiral reaction medium
Directory of Open Access Journals (Sweden)
Pégot Bruce
2006-09-01
Full Text Available Abstract The asymmetric aza-Diels-Alder reaction of chiral imines with Danishefsky's diene in chiral ionic liquids provides the corresponding cycloadduct with moderate to high diastereoselectivity. The reaction has proved to perform better at room temperature in ionic liquids without either Lewis acid catalyst or organic solvent. Chiral ionic liquids are recycled while their efficiency is preserved.
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Spetz, Johan; Rudqvist, Nils; Langen, Britta; Parris, Toshima Z; Dalmo, Johanna; Schüler, Emil; Wängberg, Bo; Nilsson, Ola; Helou, Khalil; Forssell-Aronsson, Eva
2018-05-01
Patients with neuroendocrine tumors expressing somatostatin receptors are often treated with 177 Lu[Lu]-octreotate. Despite being highly effective in animal models, 177 Lu[Lu]-octreotate-based therapies in the clinical setting can be optimized further. The aims of the study were to identify and elucidate possible optimization venues for 177 Lu[Lu]-octreotate tumor therapy by characterizing transcriptional responses in the GOT1 small intestine neuroendocrine tumor model in nude mice. GOT1-bearing female BALB/c nude mice were intravenously injected with 15 MBq 177 Lu[Lu]-octreotate (non-curative amount) or mock-treated with saline solution. Animals were killed 1, 3, 7 or 41 d after injection. Total RNA was extracted from the tumor samples and profiled using Illumina microarray expression analysis. Differentially expressed genes were identified (treated vs. control) and pathway analysis was performed. Distribution of differentially expressed transcripts indicated a time-dependent treatment response in GOT1 tumors after 177 Lu[Lu]-octreotate administration. Regulation of CDKN1A, BCAT1 and PAM at 1 d after injection was compatible with growth arrest as the initial response to treatment. Upregulation of APOE and BAX at 3 d, and ADORA2A, BNIP3, BNIP3L and HSPB1 at 41 d after injection suggests first activation and then inhibition of the intrinsic apoptotic pathway during tumor regression and regrowth, respectively. Transcriptional analysis showed radiation-induced apoptosis as an early response after 177 Lu[Lu]-octreotate administration, followed by pro-survival transcriptional changes in the tumor during the regrowth phase. Time-dependent changes in cell cycle and apoptosis-related processes suggest different time points after radionuclide therapy when tumor cells may be more susceptible to additional treatment, highlighting the importance of timing when administering multiple therapeutic agents. Copyright © 2018 The Authors. Published by Elsevier Inc. All
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Pacheco, Joshua J.; Davis, Mark E.
2014-01-01
Terephthalic acid (PTA), a monomer in the synthesis of polyethylene terephthalate (PET), is obtained by the oxidation of petroleum-derived p-xylene. There is significant interest in the synthesis of renewable, biomass-derived PTA. Here, routes to PTA starting from oxidized products of 5-hydroxymethylfurfural (HMF) that can be produced from biomass are reported. These routes involve Diels-Alder reactions with ethylene and avoid the hydrogenation of HMF to 2,5-dimethylfuran. Oxidized derivatives of HMF are reacted with ethylene over solid Lewis acid catalysts that do not contain strong Brønsted acids to synthesize intermediates of PTA and its equally important diester, dimethyl terephthalate (DMT). The partially oxidized HMF, 5-(hydroxymethyl)furoic acid (HMFA), is reacted with high pressure ethylene over a pure-silica molecular sieve containing framework tin (Sn-Beta) to produce the Diels-Alder dehydration product, 4-(hydroxymethyl)benzoic acid (HMBA), with 31% selectivity at 61% HMFA conversion after 6 h at 190 °C. If HMFA is protected with methanol to form methyl 5-(methoxymethyl)furan-2-carboxylate (MMFC), MMFC can react with ethylene in the presence of Sn-Beta for 2 h to produce methyl 4-(methoxymethyl)benzenecarboxylate (MMBC) with 46% selectivity at 28% MMFC conversion or in the presence of a pure-silica molecular sieve containing framework zirconium (Zr-Beta) for 6 h to produce MMBC with 81% selectivity at 26% MMFC conversion. HMBA and MMBC can then be oxidized to produce PTA and DMT, respectively. When Lewis acid containing mesoporous silica (MCM-41) and amorphous silica, or Brønsted acid containing zeolites (Al-Beta), are used as catalysts, a significant decrease in selectivity/yield of the Diels-Alder dehydration product is observed. PMID:24912153
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Polgar, L. M.; Fortunato, G.; Araya-Hermosilla, R.; van Duin, M.; Pucci, A.; Picchioni, F.
Furan-functionalized polyketone (PK-FU) was added to a furan-functionalized ethylene-propylene rubber (EPM-FU). The mixture was subsequently cross-linked with a bismaleimide through Diels-Alder chemistry in order to improve the mechanical properties of the rubber. Infrared spectroscopy showed the
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Protein-DNA binding dynamics predict transcriptional response to nutrients in archaea.
Todor, Horia; Sharma, Kriti; Pittman, Adrianne M C; Schmid, Amy K
2013-10-01
Organisms across all three domains of life use gene regulatory networks (GRNs) to integrate varied stimuli into coherent transcriptional responses to environmental pressures. However, inferring GRN topology and regulatory causality remains a central challenge in systems biology. Previous work characterized TrmB as a global metabolic transcription factor in archaeal extremophiles. However, it remains unclear how TrmB dynamically regulates its ∼100 metabolic enzyme-coding gene targets. Using a dynamic perturbation approach, we elucidate the topology of the TrmB metabolic GRN in the model archaeon Halobacterium salinarum. Clustering of dynamic gene expression patterns reveals that TrmB functions alone to regulate central metabolic enzyme-coding genes but cooperates with various regulators to control peripheral metabolic pathways. Using a dynamical model, we predict gene expression patterns for some TrmB-dependent promoters and infer secondary regulators for others. Our data suggest feed-forward gene regulatory topology for cobalamin biosynthesis. In contrast, purine biosynthesis appears to require TrmB-independent regulators. We conclude that TrmB is an important component for mediating metabolic modularity, integrating nutrient status and regulating gene expression dynamics alone and in concert with secondary regulators.
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Gorska, Natalia; Kowalska-Duda, Ewa; Pniewski, Filip; Latała, Adam
2018-06-01
The study has been motivated by the development of the hydroacoustic techniques for mapping and classifying the benthic habitats and for the research of the microbenthos photosynthesis in the semi-enclosed Baltic Sea, particularly sensitive to human activity. The investigation of the effect of the benthic microalgal photosynthesis on the echo signal from the Baltic sandy sediments is continuing. The study clarifies the impact of the abiotic and biotic factors on the diel variation of the backscattering caused by the benthic microalgal photosynthetic activity. Five multiday laboratory experiments, different in hydrophysical or biological conditions, were conducted. During each measurement series, the "day" (illumination) and "night" (darkness) conditions (L:D cycle) were simulated and the diel variations of the echo energy of the backscattered signal were analyzed. The hydroacoustic data were acquired along with measuring biological and biooptical parameters and oxygen concentration. The study demonstrated the impact of microphytobenthos photosynthesis on the backscattering properties of the marine sediment which is sensitive to the illumination level, benthic microalgal biomass and macrozoobenthos bioturbation.
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Effects of diel vertical migration on ephippia production in Daphnia
Directory of Open Access Journals (Sweden)
Victor ALEKSEEV
2004-09-01
Full Text Available Fish presence in experimentally simulated temperature conditions (limno-towers led to diel vertical migration and resulted in a decrease of ephippia production in Daphnia pulicaria. Diel fluctuation of food, temperature and day length similar to those experienced by migrating Daphnia were tested in laboratory experiments with flow-through-systems. Daphnids were kept under these conditions for 15 days and the proportions of females producing an ephippium were determined. In addition, maturation time, survival to maturation, size of the first clutch and female dry weight (without eggs on day 15 were traced. The most important factor affecting ephippia production in migrating Daphnia was photoperiod change, and when mother and embryo are exposed to alternating light conditions, these are thought to have the effect on the mother of acting as a signal to stop ephippia production. Such effects might be explained by the different sensitiveness to light intensity in females carrying an embryo and an embryo itself in broods. Fish presence forced Daphnia to stay in low-light conditions during daytime hours, to avoid attacks by fish. The Daphnia were able to check light intensity constantly by short vertical jumps above a light-threshold that was confirmed experimentally in limno-towers. The dim conditions were possibly light enough for adults to check day length, but were too dark for embryos shaded by the mother's body. Food conditions played a relatively small role in the process, and no effects of temperature on ephippia production were found. As expected, food affected the size of the first clutch, and temperature controlled the time to maturation. Photoperiod had a marginally significant influence on the time to maturation in Daphnia. A hypothesis on the role of photoperiod as the key factor for Daphnia life cyclic recurrence and other seasonal adaptations is proposed.
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The inverse electron demand Diels-Alder click reaction in radiochemistry.
Reiner, Thomas; Zeglis, Brian M
2014-04-01
The inverse electron-demand Diels-Alder (IEDDA) cycloaddition between 1,2,4,5-tetrazines and strained alkene dienophiles is an emergent variety of catalyst-free 'click' chemistry that has the potential to have a transformational impact on the synthesis and development of radiopharmaceuticals. The ligation is selective, rapid, high-yielding, clean, and bioorthogonal and, since its advent in 2008, has been employed in a wide variety of chemical settings. In radiochemistry, the reaction has proven particularly useful with (18) F and has already been utilized to create a number of (18) F-labeled agents, including the PARP1-targeting small molecule (18) F-AZD2281, the αv β3 integrin-targeting peptide (18) F-RGD, and the GLP-1-targeting peptide (18) F-exendin. The inherent flexibility of the ligation has also been applied to the construction of radiometal-based probes, specifically the development of a modular strategy for the synthesis of radioimmunoconjugates that effectively eliminates variability in the construction of these agents. Further, the exceptional speed and biorthogonality of the reaction have made it especially promising in the realm of in vivo pretargeted imaging and therapy, and pretargeted imaging strategies based on the isotopes (111) In, (18) F, and (64) Cu have already proven capable of producing images with high tumor contrast and low levels of uptake in background, nontarget organs. Ultimately, the characteristics of inverse electron-demand Diels-Alder click chemistry make it almost uniquely well-suited for radiochemistry, and although the field is young, this ligation has the potential to make a tremendous impact on the synthesis, development, and study of novel radiopharmaceuticals. Copyright © 2013 John Wiley & Sons, Ltd.
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Kislov, V V; Islamova, N I; Kolker, A M; Lin, S H; Mebel, A M
2005-09-01
Extensive ab initio Gaussian-3-type calculations of potential energy surfaces (PES), which are expected to be accurate within 1-2 kcal/mol, combined with statistical theory calculations of reaction rate constants have been applied to study various possible pathways in the hydrogen abstraction acetylene addition (HACA) mechanism of naphthalene and acenaphthalene formation as well as Diels-Alder pathways to acenaphthalene, phenanthrene, and pyrene. The barrier heights; reaction energies; and molecular parameters of the reactants, products, intermediates, and transition states have been generated for all types of reactions involved in the HACA and Diels-Alder mechanisms, including H abstraction from various aromatic intermediates, acetylene addition to radical sites, ring closures leading to the formation of additional aromatic rings, elimination of hydrogen atoms, H disproportionation, C2H2 cycloaddition, and H2 loss. The reactions participating in various HACA sequences (e.g., Frenklach's, alternative Frenklach's, and Bittner and Howard's routes) are demonstrated to have relatively low barriers and high rate constants under combustion conditions. A comparison of the significance of different HACA mechanisms in PAH growth can be made in the future using PES and molecular parameters obtained in the present work. The results show that the Diels-Alder mechanism cannot compete with the HACA pathways even at high combustion temperatures, because of high barriers and consequently low reaction rate constants. The calculated energetic parameters and rate constants have been compared with experimental and theoretical data available in the literature.
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Computational design of a Diels-Alderase from a thermophilic esterase: the importance of dynamics
Linder, Mats; Johansson, Adam Johannes; Olsson, Tjelvar S. G.; Liebeschuetz, John; Brinck, Tore
2012-09-01
A novel computational Diels-Alderase design, based on a relatively rare form of carboxylesterase from Geobacillus stearothermophilus, is presented and theoretically evaluated. The structure was found by mining the PDB for a suitable oxyanion hole-containing structure, followed by a combinatorial approach to find suitable substrates and rational mutations. Four lead designs were selected and thoroughly modeled to obtain realistic estimates of substrate binding and prearrangement. Molecular dynamics simulations and DFT calculations were used to optimize and estimate binding affinity and activation energies. A large quantum chemical model was used to capture the salient interactions in the crucial transition state (TS). Our quantitative estimation of kinetic parameters was validated against four experimentally characterized Diels-Alderases with good results. The final designs in this work are predicted to have rate enhancements of ≈103-106 and high predicted proficiencies. This work emphasizes the importance of considering protein dynamics in the design approach, and provides a quantitative estimate of the how the TS stabilization observed in most de novo and redesigned enzymes is decreased compared to a minimal, `ideal' model. The presented design is highly interesting for further optimization and applications since it is based on a thermophilic enzyme ( T opt = 70 °C).
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Lee, Jong-Hyuk; Kang, Byung-Hee; Jang, Hyonchol; Kim, Tae Wan; Choi, Jinmi; Kwak, Sojung; Han, Jungwon; Cho, Eun-Jung; Youn, Hong-Duk
2015-05-19
Post-translational modifications of core histones affect various cellular processes, primarily through transcription. However, their relationship with the termination of transcription has remained largely unknown. In this study, we show that DNA damage-activated AKT phosphorylates threonine 45 of core histone H3 (H3-T45). By genome-wide chromatin immunoprecipitation sequencing (ChIP-seq) analysis, H3-T45 phosphorylation was distributed throughout DNA damage-responsive gene loci, particularly immediately after the transcription termination site. H3-T45 phosphorylation pattern showed close-resemblance to that of RNA polymerase II C-terminal domain (CTD) serine 2 phosphorylation, which establishes the transcription termination signal. AKT1 was more effective than AKT2 in phosphorylating H3-T45. Blocking H3-T45 phosphorylation by inhibiting AKT or through amino acid substitution limited RNA decay downstream of mRNA cleavage sites and decreased RNA polymerase II release from chromatin. Our findings suggest that AKT-mediated phosphorylation of H3-T45 regulates the processing of the 3' end of DNA damage-activated genes to facilitate transcriptional termination. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.
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Patterns in diel habitat use of fish covering the littoral and pelagic zones in a reservoir
Czech Academy of Sciences Publication Activity Database
Říha, Milan; Ricard, Daniel; Vašek, Mojmír; Prchalová, Marie; Mrkvička, Tomáš; Jůza, Tomáš; Čech, Martin; Draštík, Vladislav; Muška, Milan; Kratochvíl, Michal; Peterka, Jiří; Tušer, Michal; Seďa, Jaromír; Blabolil, Petr; Bláha, M.; Wanzenbock, J.; Kubečka, Jan
2015-01-01
Roč. 747, č. 1 (2015), s. 111-131 ISSN 0018-8158 R&D Projects: GA MŠk(CZ) EE2.3.20.0204; GA MŠk(CZ) EE2.3.30.0032 Institutional support: RVO:60077344 Keywords : habitat use * diel period * distribution * fish diet * littoral * pelagial * reservoir Subject RIV: EG - Zoology Impact factor: 2.051, year: 2015
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Eleftheriadis, Nikolaos; Samatidou, Evanthia; Neochoritis, Constantinos G.
The Lewis acid-catalyzed Diels-Alder reactions of suitably substituted imidazole-2-thiones with dienes were studied. It was found that the electron density of the imidazole core influenced the reaction, since electron withdrawing groups led to the novel spiro-derivatives 2 whereas electron donating
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Energy Technology Data Exchange (ETDEWEB)
Song, You, E-mail: you.song@niva.no [Norwegian University of Life Sciences (NMBU), Faculty of Environmental Science and Technology, Department of Environmental Sciences (IMV), Centre for Environmental Radioactivity - CERAD, P.O. Box 5003, N-1432 Ås (Norway); Norwegian Institute for Water Research (NIVA), Gaustadalléen 21, N-0349 Oslo (Norway); Salbu, Brit; Teien, Hans-Christian; Heier, Lene Sørlie [Norwegian University of Life Sciences (NMBU), Faculty of Environmental Science and Technology, Department of Environmental Sciences (IMV), Centre for Environmental Radioactivity - CERAD, P.O. Box 5003, N-1432 Ås (Norway); Rosseland, Bjørn Olav [Norwegian University of Life Sciences (NMBU), Faculty of Environmental Science and Technology, Department of Environmental Sciences (IMV), Centre for Environmental Radioactivity - CERAD, P.O. Box 5003, N-1432 Ås (Norway); Norwegian University of Life Sciences (NMBU), Department of Ecology and Natural Resource Management, P.O. Box 5003, N-1432 Ås (Norway); Tollefsen, Knut Erik [Norwegian University of Life Sciences (NMBU), Faculty of Environmental Science and Technology, Department of Environmental Sciences (IMV), Centre for Environmental Radioactivity - CERAD, P.O. Box 5003, N-1432 Ås (Norway); Norwegian Institute for Water Research (NIVA), Gaustadalléen 21, N-0349 Oslo (Norway)
2014-11-15
Highlights: • First study on early stress responses in salmon exposed to low-dose gamma radiation. • Dramatic dose-dependent transcriptional responses characterized. • Multiple modes of action proposed for gamma radiation. - Abstract: Due to the production of free radicals, gamma radiation may pose a hazard to living organisms. The high-dose radiation effects have been extensively studied, whereas the ecotoxicity data on low-dose gamma radiation is still limited. The present study was therefore performed using Atlantic salmon (Salmo salar) to characterize effects of low-dose (15, 70 and 280 mGy) gamma radiation after short-term (48 h) exposure. Global transcriptional changes were studied using a combination of high-density oligonucleotide microarrays and quantitative real-time reverse transcription polymerase chain reaction (qPCR). Differentially expressed genes (DEGs; in this article the phrase gene expression is taken as a synonym of gene transcription, although it is acknowledged that gene expression can also be regulated, e.g., at protein stability and translational level) were determined and linked to their biological meanings predicted using both Gene Ontology (GO) and mammalian ortholog-based functional analyses. The plasma glucose level was also measured as a general stress biomarker at the organism level. Results from the microarray analysis revealed a dose-dependent pattern of global transcriptional responses, with 222, 495 and 909 DEGs regulated by 15, 70 and 280 mGy gamma radiation, respectively. Among these DEGs, only 34 were commonly regulated by all radiation doses, whereas the majority of differences were dose-specific. No GO functions were identified at low or medium doses, but repression of DEGs associated with GO functions such as DNA replication, cell cycle regulation and response to reactive oxygen species (ROS) were observed after 280 mGy gamma exposure. Ortholog-based toxicity pathway analysis further showed that 15 mGy radiation
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Directory of Open Access Journals (Sweden)
Mohamed El Missiry
Full Text Available In chronic myeloid leukemia (CML, early treatment prediction is important to identify patients with inferior overall outcomes. We examined the feasibility of using reductions in BCR-ABL1 transcript levels after 1 month of tyrosine kinase inhibitor (TKI treatment to predict therapy response. Fifty-two first-line TKI-treated CML patients were included (imatinib n = 26, dasatinib n = 21, nilotinib n = 5, and BCR-ABL1 transcript levels were measured at diagnosis (dg and 1, 3, 6, 12, 18, 24, and 36 months. The fold change of the BCR-ABL1 transcripts at 1 month compared to initial BCR-ABL1 transcript levels was used to indicate early therapy response. In our cohort, 21% of patients had no decrease in BCR-ABL1 transcript levels after 1 month and were classified as poor responders. Surprisingly, these patients had lower BCR-ABL1 transcript levels at dg compared to responders (31% vs. 48%, p = 0.0083. Poor responders also significantly more often had enlarged spleen (55% vs. 15%; p<0.01 and a higher percentage of Ph+ CD34+CD38- cells in the bone marrow (91% vs. 75%, p<0.05. The major molecular response rates were inferior in the poor responders (at 12m 18% vs. 64%, p<0.01; 18m 27% vs. 75%, p<0.01; 24m 55% vs. 87%, p<0.01. In conclusion, early treatment response analysis defines a biologically distinct patient subgroup with inferior long-term outcomes.
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Baar, Marsha R.; Falcone, Danielle; Gordon, Christopher
2010-01-01
Microwave heating enhanced the rate of three reactions typically performed in our undergraduate organic chemistry laboratory: a Diels-Alder cycloaddition, a Wittig salt formation, and a Williamson ether synthesis. Ninety-minute refluxes were shortened to 10 min using a laboratory-grade microwave oven. In addition, yields improved for the Wittig…
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Kocsis, Laura S; Benedetti, Erica; Brummond, Kay M
2012-09-07
Functionalized naphthalenes are valuable building blocks in many important areas. A microwave-assisted, intramolecular dehydrogenative Diels-Alder reaction of styrenyl derivatives to provide cyclopenta[b]naphthalene substructures not previously accessible using existing synthetic methods is described. The synthetic utility of these uniquely functionalized naphthalenes was demonstrated by a single-step conversion of one of these cycloadducts to a fluorophore bearing a structural resemblance to Prodan.
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Directory of Open Access Journals (Sweden)
Daniel eWipf
2014-12-01
Full Text Available Sulfur plays an essential role in plants’ growth and development and in their response to various abiotic and biotic stresses despite its leachability and its very low abundance in the only form that plant roots can uptake (sulfate. It is part of amino acids, glutathione (GSH, thiols of proteins and peptides, membrane sulfolipids, cell walls and secondary products, so reduced availability can drastically alter plant growth and development. The nutritional benefits of symbiotic interactions can help the plant in case of S deficiency. In particular the arbuscular mycorrhizal (AM interaction improves N, P and S plant nutrition, but the mechanisms behind these exchanges are not fully known yet. Although the transcriptional changes in the leguminous model plant Medicago truncatula have been already assessed in several biotic and/or abiotic conditions, S deficiency has not been considered so far. The aim of this work is to get a first overview on S-deficiency responses in the leaf and root tissues of plants interacting with the AM fungus Rhizophagus irregularis.Several hundred genes displayed significantly different transcript accumulation levels. Annotation and GO ID association were used to identify biological processes and molecular functions affected by sulfur starvation. Beside the beneficial effects of AM interaction, plants were greatly affected by the nutritional status, showing various differences in their transcriptomic footprints. Several pathways in which S plays an important role appeared to be differentially affected according to mycorrhizal status, with a generally reduced responsiveness to S deficiency in mycorrhized plants.
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Beniwal, Vijay; Kumar, Anil
2017-02-08
Organic reactions in general display large rate accelerations when performed under interfacial conditions, such as on water or at ionic liquid interfaces. However, a clear picture of the physicochemical factors responsible for this large rate enhancements is not available. To gain an understanding of the thermodynamic and molecular origin of these large rate enhancements, we performed a Diels-Alder reaction between cyclopentadiene and methyl acrylate at ionic liquid/n-hexane interfaces. This study describes, for the first time, a methodology for the calculation of the activation parameters of an interfacial reaction. It has been seen that the energy of activation for an interfacial reaction is much smaller than that of the corresponding homogeneous reaction, resulting into the large rate acceleration for the interfacial reaction. Furthermore, the study describes the effects of the alkyl chain length of ionic liquid cations, the extent of heterogeneity, and the polarity of ionic liquids on the rate constants and stereoselectivity of the reaction.
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Agent-based modeling of oxygen-responsive transcription factors in Escherichia coli.
Directory of Open Access Journals (Sweden)
Hao Bai
2014-04-01
Full Text Available In the presence of oxygen (O2 the model bacterium Escherichia coli is able to conserve energy by aerobic respiration. Two major terminal oxidases are involved in this process - Cyo has a relatively low affinity for O2 but is able to pump protons and hence is energetically efficient; Cyd has a high affinity for O2 but does not pump protons. When E. coli encounters environments with different O2 availabilities, the expression of the genes encoding the alternative terminal oxidases, the cydAB and cyoABCDE operons, are regulated by two O2-responsive transcription factors, ArcA (an indirect O2 sensor and FNR (a direct O2 sensor. It has been suggested that O2-consumption by the terminal oxidases located at the cytoplasmic membrane significantly affects the activities of ArcA and FNR in the bacterial nucleoid. In this study, an agent-based modeling approach has been taken to spatially simulate the uptake and consumption of O2 by E. coli and the consequent modulation of ArcA and FNR activities based on experimental data obtained from highly controlled chemostat cultures. The molecules of O2, transcription factors and terminal oxidases are treated as individual agents and their behaviors and interactions are imitated in a simulated 3-D E. coli cell. The model implies that there are two barriers that dampen the response of FNR to O2, i.e. consumption of O2 at the membrane by the terminal oxidases and reaction of O2 with cytoplasmic FNR. Analysis of FNR variants suggested that the monomer-dimer transition is the key step in FNR-mediated repression of gene expression.
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Chen, Qiansi; Li, Meng; Zhang, Zhongchun; Tie, Weiwei; Chen, Xia; Jin, Lifeng; Zhai, Niu; Zheng, Qingxia; Zhang, Jianfeng; Wang, Ran; Xu, Guoyun; Zhang, Hui; Liu, Pingping; Zhou, Huina
2017-01-10
Drought stress is one of the most severe problem limited agricultural productivity worldwide. It has been reported that plants response to drought-stress by sophisticated mechanisms at both transcriptional and post-transcriptional levels. However, the precise molecular mechanisms governing the responses of tobacco leaves to drought stress and water status are not well understood. To identify genes and miRNAs involved in drought-stress responses in tobacco, we performed both mRNA and small RNA sequencing on tobacco leaf samples from the following three treatments: untreated-control (CL), drought stress (DL), and re-watering (WL). In total, we identified 798 differentially expressed genes (DEGs) between the DL and CL (DL vs. CL) treatments and identified 571 DEGs between the WL and DL (WL vs. DL) treatments. Further analysis revealed 443 overlapping DEGs between the DL vs. CL and WL vs. DL comparisons, and, strikingly, all of these genes exhibited opposing expression trends between these two comparisons, strongly suggesting that these overlapping DEGs are somehow involved in the responses of tobacco leaves to drought stress. Functional annotation analysis showed significant up-regulation of genes annotated to be involved in responses to stimulus and stress, (e.g., late embryogenesis abundant proteins and heat-shock proteins) antioxidant defense (e.g., peroxidases and glutathione S-transferases), down regulation of genes related to the cell cycle pathway, and photosynthesis processes. We also found 69 and 56 transcription factors (TFs) among the DEGs in, respectively, the DL vs. CL and the WL vs. DL comparisons. In addition, small RNA sequencing revealed 63 known microRNAs (miRNA) from 32 families and 368 novel miRNA candidates in tobacco. We also found that five known miRNA families (miR398, miR390, miR162, miR166, and miR168) showed differential regulation under drought conditions. Analysis to identify negative correlations between the differentially expressed mi
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Directory of Open Access Journals (Sweden)
Deepak Voora, MD
2016-09-01
Full Text Available Aspirin prevents cardiovascular disease and colon cancer; however aspirin's inhibition of platelet COX-1 only partially explains its diverse effects. We previously identified an aspirin response signature (ARS in blood consisting of 62 co-expressed transcripts that correlated with aspirin's effects on platelets and myocardial infarction (MI. Here we report that 60% of ARS transcripts are regulated by RUNX1 – a hematopoietic transcription factor - and 48% of ARS gene promoters contain a RUNX1 binding site. Megakaryocytic cells exposed to aspirin and its metabolite (salicylic acid, a weak COX-1 inhibitor showed up regulation in the RUNX1 P1 isoform and MYL9, which is transcriptionally regulated by RUNX1. In human subjects, RUNX1 P1 expression in blood and RUNX1-regulated platelet proteins, including MYL9, were aspirin-responsive and associated with platelet function. In cardiovascular disease patients RUNX1 P1 expression was associated with death or MI. RUNX1 acts as a tumor suppressor gene in gastrointestinal malignancies. We show that RUNX1 P1 expression is associated with colon cancer free survival suggesting a role for RUNX1 in aspirin's protective effect in colon cancer. Our studies reveal an effect of aspirin on RUNX1 and gene expression that may additionally explain aspirin's effects in cardiovascular disease and cancer.
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Mohamed, Bahaeldeen Babikar; Aftab, Beenish; Sarwar, Muhammad Bilal; Ahmad, Zarnab; Hassan, Sameera; Husnain, Tayyab
2017-01-01
Various regulatory proteins play a fundamental role to manage the healthy plant growth under stress conditions. Differential display reverse transcriptase PCR and random amplification of cDNA ends (RACE) was used to explore the osmotic stress-responsive transcripts. We identified and characterized the salt stress-responsive R2R3 type RMYB transcription factor from Hibiscus sabdariffa which has an open reading frame of 690 bp, encoding 229 long chain amino acids. In silico analysis confirmed the conserved R2 and R3 domain as well as an NLS-1 localization site. The deduced amino acids of RMYB shared 83, 81, 80, 79, 72, 71, and 66% homology with Arabidopsis thaliana, Glycine max, Oryza sativa, Zea maize, Malus domestica, Populus tremula × Populus alba, and Medicago sativa specific MYB family, respectively. We observed the gene upregulation in stem, leaf, and root tissue in response to abiotic stress. Furthermore, RMYB gene was cloned into plant expression vector under CaMV35S promoter and transformed to Gossypium hirsutum: a local cotton cultivar. Overexpression of RMYB was observed in transgenic plants under abiotic stresses which further suggests its regulatory role in response to stressful conditions. The RMYB transcription factor-overexpressing in transgenic cotton plants may be used as potential agent for the development of stress tolerant crop cultivars. PMID:29181384
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Carbonell-Bejerano, Pablo; Diago, Maria-Paz; Martínez-Abaigar, Javier; Martínez-Zapater, José M; Tardáguila, Javier; Núñez-Olivera, Encarnación
2014-07-09
Ultraviolet (UV) radiation modulates secondary metabolism in the skin of Vitis vinifera L. berries, which affects the final composition of both grapes and wines. The expression of several phenylpropanoid biosynthesis-related genes is regulated by UV radiation in grape berries. However, the complete portion of transcriptome and ripening processes influenced by solar UV radiation in grapes remains unknown. Whole genome arrays were used to identify the berry skin transcriptome modulated by the UV radiation received naturally in a mid-altitude Tempranillo vineyard. UV radiation-blocking and transmitting filters were used to generate the experimental conditions. The expression of 121 genes was significantly altered by solar UV radiation. Functional enrichment analysis of altered transcripts mainly pointed out that secondary metabolism-related transcripts were induced by UV radiation including VvFLS1, VvGT5 and VvGT6 flavonol biosynthetic genes and monoterpenoid biosynthetic genes. Berry skin phenolic composition was also analysed to search for correlation with gene expression changes and UV-increased flavonols accumulation was the most evident impact. Among regulatory genes, novel UV radiation-responsive transcription factors including VvMYB24 and three bHLH, together with known grapevine UV-responsive genes such as VvMYBF1, were identified. A transcriptomic meta-analysis revealed that genes up-regulated by UV radiation in the berry skin were also enriched in homologs of Arabidopsis UVR8 UV-B photoreceptor-dependent UV-B -responsive genes. Indeed, a search of the grapevine reference genomic sequence identified UV-B signalling pathway homologs and among them, VvHY5-1, VvHY5-2 and VvRUP were up-regulated by UV radiation in the berry skin. Results suggest that the UV-B radiation-specific signalling pathway is activated in the skin of grapes grown at mid-altitudes. The biosynthesis and accumulation of secondary metabolites, which are appreciated in winemaking and
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Chueca, Beatriz; Pérez-Sáez, Elisa; Pagán, Rafael; García-Gonzalo, Diego
2017-09-18
DNA microarrays were used to study the mechanism of bacterial inactivation by carvacrol and citral. After 10-min treatments of Escherichia coli MG1655 cells with 100 and 50ppm of carvacrol and citral, 76 and 156 genes demonstrated significant transcriptional differences (p≤0.05), respectively. Among the up-regulated genes after carvacrol treatment, we found gene coding for multidrug efflux pumps (acrA, mdtM), genes related to phage shock response (pspA, pspB, pspC, pspD, pspF and pspG), biosynthesis of arginine (argC, argG, artJ), and purine nucleotides (purC, purM). In citral-treated cells, transcription of purH and pyrB and pyrI was 2 times higher. Deletion of several differentially expressed genes confirmed the role of ygaV, yjbO, pspC, sdhA, yejG and ygaV in the mechanisms of E. coli inactivation by carvacrol and citral. These results would indicate that citral and carvacrol treatments cause membrane damage and activate metabolism through the production of nucleotides required for DNA and RNA synthesis and metabolic processes. Comparative transcriptomics of the response of E. coli to a heat treatment, which caused a significant change of the transcription of 1422 genes, revealed a much weaker response to both individual constituents of essential oils (ICs).·Thus, inactivation by citral or carvacrol was not multitarget in nature. Copyright © 2017 Elsevier B.V. All rights reserved.
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Investigating radical cation chain processes in the electrocatalytic Diels-Alder reaction.
Imada, Yasushi; Okada, Yohei; Chiba, Kazuhiro
2018-01-01
Single electron transfer (SET)-triggered radical ion-based reactions have proven to be powerful options in synthetic organic chemistry. Although unique chain processes have been proposed in various photo- and electrochemical radical ion-based transformations, the turnover number, also referred to as catalytic efficiency, remains unclear in most cases. Herein, we disclose our investigations of radical cation chain processes in the electrocatalytic Diels-Alder reaction, leading to a scalable synthesis. A gram-scale synthesis was achieved with high current efficiency of up to 8000%. The reaction monitoring profiles showed sigmoidal curves with induction periods, suggesting the involvement of intermediate(s) in the rate determining step.
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A Tri-O-Bridged Diels-Alder Adduct from Cortex Mori Radicis
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An-Qi Lu
2018-01-01
Full Text Available Sanggenon X, an unusual tri-O-bridged Diels-Alder adduct, was isolated from Cortex Mori Radicis. Its structure was established by spectroscopic analysis, including NMR and HR-MS (High Resolution Mass Spectrometry. Sanggenon X contained three O-bridged rings, where the oxygenated bridgeheads were all quaternary carbons. Chemical methylation was carried out to deduce the linkages of the three O-bridges. The absolute configuration was determined by calculating the ECD (Electronic Circular Dichroism using the TDDFT (Time-Dependent Density Functional Theory method. Sanggenon X showed significant antioxidant activity against Fe2+-Cys-induced lipid peroxidation in rat liver microsomes, and was as effective as the positive control, curcumin.
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Saxena, Kapil; Simon, Lukas M.; Zeng, Xi-Lei; Blutt, Sarah E.; Crawford, Sue E.; Sastri, Narayan P.; Karandikar, Umesh C.; Ajami, Nadim J.; Zachos, Nicholas C.; Kovbasnjuk, Olga; Donowitz, Mark; Conner, Margaret E.; Shaw, Chad A.; Estes, Mary K.
2017-01-01
Understanding host?enteric virus interactions has been limited by the inability to culture nontransformed small intestinal epithelial cells and to infect animal models with human viruses. We report epithelial responses in human small intestinal enteroid cultures from different individuals following infection with human rotavirus (HRV), a model enteric pathogen. RNA-sequencing and functional assays revealed type III IFN as the dominant transcriptional response that activates interferon-stimula...
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Liu, Fengli; Pullarkat, Sumod A; Tan, Kien-Wee; Li, Yongxin; Leung, Pak-Hing
2009-12-07
The organoplatinum complex containing ortho-metalated (R)-(1-(dimethylamino)ethyl)-naphthalene as the chiral auxiliary has been used efficiently to promote the asymmetric [4 + 2] Diels-Alder reaction between diphenylvinylphosphine and 3-diphenylphosphinofuran to generate two chelating diphosphine endocycloadducts in the ratio 17:1. The absolute configurations of the three newly generated stereocenters have been assigned by single-crystal X-ray analysis.
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Wu, Zhi-Jun; Li, Xing-Hui; Liu, Zhi-Wei; Li, Hui; Wang, Yong-Xin; Zhuang, Jing
2016-02-01
Tea plant [Camellia sinensis (L.) O. Kuntze] is a leaf-type healthy non-alcoholic beverage crop, which has been widely introduced worldwide. Tea is rich in various secondary metabolites, which are important for human health. However, varied climate and complex geography have posed challenges for tea plant survival. The WRKY gene family in plants is a large transcription factor family that is involved in biological processes related to stress defenses, development, and metabolite synthesis. Therefore, identification and analysis of WRKY family transcription factors in tea plant have a profound significance. In the present study, 50 putative C. sinensis WRKY proteins (CsWRKYs) with complete WRKY domain were identified and divided into three Groups (Group I-III) on the basis of phylogenetic analysis results. The distribution of WRKY family transcription factors among plantae, fungi, and protozoa showed that the number of WRKY genes increased in higher plant, whereas the number of these genes did not correspond to the evolutionary relationships of different species. Structural feature and annotation analysis results showed that CsWRKY proteins contained WRKYGQK/WRKYGKK domains and C2H2/C2HC-type zinc-finger structure: D-X18-R-X1-Y-X2-C-X4-7-C-X23-H motif; CsWRKY proteins may be associated with the biological processes of abiotic and biotic stresses, tissue development, and hormone and secondary metabolite biosynthesis. Temperature stresses suggested that the candidate CsWRKY genes were involved in responses to extreme temperatures. The current study established an extensive overview of the WRKY family transcription factors in tea plant. This study also provided a global survey of CsWRKY transcription factors and a foundation of future functional identification and molecular breeding.
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Directory of Open Access Journals (Sweden)
Mujeeb A. Sultan
2016-01-01
Full Text Available Diels-Alder reaction of 10-allyl-1,8-dichloroanthracene (3 with 2-chloroacrylonitrile (4 and 1-cyanovinyl acetate (5 gives exclusively the ortho isomer while its reaction with phenyl vinyl sulfone (10 yields a mixture of two isomeric adducts with priority to ortho isomer. The reactions proceeded under microwave condition in xylene. Configurations of these isomers have been assigned with the help of NMR spectra. The results indicated that the steric effect is dominating toward the isomer regioselectivity in the Diels-Alder reaction of the present compounds.
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Directory of Open Access Journals (Sweden)
B. Biolatto
2000-03-01
Full Text Available Under high pressure conditions, the Diels-Alder reaction involving N,N-diethyl-1-tosyl-3-indoleglyoxylamide and 1-(N-acetyl-N-propylamino-1,3-butadiene produces a highly functionalized intermediate for the synthesis of Indole Alkaloids, in shorter times and higher yields than under thermal conditions.
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Diels-Alder Synthesis of endo-cis-N-phenylbicyclo[2.2.2]oct-5-en-2,3-dicarboximide
Baar, Marsha R.; Wustholz, Kristin
2005-01-01
A study investigated the Diels-Alder synthesis of endo-cis-N-phenylbicyclo [2.2.2]oct-5-en-2,3-dicarboximide. The amount of time taken by a reaction between the 1,3-cyclohexadiene and N-phenylmaleimide at room temperature and also whether the desired cycloadduct would precipitate directly from the reaction mixture was examined.
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Vos, J.B.; Sterkenburg, M.A. van; Rabe, K.F.; Schalkwijk, J.; Hiemstra, P.S.; Datson, N.A.
2005-01-01
The airway epithelium responds to microbial exposure by altering expression of a variety of genes to increase innate host defense. We aimed to delineate the early transcriptional response in human primary bronchial epithelial cells exposed for 6 h to a mixture of IL-1beta and TNF-alpha or
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Directory of Open Access Journals (Sweden)
J. Antonio Palenzuela
2007-02-01
Full Text Available A route for the preparation of 2,5-disubstituted octahydroquinolin-4-ones, synthetic precursors of the decahydroquinoline-type toxins, is presented. The key steps are an asymmetric epoxidation and an intramolecular hetero Diels-Alder reaction between an activated diene and an imine. The presence of an allylic stereogenic center induces some selectivity and thus only two cycloadducts are obtained in 70:30 ratio and good yield.
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Nekkaa, Imane; Palkó, Márta; Mándity, István M; Fülöp, Ferenc
2018-01-01
The syntheses of various pyrimidinones as potentially bioactive products by means of the highly controlled continuous-flow retro-Diels-Alder reaction of condensed pyrimidinone derivatives are presented. Noteworthy, the use of this approach allowed us to rapidly screen a selection of conditions and quickly confirm the viability of preparing the desired pyrimidinones in short reaction times. Yields typically higher than those published earlier using conventional batch or microwave processes were achieved.
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Mahmood, Kashif; Xu, Zhenhua; El-Kereamy, Ashraf; Casaretto, Jos? A.; Rothstein, Steven J.
2016-01-01
Production of anthocyanins is one of the adaptive responses employed by plants during stress conditions. During stress, anthocyanin biosynthesis is mainly regulated at the transcriptional level via a complex interplay between activators and repressors of anthocyanin biosynthesis genes. In this study, we investigated the role of a NAC transcription factor, ANAC032, in the regulation of anthocyanin biosynthesis during stress conditions. ANAC032 expression was found to be induced by exogenous su...
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Energy Technology Data Exchange (ETDEWEB)
Milan, Massimo; Pauletto, Marianna; Patarnello, Tomaso; Bargelloni, Luca [Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell' Universita 16, Legnaro (Padova) (Italy); Marin, Maria Gabriella [Department of Biology, University of Padova, Via Ugo Bassi 58/B, 35131 Padova (Italy); Matozzo, Valerio, E-mail: matozzo@bio.unipd.it [Department of Biology, University of Padova, Via Ugo Bassi 58/B, 35131 Padova (Italy)
2013-01-15
Pharmaceuticals are a class of emerging environmental contaminants that continuously enter aquatic environments. Presently, little information is available about the effects of these substances on non-target organisms, such as bivalves. We investigated the effects of ibuprofen (IBU) on the clam Ruditapes philippinarum. Clams were exposed for 1, 3, 5 and 7 days to 0, 100 and 1000 {mu}g IBU/L, and established biomarker responses (haemolymph lysozyme, gill acetylcholinesterase and digestive gland superoxide dismutase activities) as well as digestive gland transcriptome were evaluated. A two-way ANOVA revealed significant effects of both 'IBU concentration' and 'exposure duration' on biomarker responses. Overall, the enzyme activities were generally lower in IBU-exposed clams than in controls. Although limited knowledge of the mollusc transcriptome makes it difficult to interpret the effects of IBU on clams, the gene transcription analysis using DNA microarrays enabled the identification of the putative molecular mode of action of the IBU. The functional analysis of differentially transcribed genes suggests that IBU can interfere with various signalling pathways in clams, such as arachidonic acid metabolism, apoptosis, peroxisomal proliferator-activated receptors, and nuclear factor-kappa B. In addition, several genes involved in the metabolism of xenobiotics (e.g., glutathione S-transferase, sulfotransferase, cytochrome P450) were also found to be significantly affected by IBU exposure. In summary, the integrated approach of gene transcription analysis and biomarker responses facilitated the elucidation of the putative mechanisms of action of IBU in non-target species.
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International Nuclear Information System (INIS)
Milan, Massimo; Pauletto, Marianna; Patarnello, Tomaso; Bargelloni, Luca; Marin, Maria Gabriella; Matozzo, Valerio
2013-01-01
Pharmaceuticals are a class of emerging environmental contaminants that continuously enter aquatic environments. Presently, little information is available about the effects of these substances on non-target organisms, such as bivalves. We investigated the effects of ibuprofen (IBU) on the clam Ruditapes philippinarum. Clams were exposed for 1, 3, 5 and 7 days to 0, 100 and 1000 μg IBU/L, and established biomarker responses (haemolymph lysozyme, gill acetylcholinesterase and digestive gland superoxide dismutase activities) as well as digestive gland transcriptome were evaluated. A two-way ANOVA revealed significant effects of both “IBU concentration” and “exposure duration” on biomarker responses. Overall, the enzyme activities were generally lower in IBU-exposed clams than in controls. Although limited knowledge of the mollusc transcriptome makes it difficult to interpret the effects of IBU on clams, the gene transcription analysis using DNA microarrays enabled the identification of the putative molecular mode of action of the IBU. The functional analysis of differentially transcribed genes suggests that IBU can interfere with various signalling pathways in clams, such as arachidonic acid metabolism, apoptosis, peroxisomal proliferator-activated receptors, and nuclear factor-kappa B. In addition, several genes involved in the metabolism of xenobiotics (e.g., glutathione S-transferase, sulfotransferase, cytochrome P450) were also found to be significantly affected by IBU exposure. In summary, the integrated approach of gene transcription analysis and biomarker responses facilitated the elucidation of the putative mechanisms of action of IBU in non-target species.
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Yang, Baochao; Lin, Kuaikuai; Shi, Yingbo; Gao, Shuanhu
2017-09-20
Stereoselective construction of polycyclic rings with all-carbon quaternary centers, and vicinal all-carbon quaternary stereocenters, remains a significant challenge in organic synthesis. These structures can be found in a wide range of polycyclic natural products and drug molecules. Here we report a Ti(Oi-Pr) 4 -promoted photoenolization/Diels-Alder (PEDA) reaction to construct hydroanthracenol and related polycyclic rings bearing all-carbon quaternary centers. This photolysis proceeds under mild conditions and generates a variety of photo-cycloaddition products in good reaction efficiency and stereoselectivity (48 examples), and has been successfully used in the construction of core skeleton of oncocalyxones, tetracycline and pleurotin. It also provides a reliable method for the late-stage modification of natural products bearing enone groups, such as steroids. The total synthesis of oncocalyxone B was successfully achieved using this PEDA approach.Anthracenols with multiple chiral centres are common motifs in natural products. Here, the authors show a highly stereoselective photoenolization/Diels-Alder methodology involving a key Lewis acid reagent enabling the efficient construction of a family of anthracenol derivatives with quaternary centers.
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Li, Jinling; Jiao, Chongjun; Huang, Kuo-Wei; Wu, Jishan
2011-01-01
Diels-Alder cycloaddition reactions at the bay regions of bisanthene (1) with dienophiles such as 1,4-naphthoquinone have been investigated. The products were submitted to nucleophilic addition followed by reductive aromatization reactions to afford the laterally extended bisanthene derivatives 2 and 3. Attempted synthesis of a larger expanded bisanthene 4 revealed an unexpected hydrogenation reaction at the last reductive aromatization step. Unusual Michael addition was observed on quinone 14, which was obtained by Diels-Alder reaction between 1 and 1,4-anthraquinone. Compounds 1-3 exhibited near-infrared (NIR) absorption and emission with high-to-moderate fluorescent quantum yields. Their structures and absorption spectra were studied by density function theory and non-planar twisted structures were calculated for 2 and 3. All compounds showed amphoteric redox behavior with multiple oxidation/reduction waves. Oxidative titration with SbCl 5 gave stable radical cations, and the process was followed by UV/Vis/NIR spectroscopic measurements. Their photostability was measured and correlated to their different geometries and electronic structures. © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Li, Jinling
2011-11-14
Diels-Alder cycloaddition reactions at the bay regions of bisanthene (1) with dienophiles such as 1,4-naphthoquinone have been investigated. The products were submitted to nucleophilic addition followed by reductive aromatization reactions to afford the laterally extended bisanthene derivatives 2 and 3. Attempted synthesis of a larger expanded bisanthene 4 revealed an unexpected hydrogenation reaction at the last reductive aromatization step. Unusual Michael addition was observed on quinone 14, which was obtained by Diels-Alder reaction between 1 and 1,4-anthraquinone. Compounds 1-3 exhibited near-infrared (NIR) absorption and emission with high-to-moderate fluorescent quantum yields. Their structures and absorption spectra were studied by density function theory and non-planar twisted structures were calculated for 2 and 3. All compounds showed amphoteric redox behavior with multiple oxidation/reduction waves. Oxidative titration with SbCl 5 gave stable radical cations, and the process was followed by UV/Vis/NIR spectroscopic measurements. Their photostability was measured and correlated to their different geometries and electronic structures. © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Bai, Xuejia; Huang, Wenqiu; Zhang, Chenguang; Niu, Jing; Ding, Wei
2016-03-01
One of the basic leucine zipper transcription factors, BATF2, has been found to suppress cancer growth and migration. However, little is known about the genes downstream of BATF2. HeLa cells were stably transfected with BATF2, then chromatin immunoprecipitation-sequencing was employed to identify the DNA motifs responsive to BATF2. Comprehensive bioinformatics analyses indicated that the most significant motif discovered as TTCCATT[CT]GATTCCATTC[AG]AT was primarily distributed among the chromosome centromere regions and mostly within human type II satellite DNA. Such motifs were able to prime the transcription of type II satellite DNA in a directional and asymmetrical manner. Consistently, satellite II transcription was up-regulated in BATF2-overexpressing cells. The present study provides insight into understanding the role of BATF2 in tumours and the importance of satellite DNA in the maintenance of genomic stability. Copyright© 2016 International Institute of Anticancer Research (Dr. John G. Delinassios), All rights reserved.
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Laurence A. Marchat; Elena Aréchaga Ocampo; Mavil López Casamichana; Carlos Pérez-Plasencia; César López-Camarillo; Elizbeth Álvarez-Sánchez
2011-01-01
Solar ultraviolet (UV) radiation is an important environmental factor that leads to immune suppression, inflammation, photoaging, and skin carcinogenesis. Here, we reviewed the specific signal transduction pathways and transcription factors involved in the cellular response to UV-irradiation. Increasing experimental data supporting a role for p38, MAPK, JNK, ERK1/2, and ATM kinases in the response network to UV exposure is discussed. We also reviewed the participation of NF-?B, AP-1, and NRF2...
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Polgar, L. M.; van Duin, M.; Broekhuis, A. A.; Picchioni, F.
2015-01-01
A proof of principle for the use of Diels-Alder chemistry as a thermoreversible cross-linking tool for rubber products is demonstrated. A commercial ethylene-propylene rubber grafted with maleic anhydride has been thermoreversibly cross-linked in two steps. The pending anhydride rings were first
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Meta-Analysis of Transcriptional Responses to Mastitis-Causing Escherichia coli.
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Sidra Younis
Full Text Available Bovine mastitis is a widespread disease in dairy cows, and is often caused by bacterial mammary gland infection. Mastitis causes reduced milk production and leads to excessive use of antibiotics. We present meta-analysis of transcriptional profiles of bovine mastitis from 10 studies and 307 microarrays, allowing identification of much larger sets of affected genes than any individual study. Combining multiple studies provides insight into the molecular effects of Escherichia coli infection in vivo and uncovers differences between the consequences of E. coli vs. Staphylococcus aureus infection of primary mammary epithelial cells (PMECs. In udders, live E. coli elicits inflammatory and immune defenses through numerous cytokines and chemokines. Importantly, E. coli infection causes downregulation of genes encoding lipid biosynthesis enzymes that are involved in milk production. Additionally, host metabolism is generally suppressed. Finally, defensins and bacteria-recognition genes are upregulated, while the expression of the extracellular matrix protein transcripts is silenced. In PMECs, heat-inactivated E. coli elicits expression of ribosomal, cytoskeletal and angiogenic signaling genes, and causes suppression of the cell cycle and energy production genes. We hypothesize that heat-inactivated E. coli may have prophylactic effects against mastitis. Heat-inactivated S. aureus promotes stronger inflammatory and immune defenses than E. coli. Lipopolysaccharide by itself induces MHC antigen presentation components, an effect not seen in response to E. coli bacteria. These results provide the basis for strategies to prevent and treat mastitis and may lead to the reduction in the use of antibiotics.
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International Nuclear Information System (INIS)
Sappal, Ravinder; Fast, Mark; Purcell, Sara; MacDonald, Nicole; Stevens, Don; Kibenge, Fred; Siah, Ahmed; Kamunde, Collins
2016-01-01
To survive in changing environments fish utilize a wide range of biological responses that require energy. We examined the effect of warm acclimation on the electron transport system (ETS) enzymes and transcriptional responses to hypoxia and copper (Cu) exposure in fish. Rainbow trout (Oncorhynchus mykiss) were acclimated to cold (11 °C; control) and warm (20 °C) temperatures for 3 weeks followed by exposure to Cu, hypoxia or both for 24 h. Activities of ETS enzyme complexes I-IV (CI–CIV) were measured in liver and gill mitochondria. Analyses of transcripts encoding for proteins involved in mitochondrial respiration (cytochrome c oxidase subunits 4-1 and 2: COX4-1 and COX4-2), metal detoxification/stress response (metallothioneins A and B: MT-A and MT-B) and energy sensing (AMP-activated protein kinase α1: AMPKα1) were done in liver mitochondria, and in whole liver and gill tissues by RT-qPCR. Warm acclimation inhibited activities of ETS enzymes while effects of Cu and hypoxia depended on the enzyme and thermal acclimation status. The genes encoding for COX4-1, COX4-2, MT-A, MT-B and AMPKα1 were strongly and tissue-dependently altered by warm acclimation. While Cu and hypoxia clearly increased MT-A and MT-B transcript levels in all tissues, their effects on COX4-1, COX4-2 and AMPKα1 mRNA levels were less pronounced. Importantly, warm acclimation differentially altered COX4-2/COX4-1 ratio in liver mitochondria and gill tissue. The three stressors showed both independent and joint actions on activities of ETS enzymes and transcription of genes involved in energy metabolism, stress response and metals homeostasis. Overall, we unveiled novel interactive effects that should not be overlooked in real world situations wherein fish normally encounter multiple stress factors. - Highlights: • Joint and individual effects of copper, hypoxia and warm acclimation differ quantitatively. • Energy metabolism genes are differentially altered by multiple stressors.
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Dypvik, Eivind
2012-11-13
The vertical migration and diel feeding periodicity of the skinnycheek lanternfish (Benthosema pterotum) were studied by use of a hull-mounted 38 kHz echo sounder, ROV-deployments and net-sampling at two locations (∼24°48′N, ∼36°15′E and ∼21°27′N, ∼38°5′E) in the central Red Sea. The mesopelagic zone of the Red Sea represents an unusual environment with very high temperatures (∼22 °C) and low zooplankton concentrations (<10 individuals m−3 below 600 m). The skinnycheek lanternfish performed normal diel vertical migration from ∼500 to 750 m during daytime to the epipelagic zone (upper ∼200 m) at night. A strict feeding periodicity occurred; with the skinnycheek lanternfish foraging on zooplankton throughout the night, while rapidly digesting the preceding nocturnal meal in the warm mesopelagic region. We hypothesize that the constrained epipelagic distribution of zooplankton and the unusual warm waters of the Red Sea force the whole population to ascend and feed in epipelagic waters every night, as the prey-ration eaten each night is fully digested at mesopelagic depths during daytime.
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Jia, Yang; Fan, Ming; Chen, Huinan; Miao, Yuting; Xing, Lian; Jiang, Bohong; Cheng, Qifan; Liu, Dongwei; Bao, Weikang; Qian, Bin; Wang, Jionglu; Xing, Xiaodong; Tan, Huaping; Ling, Zhonghua; Chen, Yong
2015-11-15
Biopolymer-based nanospheres have great potential in the field of drug delivery and tissue regenerative medicine. In this work, we present a flexible way to conjugate a magnetic hyaluronic acid (HA) nanosphere system that are capable of vectoring delivery of adipogenic factor, e.g. dexamethasone, for adipose tissue engineering. Conjugation of nanospheres was established by aqueous Diels-Alder chemistry between furan and maleimide of HA derivatives. Simultaneously, a furan functionalized dexamethasone peptide, GQPGK, was synthesized and covalently immobilized into the nanospheres. The magnetic HA nanospheres were fabricated by encapsulating super-paramagnetic iron oxide nanoparticles, which exhibited quick magnetic sensitivity. The aqueous Diels-Alder chemistry made nanospheres high binding efficiency of dexamethasone, and the vectoring delivery of dexamethasone could be easily controlled by a external magnetic field. The potential application of the magnetic HA nanospheres on vectoring delivery of adipogenic factor was confirmed by co-culture of human adipose-derived stem cells (ASCs). In vitro cytotoxicity tests demonstrated that incorporation of dexamethasone into magnetic HA nanospheres showed high efficiency to promote ASCs viabilities, in particular under a magnetic field, which suggested a promising future for adipose regeneration applications. Copyright © 2015 Elsevier Inc. All rights reserved.
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Post-transcription cleavage generates the 3' end of F17R transcripts in vaccinia virus
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D'Costa, Susan M.; Antczak, James B.; Pickup, David J.; Condit, Richard C.
2004-01-01
Most vaccinia virus intermediate and late mRNAs possess 3' ends that are extremely heterogeneous in sequence. However, late mRNAs encoding the cowpox A-type inclusion protein (ATI), the second largest subunit of the RNA polymerase, and the late telomeric transcripts possess homogeneous 3' ends. In the case of the ATI mRNA, it has been shown that the homogeneous 3' end is generated by a post-transcriptional endoribonucleolytic cleavage event. We have determined that the F17R gene also produces homogeneous transcripts generated by a post-transcriptional cleavage event. Mapping of in vivo mRNA shows that the major 3' end of the F17R transcript maps 1262 nt downstream of the F17R translational start site. In vitro transcripts spanning the in vivo 3' end are cleaved in an in vitro reaction using extracts from virus infected cells, and the site of cleavage is the same both in vivo and in vitro. Cleavage is not observed using extract from cells infected in the presence of hydroxyurea; therefore, the cleavage factor is either virus-coded or virus-induced during the post-replicative phase of virus replication. The cis-acting sequence responsible for cleavage is orientation specific and the factor responsible for cleavage activity has biochemical properties similar to the factor required for cleavage of ATI transcripts. Partially purified cleavage factor generates cleavage products of expected size when either the ATI or F17R substrates are used in vitro, strongly suggesting that cleavage of both transcripts is mediated by the same factor
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Transcriptional feedback regulation of YUCCA genes in response to auxin levels in Arabidopsis.
Suzuki, Masashi; Yamazaki, Chiaki; Mitsui, Marie; Kakei, Yusuke; Mitani, Yuka; Nakamura, Ayako; Ishii, Takahiro; Soeno, Kazuo; Shimada, Yukihisa
2015-08-01
The IPyA pathway, the major auxin biosynthesis pathway, is transcriptionally regulated through a negative feedback mechanism in response to active auxin levels. The phytohormone auxin plays an important role in plant growth and development, and levels of active free auxin are determined by biosynthesis, conjugation, and polar transport. Unlike conjugation and polar transport, little is known regarding the regulatory mechanism of auxin biosynthesis. We discovered that expression of genes encoding indole-3-pyruvic acid (IPyA) pathway enzymes is regulated by elevated or reduced active auxin levels. Expression levels of TAR2, YUC1, YUC2, YUC4, and YUC6 were downregulated in response to synthetic auxins [1-naphthaleneacetic acid (NAA) and 2,4-dichlorophenoxyacetic acid (2,4-D)] exogenously applied to Arabidopsis thaliana L. seedlings. Concomitantly, reduced levels of endogenous indole-3-acetic acid (IAA) were observed. Alternatively, expression of these YUCCA genes was upregulated by the auxin biosynthetic inhibitor kynurenine in Arabidopsis seedlings, accompanied by reduced IAA levels. These results indicate that expression of YUCCA genes is regulated by active auxin levels. Similar results were also observed in auxin-overproduction and auxin-deficient mutants. Exogenous application of IPyA to Arabidopsis seedlings preincubated with kynurenine increased endogenous IAA levels, while preincubation with 2,4-D reduced endogenous IAA levels compared to seedlings exposed only to IPyA. These results suggest that in vivo conversion of IPyA to IAA was enhanced under reduced auxin levels, while IPyA to IAA conversion was depressed in the presence of excess auxin. Based on these results, we propose that the IPyA pathway is transcriptionally regulated through a negative feedback mechanism in response to active auxin levels.
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International Nuclear Information System (INIS)
Taylor, Daisy A.; Thompson, Emma L.; Nair, Sham V.; Raftos, David A.
2013-01-01
Environmental contamination by metals is a serious threat to the biological sustainability of coastal ecosystems. Our current understanding of the potential biological effects of metals in these ecosystems is limited. This study tested the transcriptional expression of immune- and stress-response genes in Sydney Rock oysters (Saccostrea glomerata). Oysters were exposed to four metals (cadmium, copper, lead and zinc) commonly associated with anthropogenic pollution in coastal waterways. Seven target genes (superoxide dismutase, ferritin, ficolin, defensin, HSP70, HSP90 and metallothionein) were selected. Quantitative (real-time) PCR analyses of the transcript expression of these genes showed that each of the different metals elicited unique transcriptional profiles. Significant changes in transcription were found for 18 of the 28 combinations tested (4 metals × 7 genes). Of these, 16 reflected down-regulation of gene transcription. HSP90 was the only gene significantly up-regulated by metal contamination (cadmium and zinc only), while defensin expression was significantly down-regulated by exposure to all four metals. This inhibition could have a significant negative effect on the oyster immune system, promoting susceptibility to opportunistic infections and disease. -- Highlights: ► Oysters were exposed to Cd, Cu, Pb or Zn, all commonly associated with coastal pollution. ► qPCR identified significant down-regulation in stress- and immune-response genes in oysters exposed to these metals. ► qPCR showed that each of the different metals elicited unique transcriptional profiles. ► The genes identified have the potential to lead to increased disease susceptibility in oysters. -- qPCR identified significant down-regulation in stress- and immune-response genes in oysters exposed to metals, which could lead to increased disease susceptibility
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Strain specific transcriptional response in Mycobacterium tuberculosis infected macrophages
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Koo Mi-Sun
2012-01-01
Full Text Available Abstract Background Tuberculosis (TB, a bacterial infection caused by Mycobacterium tuberculosis (Mtb remains a significant health problem worldwide with a third of the world population infected and nearly nine million new cases claiming 1.1 million deaths every year. The outcome following infection by Mtb is determined by a complex and dynamic host-pathogen interaction in which the phenotype of the pathogen and the immune status of the host play a role. However, the molecular mechanism by which Mtb strains induce different responses during intracellular infection of the host macrophage is not fully understood. To explore the early molecular events triggered upon Mtb infection of macrophages, we studied the transcriptional responses of murine bone marrow-derived macrophages (BMM to infection with two clinical Mtb strains, CDC1551 and HN878. These strains have previously been shown to differ in their virulence/immunogenicity in the mouse and rabbit models of pulmonary TB. Results In spite of similar intracellular growth rates, we observed that compared to HN878, infection by CDC1551 of BMM was associated with an increased global transcriptome, up-regulation of a specific early (6 hours immune response network and significantly elevated nitric oxide production. In contrast, at 24 hours post-infection of BMM by HN878, more host genes involved in lipid metabolism, including cholesterol metabolism and prostaglandin synthesis were up-regulated, compared to infection with CDC1551. In association with the differences in the macrophage responses to infection with the 2 Mtb strains, intracellular CDC1551 expressed higher levels of stress response genes than did HN878. Conclusions In association with the early and more robust macrophage activation, intracellular CDC1551 cells were exposed to a higher level of stress leading to increased up-regulation of the bacterial stress response genes. In contrast, sub-optimal activation of macrophages and induction of
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Kim, June-Sik; Mizoi, Junya; Yoshida, Takuya; Fujita, Yasunari; Nakajima, Jun; Ohori, Teppei; Todaka, Daisuke; Nakashima, Kazuo; Hirayama, Takashi; Shinozaki, Kazuo; Yamaguchi-Shinozaki, Kazuko
2011-12-01
In plants, osmotic stress-responsive transcriptional regulation depends mainly on two major classes of cis-acting elements found in the promoter regions of stress-inducible genes: ABA-responsive elements (ABREs) and dehydration-responsive elements (DREs). ABRE has been shown to perceive ABA-mediated osmotic stress signals, whereas DRE is known to be involved in an ABA-independent pathway. Previously, we reported that the transcription factor DRE-BINDING PROTEIN 2A (DREB2A) regulates DRE-mediated transcription of target genes under osmotic stress conditions in Arabidopsis (Arabidopsis thaliana). However, the transcriptional regulation of DREB2A itself remains largely uncharacterized. To elucidate the transcriptional mechanism associated with the DREB2A gene under osmotic stress conditions, we generated a series of truncated and base-substituted variants of the DREB2A promoter and evaluated their transcriptional activities individually. We found that both ABRE and coupling element 3 (CE3)-like sequences located approximately -100 bp from the transcriptional initiation site are necessary for the dehydration-responsive expression of DREB2A. Coupling our transient expression analyses with yeast one-hybrid and chromatin immunoprecipitation (ChIP) assays indicated that the ABRE-BINDING PROTEIN 1 (AREB1), AREB2 and ABRE-BINDING FACTOR 3 (ABF3) bZIP transcription factors can bind to and activate the DREB2A promoter in an ABRE-dependent manner. Exogenous ABA application induced only a modest accumulation of the DREB2A transcript when compared with the osmotic stress treatment. However, the osmotic stress-induced DREB2A expression was found to be markedly impaired in several ABA-deficient and ABA-insensitive mutants. These results suggest that in addition to an ABA-independent pathway, the ABA-dependent pathway plays a positive role in the osmotic stress-responsive expression of DREB2A.
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Vineetha, G.
2015-04-03
Monsoonal estuaries, located along the coastline of the Indian subcontinent, differ from other estuaries by their time dependence on the salinity characteristics. Effective sustenance and retention of the mesozooplankton community in the estuarine habitats is often determined by their dominant behavioral patterns: diel vertical migration (DVM) and tidal vertical migration (TVM). The modes of these endogenous rhythms often vary among estuaries based on the river runoff and tidal characteristics. The present study is a pioneering attempt to depict the vertical migration pattern of zooplankton along a diel and tidal scale in a tropical, microtidal, monsoonal estuary. We observed that in spite of the prominent asymmetry in the magnitude of the river runoff between the seasons, most of the zooplankton groups exhibited strong DVM, with a clear increase in biomass and abundance in surface waters during night. The peak increase in biomass and abundance at night always synchronized with the slack periods in the tidal cycles, which differed from the general concepts of downward migration during ebb tide and upward migration during flood tide in estuarine systems. The weak currents during the slack period might have favored the effective vertical migration of the mesozooplankton community in this monsoonal estuarine system. © 2015 Society of Wetland Scientists
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Qi, Jun; Roush, William R.
2008-01-01
A direct synthesis of the α-hydroxyaldehyde exo-5, a precursor of the exo-spirotetronate subunit o f the quartromicins, was achieved through an exo-selective Lewis acid-catalyzed Diels-Alder reaction of dienophile 12a and diene 1. PMID:16774259
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Valero Francisco
2007-07-01
Full Text Available Abstract Background The analysis of transcriptional levels of the genes involved in protein synthesis and secretion is a key factor to understand the host organism's responses to recombinant protein production, as well as their interaction with the cultivation conditions. Novel techniques such as the sandwich hybridization allow monitoring quantitatively the dynamic changes of specific RNAs. In this study, the transcriptional levels of some genes related to the unfolded protein response (UPR and central metabolism of Pichia pastoris were analysed during batch and fed-batch cultivations using an X-33-derived strain expressing a Rhizopus oryzae lipase under control of the formaldehyde dehydrogenase promoter (FLD1, namely the alcohol oxidase gene AOX1, the formaldehyde dehydrogenase FLD1, the protein disulfide isomerase PDI, the KAR2 gene coding for the BiP chaperone, the 26S rRNA and the R. oryzae lipase gene ROL. Results The transcriptional levels of the selected set of genes were first analysed in P. pastoris cells growing in shake flask cultures containing different carbon and nitrogen sources combinations, glycerol + ammonium, methanol + methylamine and sorbitol + methylamine. The transcriptional levels of the AOX1 and FLD1 genes were coherent with the known regulatory mechanism of C1 substrates in P. pastoris, whereas ROL induction lead to the up-regulation of KAR2 and PDI transcriptional levels, thus suggesting that ROL overexpression triggers the UPR. This was further confirmed in fed-batch cultivations performed at different growth rates. Transcriptional levels of the analysed set of genes were generally higher at higher growth rates. Nevertheless, when ROL was overexpressed in a strain having the UPR constitutively activated, significantly lower relative induction levels of these marker genes were detected. Conclusion The bead-based sandwich hybridization assay has shown its potential as a reliable instrument for quantification of
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Directory of Open Access Journals (Sweden)
Fatma Kaplan
Full Text Available BACKGROUND: In tightly closed human habitats such as space stations, locations near volcano vents and closed culture vessels, atmospheric CO(2 concentration may be 10 to 20 times greater than Earth's current ambient levels. It is known that super-elevated (SE CO(2 (>1,200 µmol mol(-1 induces physiological responses different from that of moderately elevated CO(2 (up to 1,200 µmol mol(-1, but little is known about the molecular responses of plants to supra-optimal [CO(2]. METHODOLOGY/PRINCIPAL FINDINGS: To understand the underlying molecular causes for differential physiological responses, metabolite and transcript profiles were analyzed in aerial tissue of Arabidopsis plants, which were grown under ambient atmospheric CO(2 (400 µmol mol(-1, elevated CO(2 (1,200 µmol mol(-1 and SE CO(2 (4,000 µmol mol(-1, at two developmental stages early and late vegetative stage. Transcript and metabolite profiling revealed very different responses to elevated versus SE [CO(2]. The transcript profiles of SE CO(2 treated plants were closer to that of the control. Development stage had a clear effect on plant molecular response to elevated and SE [CO(2]. Photosynthetic acclimation in terms of down-regulation of photosynthetic gene expression was observed in response to elevated [CO(2], but not that of SE [CO(2] providing the first molecular evidence that there appears to be a fundamental disparity in the way plants respond to elevated and SE [CO(2]. Although starch accumulation was induced by both elevated and SE [CO(2], the increase was less at the late vegetative stage and accompanied by higher soluble sugar content suggesting an increased starch breakdown to meet sink strength resulting from the rapid growth demand. Furthermore, many of the elevated and SE CO(2-responsive genes found in the present study are also regulated by plant hormone and stress. CONCLUSIONS/SIGNIFICANCE: This study provides new insights into plant acclimation to elevated and SE [CO
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International Nuclear Information System (INIS)
Silva, Fernando de C. da; Ferreira, Sabrina B.; Ferreira, Vitor F.; Kaiser, Carlos R.; Pinto, Angelo C.
2009-01-01
Methylene and aryl o-quinone methides (o-QMs) generated by Knoevenagel condensation of 2-hydroxy-1,4-naphthoquinone with formaldehyde and arylaldehydes, undergo facile hetero Diels-Alder reaction with some substituted styrenes (as dienophiles) in aqueous ethanol media providing derivatives of α- and β-lapachone (author)
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Directory of Open Access Journals (Sweden)
Close Timothy J
2009-08-01
Full Text Available Abstract Background Rice and barley are both members of Poaceae (grass family but have a marked difference in salt tolerance. The molecular mechanism underlying this difference was previously unexplored. This study employs a comparative genomics approach to identify analogous and contrasting gene expression patterns between rice and barley. Results A hierarchical clustering approach identified several interesting expression trajectories among rice and barley genotypes. There were no major conserved expression patterns between the two species in response to salt stress. A wheat salt-stress dataset was queried for comparison with rice and barley. Roughly one-third of the salt-stress responses of barley were conserved with wheat while overlap between wheat and rice was minimal. These results demonstrate that, at transcriptome level, rice is strikingly different compared to the more closely related barley and wheat. This apparent lack of analogous transcriptional programs in response to salt stress is further highlighted through close examination of genes associated with root growth and development. Conclusion The analysis provides support for the hypothesis that conservation of transcriptional signatures in response to environmental cues depends on the genetic similarity among the genotypes within a species, and on the phylogenetic distance between the species.
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Directory of Open Access Journals (Sweden)
Erica Bree Rosenblum
Full Text Available Emerging infectious diseases are of great concern for both wildlife and humans. Several highly virulent fungal pathogens have recently been discovered in natural populations, highlighting the need for a better understanding of fungal-vertebrate host-pathogen interactions. Because most fungal pathogens are not fatal in the absence of other predisposing conditions, host-pathogen dynamics for deadly fungal pathogens are of particular interest. The chytrid fungus Batrachochytrium dendrobatidis (hereafter Bd infects hundreds of species of frogs in the wild. It is found worldwide and is a significant contributor to the current global amphibian decline. However, the mechanism by which Bd causes death in amphibians, and the response of the host to Bd infection, remain largely unknown. Here we use whole-genome microarrays to monitor the transcriptional responses to Bd infection in the model frog species, Silurana (Xenopus tropicalis, which is susceptible to chytridiomycosis. To elucidate the immune response to Bd and evaluate the physiological effects of chytridiomycosis, we measured gene expression changes in several tissues (liver, skin, spleen following exposure to Bd. We detected a strong transcriptional response for genes involved in physiological processes that can help explain some clinical symptoms of chytridiomycosis at the organismal level. However, we detected surprisingly little evidence of an immune response to Bd exposure, suggesting that this susceptible species may not be mounting efficient innate and adaptive immune responses against Bd. The weak immune response may be partially explained by the thermal conditions of the experiment, which were optimal for Bd growth. However, many immune genes exhibited decreased expression in Bd-exposed frogs compared to control frogs, suggesting a more complex effect of Bd on the immune system than simple temperature-mediated immune suppression. This study generates important baseline data for ongoing
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Menezes, Regina Andrade; Pimentel, Catarina; Silva, Ana Rita Courelas; Amaral, Catarina; Merhej, Jawad; Devaux, Frédéric; Rodrigues-Pousada, Claudina
2017-04-01
Response to arsenic stress in Saccharomyces cerevisiae is orchestrated by the regulatory protein Yap8, which mediates transcriptional activation of ACR2 and ACR3. This study contributes to the state of art knowledge of the molecular mechanisms underlying yeast stress response to arsenate as it provides the genetic and biochemical evidences that Yap8, through cysteine residues 132, 137, and 274, is the sensor of presence of arsenate in the cytosol. Moreover, it is here reported for the first time the essential role of the Mediator complex in the transcriptional activation of ACR2 by Yap8. Based on our data, we propose an order-of-function map to recapitulate the sequence of events taking place in cells injured with arsenate. Modification of the sulfhydryl state of these cysteines converts Yap8 in its activated form, triggering the recruitment of the Mediator complex to the ACR2/ACR3 promoter, through the interaction with the tail subunit Med2. The Mediator complex then transfers the regulatory signals conveyed by Yap8 to the core transcriptional machinery, which culminates with TBP occupancy, ACR2 upregulation and cell adaptation to arsenate stress. Additional co-factors are required for the transcriptional activation of ACR2 by Yap8, particularly the nucleosome remodeling activity of SWI/SNF and SAGA complexes. Copyright © 2017. Published by Elsevier B.V.
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Salat-Canela, Clàudia; Paulo, Esther; Sánchez-Mir, Laura; Carmona, Mercè; Ayté, José; Oliva, Baldo; Hidalgo, Elena
2017-08-18
Adaptation to stress triggers the most dramatic shift in gene expression in fission yeast ( Schizosaccharomyces pombe ), and this response is driven by signaling via the MAPK Sty1. Upon activation, Sty1 accumulates in the nucleus and stimulates expression of hundreds of genes via the nuclear transcription factor Atf1, including expression of atf1 itself. However, the role of stress-induced, Sty1-mediated Atf1 phosphorylation in transcriptional activation is unclear. To this end, we expressed Atf1 phosphorylation mutants from a constitutive promoter to uncouple Atf1 activity from endogenous, stress-activated Atf1 expression. We found that cells expressing a nonphosphorylatable Atf1 variant are sensitive to oxidative stress because of impaired transcription of a subset of stress genes whose expression is also controlled by another transcription factor, Pap1. Furthermore, cells expressing a phospho-mimicking Atf1 mutant display enhanced stress resistance, and although expression of the Pap1-dependent genes still relied on stress induction, another subset of stress-responsive genes was constitutively expressed in these cells. We also observed that, in cells expressing the phospho-mimicking Atf1 mutant, the presence of Sty1 was completely dispensable, with all stress defects of Sty1-deficient cells being suppressed by expression of the Atf1 mutant. We further demonstrated that Sty1-mediated Atf1 phosphorylation does not stimulate binding of Atf1 to DNA but, rather, establishes a platform of interactions with the basal transcriptional machinery to facilitate transcription initiation. In summary, our results provide evidence that Atf1 phosphorylation by the MAPK Sty1 is required for oxidative stress responses in fission yeast cells by promoting transcription initiation. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.
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Michelle T Juarez
2011-12-01
Full Text Available The epidermis is the largest organ of the body for most animals, and the first line of defense against invading pathogens. A breach in the epidermal cell layer triggers a variety of localized responses that in favorable circumstances result in the repair of the wound. Many cellular and genetic responses must be limited to epidermal cells that are close to wounds, but how this is regulated is still poorly understood. The order and hierarchy of epidermal wound signaling factors are also still obscure. The Drosophila embryonic epidermis provides an excellent system to study genes that regulate wound healing processes. We have developed a variety of fluorescent reporters that provide a visible readout of wound-dependent transcriptional activation near epidermal wound sites. A large screen for mutants that alter the activity of these wound reporters has identified seven new genes required to activate or delimit wound-induced transcriptional responses to a narrow zone of cells surrounding wound sites. Among the genes required to delimit the spread of wound responses are Drosophila Flotillin-2 and Src42A, both of which are transcriptionally activated around wound sites. Flotillin-2 and constitutively active Src42A are also sufficient, when overexpressed at high levels, to inhibit wound-induced transcription in epidermal cells. One gene required to activate epidermal wound reporters encodes Dual oxidase, an enzyme that produces hydrogen peroxide. We also find that four biochemical treatments (a serine protease, a Src kinase inhibitor, methyl-ß-cyclodextrin, and hydrogen peroxide are sufficient to globally activate epidermal wound response genes in Drosophila embryos. We explore the epistatic relationships among the factors that induce or delimit the spread of epidermal wound signals. Our results define new genetic functions that interact to instruct only a limited number of cells around puncture wounds to mount a transcriptional response, mediating
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Noncanonical ATM Activation and Signaling in Response to Transcription-Blocking DNA Damage.
Marteijn, Jurgen A; Vermeulen, Wim; Tresini, Maria
2017-01-01
Environmental genotoxins and metabolic byproducts generate DNA lesions that can cause genomic instability and disrupt tissue homeostasis. To ensure genomic integrity, cells employ mechanisms that convert signals generated by stochastic DNA damage into organized responses, including activation of repair systems, cell cycle checkpoints, and apoptotic mechanisms. DNA damage response (DDR) signaling pathways coordinate these responses and determine cellular fates in part, by transducing signals that modulate RNA metabolism. One of the master DDR coordinators, the Ataxia Telangiectasia Mutated (ATM) kinase, has a fundamental role in mediating DNA damage-induced changes in mRNA synthesis. ATM acts by modulating a variety of RNA metabolic pathways including nascent RNA splicing, a process catalyzed by the spliceosome. Interestingly, ATM and the spliceosome influence each other's activity in a reciprocal manner by a pathway that initiates when transcribing RNA polymerase II (RNAPII) encounters DNA lesions that prohibit forward translocation. In response to stalling of RNAPII assembly of late-stage spliceosomes is disrupted resulting in increased splicing factor mobility. Displacement of spliceosomes from lesion-arrested RNA polymerases facilitates formation of R-loops between the nascent RNA and DNA adjacent to the transcription bubble. R-loops signal for noncanonical ATM activation which in quiescent cells occurs in absence of detectable dsDNA breaks. In turn, activated ATM signals to regulate spliceosome dynamics and AS genome wide.This chapter describes the use of fluorescence microscopy methods that can be used to evaluate noncanonical ATM activation by transcription-blocking DNA damage. First, we present an immunofluorescence-detection method that can be used to evaluate ATM activation by autophosphorylation, in fixed cells. Second, we present a protocol for Fluorescence Recovery After Photobleaching (FRAP) of GFP-tagged splicing factors, a highly sensitive and
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Hoang, Giang T.; Kubo, Tomohiro; Young, Victor G., Jr.; Kautzky, Jacob A.; Wissinger, Jane E.
2015-01-01
Two introductory organic chemistry laboratory experiments are described based on the Diels-Alder reaction of 2,3,4,5-tetraphenylcyclopentadienone, which is synthesized prior to or in a one-pot reaction, with styrene. Students are presented with three possible products, the "endo" and "exo" diastereomers and the decarbonylated…
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Kotha, Sambasivarao; Ravikumar, Ongolu
2015-01-01
Atom efficient processes such as the Diels-Alder reaction (DA) and the ring-rearrangement metathesis (RRM) have been used to design new polycycles. In this regard, ruthenium alkylidene catalysts are effective in realizing the RRM of bis-norbornene derivatives prepared by DA reaction and Grignard addition. Here, fused polycycles are assembled which are difficult to produce by conventional synthetic routes.
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Flores-Conde, Maria Ines; Reyes, Leonor; Herrera, Rafael; Rios, Hulme; Vazquez, Miguel A.; Miranda, Rene; Tamariz, Joaquin; Delgado, Francisco
2012-01-01
Infrared irradiation promoted the Diels-Alder cycloadditions of exo-2-oxazolidinone dienes 1–3 with the Knoevenagel adducts 4–6, as dienophiles, leading to the synthesis of new 3,5-diphenyltetrahydrobenzo[d]oxazol-2-one derivatives (7, 9, 11 and 13–17), under solvent-free conditions. These cycloadditions were performed with good regio- and stereoselectivity, favoring the para-endo cycloadducts. We also evaluated the one-pot three-component reaction of active methylene compounds 20, benzaldehydes 21 and exo-2-oxazolidinone diene 2 under the same reaction conditions. A cascade Knoevenagel condensation/Diels-Alder cycloaddition reaction was observed, resulting in the final adducts 13–16 in similar yields. These procedures are environmentally benign, because no solvent and no catalyst were employed in these processes. The regioselectivity of these reactions was rationalized by Frontier Molecular Orbital (FMO) calculations. PMID:22489113
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Directory of Open Access Journals (Sweden)
Francisco Delgado
2012-02-01
Full Text Available Infrared irradiation promoted the Diels-Alder cycloadditions of exo-2-oxazolidinone dienes 1–3 with the Knoevenagel adducts 4–6, as dienophiles, leading to the synthesis of new 3,5-diphenyltetrahydrobenzo[d]oxazol-2-one derivatives (7, 9, 11 and 13–17, under solvent-free conditions. These cycloadditions were performed with good regio- and stereoselectivity, favoring the para-endo cycloadducts. We also evaluated the one-pot three-component reaction of active methylene compounds 20, benzaldehydes 21 and exo-2-oxazolidinone diene 2 under the same reaction conditions. A cascade Knoevenagel condensation/Diels-Alder cycloaddition reaction was observed, resulting in the final adducts 13–16 in similar yields. These procedures are environmentally benign, because no solvent and no catalyst were employed in these processes. The regioselectivity of these reactions was rationalized by Frontier Molecular Orbital (FMO calculations.
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Research of angelica sinensis (Oliv) diels new strain DGA2000-02 selection
International Nuclear Information System (INIS)
Xie Hongmei; Li Wenjian; Hao Jifang; Liu Jing; Liu Xiaorui; Jing Yanming; Shang Hushan; Liu Rongqing; He Baogang; Wang Chunming; Zhang Guoli; Chen Shuzhen
2008-01-01
Angelica sinensis(Oliv)Diets new strain DGA2000-02 was selected successfully by Institute of Modern Physics, Chinese Academy of Sciences, Dryland Farming Research and Extension Center of Dingxi Prefecture, etc. According to the program of new strain selection, this new strain was selected for several year's after the dry seeds of Gansu Angelica sinensis(Oliv)Diels 90-01 was irradiated by ions of 55 MeV/u 40 Ar +15 . During the period of year 2005-2007, region experiments of Angelica sinensis (Oliv)Diels new strain DGA2000-02 were developed in Minxian, Weiyuan, Zhangxian and Longxi etc. Average yield of the fresh DGA2000-02 Angelica was 10 621.5 kg/hm 2 , and 15.0% production was increased more than control (for 1 386.0 kg/hm 2 of 90-01). The growth stage of the DGA2000-02 was 790 d, and it has deep purple stem and yellow-white root. The quality analysis results are as follows: total ash content is 4.2% and acidast ash content is 0.4%, 16% and 33.3% better than control, respectively; the lixivium is 61.4%, i.e., 4.4% more than the standard of Pharmacopoeia of People's Republic of China (2005 edition); the ferullc acid content is 0.148%, i.e., 2.96 times ligher than the standard. All these results showed that the quality of the DGA2000-02 was better significantly than both control and the standard. It can be grown appropriately at the high, cold and dankness regions at the altitude of 2000-2600 m and with a annual precipitation of 500-600 mm. (authors)
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International Nuclear Information System (INIS)
Clark, Catherine D.; De Bruyn, Warren J.; Hirsch, Charlotte M.; Aiona, Paige
2010-01-01
Hydrogen peroxide is photochemically produced in natural waters. It has been implicated in the oxidative-induced mortality of fecal indicator bacteria (FIB), a microbial water quality measure. To assess levels and cycling of peroxide in beach waters monitored for FIB, diel studies were carried out in surf zone waters in July 2009 at Crystal Cove State Beach, Southern California, USA. Maximum concentrations of 160-200 nM were obtained within 1 h of solar noon. Levels dropped at night to 20-40 nM, consistent with photochemical production from sunlight. Day-time production and night-time dark loss rates averaged 16 ± 3 nM h -1 and 12 ± 4 nM h -1 respectively. Apparent quantum yields averaged 0.07 ± 0.02. Production was largely dominated by sunlight, with some dependence on chromophoric dissolved organic matter (CDOM) levels in waters with high absorption coefficients. Peroxide levels measured here are sufficient to cause oxidative-stress-induced mortality of bacteria, affect FIB diel cycling and impact microbial water quality in marine bathing waters.
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Fan, Ming; Ma, Ye; Zhang, Ziwei; Mao, Jiahui; Tan, Huaping; Hu, Xiaohong
2015-11-01
A robust synthetic strategy of biopolymer-based hydrogels has been developed where hyaluronic acid derivatives reacted through aqueous Diels-Alder chemistry without the involvement of chemical catalysts, allowing for control and sustain release of dexamethasone. To conjugate the hydrogel, furan and maleimide functionalized hyaluronic acid were synthesized, respectively, as well as furan functionalized dexamethasone, for the covalent immobilization. Chemical structure, gelation time, morphologies, swelling kinetics, weight loss, compressive modulus and dexamethasone release of the hydrogel system in PBS at 37°C were studied. The results demonstrated that the aqueous Diels-Alder chemistry provides an extremely selective reaction and proceeds with high efficiency for hydrogel conjugation and covalent immobilization of dexamethasone. Cell culture results showed that the dexamethasone immobilized hydrogel was noncytotoxic and preserved proliferation of entrapped human adipose-derived stem cells. This synthetic approach uniquely allows for the direct fabrication of biologically functionalized gel scaffolds with ideal structures for adipose tissue engineering, which provides a competitive alternative to conventional conjugation techniques such as copper mediated click chemistry. Copyright © 2015. Published by Elsevier B.V.
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Batista, Marcelo Bueno; Chandra, Govind; Monteiro, Rose Adele; de Souza, Emanuel Maltempi; Dixon, Ray
2018-05-04
Bacteria adjust the composition of their electron transport chain (ETC) to efficiently adapt to oxygen gradients. This involves differential expression of various ETC components to optimize energy generation. In Herbaspirillum seropedicae, reprogramming of gene expression in response to oxygen availability is controlled at the transcriptional level by three Fnr orthologs. Here, we characterised Fnr regulons using a combination of RNA-Seq and ChIP-Seq analysis. We found that Fnr1 and Fnr3 directly regulate discrete groups of promoters (Groups I and II, respectively), and that a third group (Group III) is co-regulated by both transcription factors. Comparison of DNA binding motifs between the three promoter groups suggests Group III promoters are potentially co-activated by Fnr3-Fnr1 heterodimers. Specific interaction between Fnr1 and Fnr3, detected in two-hybrid assays, was dependent on conserved residues in their dimerization interfaces, indicative of heterodimer formation in vivo. The requirements for co-activation of the fnr1 promoter, belonging to Group III, suggest either sequential activation by Fnr3 and Fnr1 homodimers or the involvement of Fnr3-Fnr1 heterodimers. Analysis of Fnr proteins with swapped activation domains provides evidence that co-activation by Fnr1 and Fnr3 at Group III promoters optimises interactions with RNA polymerase to fine-tune transcription in response to prevailing oxygen concentrations.
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C2-symmetric bisamidines: Chiral Brønsted bases catalysing the Diels-Alder reaction of anthrones
Directory of Open Access Journals (Sweden)
2008-08-01
Full Text Available C2-symmetric bisamidines 8 have been tested as chiral Brønsted bases in the Diels-Alder reaction of anthrones and N-substituted maleimides. High yields of cycloadducts and significant asymmetric inductions up to 76% ee are accessible. The proposed mechanism involves proton transfer between anthrone and bisamidine, association of the resulting ions and finally a cycloaddition step stereoselectively controlled by the chiral ion pair.
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A 11-Steps Total Synthesis of Magellanine through a Gold(I)-Catalyzed Dehydro Diels-Alder Reaction.
McGee, Philippe; Bétournay, Geneviève; Barabé, Francis; Barriault, Louis
2017-05-22
We have developed an innovative strategy for the formation of angular carbocycles via a gold(I)-catalyzed dehydro Diels-Alder reaction. This transformation provides rapid access to a variety of complex angular cores in excellent diastereoselectivities and high yields. The usefulness of this Au I -catalyzed cycloaddition was further demonstrated by accomplishing a 11-steps total synthesis of (±)-magellanine. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Directory of Open Access Journals (Sweden)
Head Steven R
2011-06-01
Full Text Available Abstract Background Cyanobacteria are potential sources of renewable chemicals and biofuels and serve as model organisms for bacterial photosynthesis, nitrogen fixation, and responses to environmental changes. Anabaena (Nostoc sp. strain PCC 7120 (hereafter Anabaena is a multicellular filamentous cyanobacterium that can "fix" atmospheric nitrogen into ammonia when grown in the absence of a source of combined nitrogen. Because the nitrogenase enzyme is oxygen sensitive, Anabaena forms specialized cells called heterocysts that create a microoxic environment for nitrogen fixation. We have employed directional RNA-seq to map the Anabaena transcriptome during vegetative cell growth and in response to combined-nitrogen deprivation, which induces filaments to undergo heterocyst development. Our data provide an unprecedented view of transcriptional changes in Anabaena filaments during the induction of heterocyst development and transition to diazotrophic growth. Results Using the Illumina short read platform and a directional RNA-seq protocol, we obtained deep sequencing data for RNA extracted from filaments at 0, 6, 12, and 21 hours after the removal of combined nitrogen. The RNA-seq data provided information on transcript abundance and boundaries for the entire transcriptome. From these data, we detected novel antisense transcripts within the UTRs (untranslated regions and coding regions of key genes involved in heterocyst development, suggesting that antisense RNAs may be important regulators of the nitrogen response. In addition, many 5' UTRs were longer than anticipated, sometimes extending into upstream open reading frames (ORFs, and operons often showed complex structure and regulation. Finally, many genes that had not been previously identified as being involved in heterocyst development showed regulation, providing new candidates for future studies in this model organism. Conclusions Directional RNA-seq data were obtained that provide
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Deeper Insight into the Diels-Alder Reaction through the Activation Strain Model.
Fernández, Israel; Bickelhaupt, F Matthias
2016-12-06
In this Focus Review, we present the application of the so-called Activation Strain Model of chemical reactivity to the Diels-Alder cycloaddition reaction. To this end, representative recent examples have been selected to illustrate the power of this new computational approach to gain a deeper quantitative understanding of this fundamental process in chemistry. We cover a wide range of issues, such as, the "endo-rule", reactivity trends emerging from systematic variation in the reactants' strain, and cycloaddition reactions involving relevant species in material science, that is, fullerenes, polycyclic aromatic hydrocarbons and nanotubes. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Velásquez, Sonia Y; Opelz, Gerhard; Rojas, Mauricio; Süsal, Caner; Alvarez, Cristiam M
2016-05-01
High serum sCD30 levels are associated with inflammatory disorders and poor outcome in renal transplantation. The contribution to these phenomena of transcripts and proteins related to CD30-activation and -cleavage is unknown. We assessed in peripheral blood of end-stage renal disease patients (ESRDP) transcripts of CD30-activation proteins CD30 and CD30L, CD30-cleavage proteins ADAM10 and ADAM17, and Th1- and Th2-type immunity-related factors t-bet and GATA3. Additionally, we evaluated the same transcripts and release of sCD30 and 32 cytokines after allogeneic and polyclonal T-cell activation. In peripheral blood, ESRDP showed increased levels of t-bet and GATA3 transcripts compared to healthy controls (HC) (both PCD30, CD30L, ADAM10 and ADAM17 transcripts were similar. Polyclonal and allogeneic stimulation induced higher levels of CD30 transcripts in ESRDP than in HC (both PsCD30, the Th-1 cytokine IFN-γ, MIP-1α, RANTES, sIL-2Rα, MIP-1β, TNF-β, MDC, GM-CSF and IL-5, and another one consisting of CD30 and t-bet transcripts, IL-13 and proinflammatory proteins IP-10, IL-8, IL-1Rα and MCP-1. Reflecting an activated immune state, ESRDP exhibited after allostimulation upregulation of CD30 transcripts in T cells, which was associated with Th1 and proinflammatory responses. Copyright © 2016 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved.
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Sexton, Thomas; Kraka, Elfi; Cremer, Dieter
2016-02-25
The Diels-Alder reaction between 1,3-butadiene and ethene is investigated from far-out in the entrance channel to the very last step in the exit channel thus passing two bifurcation points and extending the range of the reaction valley studied with URVA (Unified Reaction Valley Approach) by 300% compared to previous studies. For the first time, the pre- and postchemical steps of the reaction are analyzed at the same level of theory as the actual chemical processes utilizing the path curvature and its decomposition into internal coordinate or curvilinear coordinate components. A first smaller charge transfer to the dienophile facilitates the rotation of gauche butadiene into its cis form. The actual chemical processes are initiated by a second larger charge transfer to the dienophile that facilitates pyramidalization of the reacting carbon centers, bond equalization, and biradicaloid formation of the reactants. The transition state is aromatically stabilized and moved by five path units into the entrance channel in line with the Hammond-Leffler postulate. The pseudorotation of the boat form into the halfchair of cyclohexene is analyzed. Predictions are made for the Diels-Alder reaction based on a 11-phase mechanism obtained by the URVA analysis.
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Yan, Chao-Xian; Yang, Fan; Yang, Xing; Zhou, Da-Gang; Zhou, Pan-Pan
2017-03-17
The Diels-Alder reaction between 3-vinylindoles and methyleneindolinone can proceed both under catalyst-free conditions and with bisthiourea as the catalyst. The reaction with bisthiourea is much faster and results in higher stereoselectivity of the product. The reaction mechanism, origin of stereoselectivity, and role of the catalyst were elaborated based on quantum mechanical calculations and theoretical methods of reactivity indices, NCI, QTAIM, and distortion/interaction models. In the uncatalyzed reaction, the two C-C bonds that are formed undergo conversion from noncovalent to covalent bonding via a concerted asynchronous mechanism. The weak intermolecular interactions formed in the transition state play important roles. The difference between the interaction and distortion energies is responsible for the stereoselectivity. In the catalyzed reaction, bisthiourea induces both the diene and dienophile to approach it via weak intermolecular interactions, which greatly lowers the energy barrier of the reaction and leads to the product with excellent stereoselectivity. The possible pathways of this reaction were explored, which suggested that the formation of the two C-C bonds goes through either a stepwise or concerted asynchronous mechanism. These results detail the reaction mechanism and shed light on both the significant role of the bisthiourea catalyst and the origin of stereoselectivity for this type of Diels-Alder reaction and related ones.
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Mono- and polyadducts of C60 with anthracenes by Diels-Alder-reactions
International Nuclear Information System (INIS)
Duarte-Ruiz, A.
2000-09-01
This work describes the synthesis and characterization of seven new mono-adducts of 9-methylanthracene, 9,10-dimethylanthracene, 9-bromoanthracene. 2,3,6,7-tetramethylanthracene, 1-methylanthracene, 2,6-di-tert-butylanthracen, as well as 2-methylanthracene to fullerene C60 in solution at r.t. by means of [4+2] Diels-Alder reactions. It could be shown that the mono-adducts with 9-methylanthracene, 9,10-dimethylanthracene, and 1-methylanthracene form the corresponding antipodal bis-adduct 'trans-1' on heating the solid to 180 o C. Furthermore the functionalization of fullerene C60 anthracene mono-adduct (C60C14H10) with anthracene through [4+2] Diels-Alder reactions was investigated which made it possible to separate and to characterize the five possible bis-adducts ('trans-1', 'trans-2', 'trans-3', 'trans-4', and 'e') that can form when the second anthracene adds either 'trans' to the opposite hemisphere (compared to the first addition of anthracene) or to an equatorial position. An exact identification of the bis-adducts 'trans-2' and 'trans-4' could only be acquired with spectroscopic methods, fortunately the bis-adducts 'trans-4', 'trans-3', and 'e' could also be examined by x-ray, thus all five could be fully characterized. No bis-adducts on the same hemisphere ('cis') were found. UV/VIS-spectra of the bis-adducts opened up the possibility to identify other [4+2] Diels-Alder products in the future. It has been noticed that the eluation sequence of the bis-adducts ('trans-1' before 'trans-2' before 'trans-4' before 'trans-3' before 'e') doesn't strictly correlate with the dipole moments. Furthermore six new tris-adducts ('t4t4t2', 't3t3t3', 't3t3t4', 'et3t2', 'et3t4', and 'eee') and one tetra-adduct ('eeet3') were separated and characterized. The tris-adduct 't3t3t3' was additionally characterized by x-ray which showed that the crystal contains only one enatiomer. All bis- and tris-adducts form the antipodal bis-adduct 'trans-1' on heating to 180 o C for 10 min
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Transcriptional Response of Human Cells to Microbeam Irradiation with 2.1 MeV Alpha Particles
Hellweg, C. E.; Bogner, S.; Spitta, L.; Arenz, A.; Baumstark-Khan, C.; Greif, K. D.; Giesen, U.
Within the next decades an increasing number of human beings in space will be simultaneously exposed to different stimuli especially microgravity and radiation To assess the risks for humans during long-duration space missions the complex interplay of these parameters at the cellular level must be understood Cellular stress protection responses lead to increased transcription of several genes via modulation of transcription factors Activation of the Nuclear Factor kappa B NF- kappa B pathway as a possible anti-apoptotic route represents such an important cellular stress response A screening assay for detection of NF- kappa B-dependent gene activation using the destabilized variant of Enhanced Green Fluorescent Protein d2EGFP as reporter protein had been developed It consists of Human Embryonic Kidney HEK 293 Cells stably transfected with a receptor-reporter-construct carrying d2EGFP under the control of a NF- kappa B response element Clones positive for Tumor Necrosis Factor alpha TNF- alpha inducible d2EGFP expression were selected as cellular reporters Irradiation was performed either with X-rays 150 kV 19 mA at DLR Cologne or with 2 1 MeV alpha particles LET sim 160 keV mu m at PTB Braunschweig After irradiation the following biological endpoints were determined i cell survival via the colony forming ability test ii time-dependent activation of NF- kappa B dependent d2EGFP gene expression using flow cytometry iii quantitative RT-PCR
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Saavedra, Diana I; Rencher, Benjamin D; Kwon, Doo-Hyun; Smith, Stacey J; Ess, Daniel H; Andrus, Merritt B
2018-02-16
Deoxypodophyllotoxin is a secondary metabolite lignan possessing potent anticancer activity with potential as a precursor for known anticancer drugs, but its use is limited by scarcity from natural sources. We here report the total synthesis of racemic deoxypodophyllotoxin in seven steps using an intramolecular styryl Diels-Alder reaction strategy uniquely suited to assemble the deoxypodophyllotoxin core. Density functional theory was used to analyze concerted, polar, and singlet-open-shell diradical reaction pathways, which identified a low-energy concerted [4 + 2] Diels-Alder pathway followed by a faster di-t-butylhydroxytoluene assisted [1,3]-formal hydrogen shift.
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Rickettsia conorii transcriptional response within inoculation eschar.
Directory of Open Access Journals (Sweden)
Patricia Renesto
Full Text Available BACKGROUND: Rickettsia conorii, the causative agent of the Mediterranean spotted fever, is transmitted to humans by the bite of infected ticks Rhipicephalus sanguineus. The skin thus constitutes an important barrier for the entry and propagation of R. conorii. Given this, analysis of the survival strategies used by the bacterium within infected skin is critical for our understanding of rickettsiosis. METHODOLOGY/PRINCIPAL FINDINGS: Here, we report the first genome-wide analysis of R. conorii gene expression from infected human skin biopsies. Our data showed that R. conorii exhibited a striking transcript signature that is remarkably conserved across patients, regardless of genotype. The expression profiles obtained using custom Agilent microarrays were validated by quantitative RT-PCR. Within eschars, the amount of detected R. conorii transcripts was of 55%, this value being of 74% for bacteria grown in Vero cells. In such infected host tissues, approximately 15% (n = 211 of the total predicted R. conorii ORFs appeared differentially expressed compared to bacteria grown in standard laboratory conditions. These genes are mostly down-regulated and encode proteins essential for bacterial replication. Some of the strategies displayed by rickettsiae to overcome the host defense barriers, thus avoiding killing, were also pointed out. The observed up-regulation of rickettsial genes associated with DNA repair is likely to correspond to a DNA-damaging agent enriched environment generated by the host cells to eradicate the pathogens. Survival of R. conorii within eschars also involves adaptation to osmotic stress, changes in cell surface proteins and up-regulation of some virulence factors. Interestingly, in contrast to down-regulated transcripts, we noticed that up-regulated ones rather exhibit a small nucleotide size, most of them being exclusive for the spotted fever group rickettsiae. CONCLUSION/SIGNIFICANCE: Because eschar is a site for rickettsial
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Directory of Open Access Journals (Sweden)
O. V. Blazhenko
2014-02-01
Full Text Available In a previous study we cloned GSH2 gene, encoding γ-glutamylcysteine synthetase (γGCS in the yeast Hansenula рolymorpha. In this study an analysis of molecular organisation of the H. рolymorpha GSH2 gene promoter was conducted and the potential binding sites of Yap1, Skn7, Creb/Atf1, and Cbf1 transcription factors were detected. It was established that full regulation of GSH2 gene expression in the response to cadmium and oxidative stress requires the length of GSH2 promoter to be longer than 450 bp from the start of translation initiation. To study the transcriptional regulation of H. polymorpha GSH2 gene recombinant strain, harbouring a reporter system, in which 1.832 kb regulatory region of GSH2 gene was fused to structural and terminatory regions of alcohol oxidase gene, was constructed. It was shown that maximum increase in H. polymorpha GSH2 gene transcription by 33% occurs in the rich medium under four-hour incubation with 1 μM concentration of cadmium ions. In the minimal medium the GSH2 gene expression does not correlate with the increased total cellular glutathione levels under cadmium ion treatment. We assume that the increased content of total cellular glutathione under cadmium stress in the yeast H. polymorpha probably is not controlled on the level of GSH2 gene transcription.
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Vegetation induced diel signal and its meaning in recharge and discharge regions
Gribovszki, Zoltán; Tóth, Tibor; Csáfordi, Péter; Szabó, András; Móricz, Norbert; Kalicz, Péter
2017-04-01
Afforestation, promoted by the European Union is planned in Hungary in the next decades. One of the most important region for afforestation is the Hungarian Great Plain where the precipitation is far below potential ET so forests can not survive without significant water uptake from shallow groundwater. Diel fluctuations of hydrological variables (e.g., soil moisture, shallow groundwater level, streamflow rate) are rarely investigated in the hydrologic literature although these short-term fluctuations may incorporate useful information (like groundwater uptake) about hydro-ecological systems in shallow groundwater areas. Vegetation induced diel fluctuations are rarely compared under varying hydrologic conditions (such as recharge and discharge zones). In this study, the data of soil moisture and shallow groundwater monitoring under different surface covers (forest and neighboring agricultural plots) in discharge and recharge regions were analyzed to gain a better understanding of the vegetation hydrological impact or water uptake in changing climate. The pilot areas of the study are located in Hungarian Great Plain and in Western Hungary. The water table under the forest displayed a typical night-time recovery in the discharge region, indicating a significant groundwater supply. Certainly, the root system of the forest was able to tap the groundwater in depths measuring a few metres, while the shallower roots of the herbaceous vegetation generally did not reach the groundwater reservoir at these depths. In the recharge zone the water table under the forest showed step-like diel pattern that refer to a lack of additional groundwater supply from below. The low groundwater evapotranspiration of the forest in the recharge zone was due to the lack of the groundwater supply in the recharge area. Similar patterns can be detected in the soil moisture of recharge and discharge zones as well. Our results suggest that local estimations of groundwater evapotranspiration from
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Hayashi, Yujiro; Bondzic, Bojan P; Yamazaki, Tatsuya; Gupta, Yogesh; Ogasawara, Shin; Taniguchi, Tohru; Monde, Kenji
2016-10-24
The asymmetric Diels-Alder reaction of α-substituted acrolein proceeds in the presence of the trifluoroacetic acid salt of trifluoromethyl-substituted diarylprolinol silyl ether to afford the exo-isomer with both excellent diastereoselectivity and high enantioselectivity. In the Diels-Alder reaction of a β,β-disubstituted α,β-unsaturated aldehyde, good exo-selectivity and excellent enantioselectivity was obtained when the perchloric acid salt of the bulky triisopropyl silyl ether of trifluoromethyl substituted diarylprolinol was employed as an organocatalyst in the presence of water. In both cases, all-carbon quaternary stereocenters are constructed enantioselectively. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Radiation activation of transcription factors in mammalian cells
International Nuclear Information System (INIS)
Kraemer, M.; Stein, B.; Mai, S.; Kunz, E.; Koenig, H.; Ponta, H.; Herrlich, P.; Rahmsdorf, H.J.; Loferer, H.; Grunicke, H.H.
1990-01-01
In mammalian cells radiation induces the enhanced transcription of several genes. The cis acting elements in the control region of inducible genes have been delimited by site directed mutagenesis. Several different elements have been found in different genes. They do not only activate gene transcription in response to radiation but also in response to growth factors and to tumor promoter phorbol esters. The transcription factors binding to these elements are present also in non-irradiated cells, but their DNA binding activity and their transactivating capability is increased upon irradiation. The signal chain linking the primary radiation induced signal (damaged DNA) to the activation of transcription factors involves the action of (a) protein kinase(s). (orig.)
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The Transcriptional Response of Diverse Saccharomyces cerevisiae Strains to Simulated Microgravity
Neff, Lily S.; Fleury, Samantha T.; Galazka, Jonathan M.
2018-01-01
Spaceflight imposes multiple stresses on biological systems resulting in genome-scale adaptations. Understanding these adaptations and their underlying molecular mechanisms is important to clarifying and reducing the risks associated with spaceflight. One such risk is infection by microbes present in spacecraft and their associated systems and inhabitants. This risk is compounded by results suggesting that some microbes may exhibit increased virulence after exposure to spaceflight conditions. The yeast, S. cerevisiae, is a powerful microbial model system, and its response to spaceflight has been studied for decades. However, to date, these studies have utilized common lab strains. Yet studies on trait variation in S. cerevisiae demonstrate that these lab strains are not representative of wild yeast and instead respond to environmental stimuli in an atypical manner. Thus, it is not clear how transferable these results are to the wild S. cerevisiae strains likely to be encountered during spaceflight. To determine if diverse S. cerevisiae strains exhibit a conserved response to simulated microgravity, we will utilize a collection of 100 S. cerevisiae strains isolated from clinical, environmental and industrial settings. We will place selected S. cerevisiae strains in simulated microgravity using a high-aspect rotating vessel (HARV) and document their transcriptional response by RNA-sequencing and quantify similarities and differences between strains. Our research will have a strong impact on the understanding of how genetic diversity of microorganisms effects their response to spaceflight, and will serve as a platform for further studies.
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Jayakumar, Samydurai; Louven, Kathrin; Strohmann, Carsten; Kumar, Kamal
2017-12-11
The active complexes of chiral N,N'-dioxide ligands with dysprosium and magnesium salts catalyze the hetero-Diels-Alder reaction between 2-aza-3-silyloxy-butadienes and alkylidene oxindoles to selectively form 3,3'- and 3,4'-piperidinoyl spirooxindoles, respectively, in very high yields and with excellent enantioselectivities. The exo-selective asymmetric cycloaddition successfully regaled the construction of sp 3 -rich and highly substituted natural-product-based spirooxindoles supporting many chiral centers, including contiguous all-carbon quaternary centers. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Directory of Open Access Journals (Sweden)
Özgür Yılmaz
2017-10-01
Full Text Available The reaction between 1,3-cyclohexadiene and dimethyl 7-oxabicyclo[2.2.1]hepta-2,5-diene-2,3-dicarboxylate both without a catalyst and with different catalysts, in both atmospheric and at high pressure, over 20 days were studied. At the end of the reactions, different products (retro Diels-Alder addition product 5 and Diels-Alder addition product 6 were obtained in different yields. When we look at the percentage of the addition product, it is observed that the yield of reaction at high pressure in water is the highest. All structures of these products were characterized by 1H-NMR, 13C-NMR, MS, and IR spectroscopy.
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Sizemore, Nicholas; Rychnovsky, Scott D
2014-02-07
A synthetic route to the isotwistane core of palhinine lycopodium alkaloids is described. A Morita-Baylis-Hillman/intramolecular Diels-Alder (IMDA) strategy sets the vicinal all-carbon quaternary centers present in this family of natural products. The regioselectivity of the IMDA reaction is dictated by the conditions employed for silyl enol ether formation, with one set of conditions providing the core of cardionine and alternate conditions generating the desired isotwistane core of isopalhinine.
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Dynamic cyanobacterial response to hydration and dehydration in a desert biological soil crust.
Rajeev, Lara; da Rocha, Ulisses Nunes; Klitgord, Niels; Luning, Eric G; Fortney, Julian; Axen, Seth D; Shih, Patrick M; Bouskill, Nicholas J; Bowen, Benjamin P; Kerfeld, Cheryl A; Garcia-Pichel, Ferran; Brodie, Eoin L; Northen, Trent R; Mukhopadhyay, Aindrila
2013-11-01
Biological soil crusts (BSCs) cover extensive portions of the earth's deserts. In order to survive desiccation cycles and utilize short periods of activity during infrequent precipitation, crust microorganisms must rely on the unique capabilities of vegetative cells to enter a dormant state and be poised for rapid resuscitation upon wetting. To elucidate the key events involved in the exit from dormancy, we performed a wetting experiment of a BSC and followed the response of the dominant cyanobacterium, Microcoleus vaginatus, in situ using a whole-genome transcriptional time course that included two diel cycles. Immediate, but transient, induction of DNA repair and regulatory genes signaled the hydration event. Recovery of photosynthesis occurred within 1 h, accompanied by upregulation of anabolic pathways. Onset of desiccation was characterized by the induction of genes for oxidative and photo-oxidative stress responses, osmotic stress response and the synthesis of C and N storage polymers. Early expression of genes for the production of exopolysaccharides, additional storage molecules and genes for membrane unsaturation occurred before drying and hints at preparedness for desiccation. We also observed signatures of preparation for future precipitation, notably the expression of genes for anaplerotic reactions in drying crusts, and the stable maintenance of mRNA through dormancy. These data shed light on possible synchronization between this cyanobacterium and its environment, and provides key mechanistic insights into its metabolism in situ that may be used to predict its response to climate, and or, land-use driven perturbations.
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Snijders, Antoine M; Marchetti, Francesco; Bhatnagar, Sandhya; Duru, Nadire; Han, Ju; Hu, Zhi; Mao, Jian-Hua; Gray, Joe W; Wyrobek, Andrew J
2012-01-01
High dose ionizing radiation (IR) is a well-known risk factor for breast cancer but the health effects after low-dose (LD, differences in their sensitivity to radiation-induced mammary cancer (BALB/c and C57BL/6) for the purpose of identifying mechanisms of mammary cancer susceptibility. Unirradiated mammary and blood tissues of these strains differed significantly in baseline expressions of DNA repair, tumor suppressor, and stress response genes. LD exposures of 7.5 cGy (weekly for 4 weeks) did not induce detectable genomic instability in either strain. However, the mammary glands of the sensitive strain but not the resistant strain showed early transcriptional responses involving: (a) diminished immune response, (b) increased cellular stress, (c) altered TGFβ-signaling, and (d) inappropriate expression of developmental genes. One month after LD exposure, the two strains showed opposing responses in transcriptional signatures linked to proliferation, senescence, and microenvironment functions. We also discovered a pre-exposure expression signature in both blood and mammary tissues that is predictive for poor survival among human cancer patients (p = 0.0001), and a post-LD-exposure signature also predictive for poor patient survival (pidentify genetic features that predispose or protect individuals from LD-induced breast cancer.
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Takii, Ryosuke; Fujimoto, Mitsuaki; Tan, Ke; Takaki, Eiichi; Hayashida, Naoki; Nakato, Ryuichiro; Shirahige, Katsuhiko
2014-01-01
The heat shock response is an evolutionally conserved adaptive response to high temperatures that controls proteostasis capacity and is regulated mainly by an ancient heat shock factor (HSF). However, the regulation of target genes by the stress-inducible HSF1 transcription complex has not yet been examined in detail in mammalian cells. In the present study, we demonstrated that HSF1 interacted with members of the ATF1/CREB family involved in metabolic homeostasis and recruited them on the HSP70 promoter in response to heat shock. The HSF1 transcription complex, including the chromatin-remodeling factor BRG1 and lysine acetyltransferases p300 and CREB-binding protein (CBP), was formed in a manner that was dependent on the phosphorylation of ATF1. ATF1-BRG1 promoted the establishment of an active chromatin state and HSP70 expression during heat shock, whereas ATF1-p300/CBP accelerated the shutdown of HSF1 DNA-binding activity during recovery from acute stress, possibly through the acetylation of HSF1. Furthermore, ATF1 markedly affected the resistance to heat shock. These results revealed the unanticipated complexity of the primitive heat shock response mechanism, which is connected to metabolic adaptation. PMID:25312646
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Gibberellic acid and cGMP-dependent transcriptional regulation in arabidopsis thaliana
Bastian, René
2010-03-01
An ever increasing amount of transcriptomic data and analysis tools provide novel insight into complex responses of biological systems. Given these resources we have undertaken to review aspects of transcriptional regulation in response to the plant hormone gibberellic acid (GA) and its second messenger guanosine 3\\',5\\'-cyclic monophosphate (cGMP) in Arabidopsis thaliana, both wild type and selected mutants. Evidence suggests enrichment of GA-responsive (GARE) elements in promoters of genes that are transcriptionally upregulated in response to cGMP but downregulated in a GA insensitive mutant (ga1-3). In contrast, in the genes upregulated in the mutant, no enrichment in the GARE is observed suggesting that GARE motifs are diagnostic for GA-induced and cGMP-dependent transcriptional upregulation. Further, we review how expression studies of GA-dependent transcription factors and transcriptional networks based on common promoter signatures derived from ab initio analyses can contribute to our understanding of plant responses at the systems level. © 2010 Landes Bioscience.
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Sultan, Mujeeb A; Karama, Usama; Almansour, Abdulrahman I; Soliman, Saied M
2016-09-23
A theoretical study of the regioselectivity of the Diels-Alder reaction between 1,8-dichloroanthracene and acrolein is performed using DFT at the B3LYP/6-31G(d,p) level of theory. The FMO analysis, global and local reactivity indices confirmed the reported experimental results. Potential energy surface analysis showed that the cycloadditions (CAs) favor the formation of the anti product. These results are in good agreement with the reported results obtained experimentally where the anti is the major product.
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Ruchko, Mykhaylo V; Gorodnya, Olena M; Pastukh, Viktor M; Swiger, Brad M; Middleton, Natavia S; Wilson, Glenn L; Gillespie, Mark N
2009-02-01
Reactive oxygen species (ROS) generated in hypoxic pulmonary artery endothelial cells cause transient oxidative base modifications in the hypoxia-response element (HRE) of the VEGF gene that bear a conspicuous relationship to induction of VEGF mRNA expression (K.A. Ziel et al., FASEB J. 19, 387-394, 2005). If such base modifications are indeed linked to transcriptional regulation, then they should be detected in HRE sequences associated with transcriptionally active nucleosomes. Southern blot analysis of the VEGF HRE associated with nucleosome fractions prepared by micrococcal nuclease digestion indicated that hypoxia redistributed some HRE sequences from multinucleosomes to transcriptionally active mono- and dinucleosome fractions. A simple PCR method revealed that VEGF HRE sequences harboring oxidative base modifications were found exclusively in mononucleosomes. Inhibition of hypoxia-induced ROS generation with myxathiozol prevented formation of oxidative base modifications but not the redistribution of HRE sequences into mono- and dinucleosome fractions. The histone deacetylase inhibitor trichostatin A caused retention of HRE sequences in compacted nucleosome fractions and prevented formation of oxidative base modifications. These findings suggest that the hypoxia-induced oxidant stress directed at the VEGF HRE requires the sequence to be repositioned into mononucleosomes and support the prospect that oxidative modifications in this sequence are an important step in transcriptional activation.
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New 30-Noroleanane Triterpenoid Saponins from Holboellia coriacea Diels
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Wenbing Ding
2016-06-01
Full Text Available Three new 30-noroleanane triterpenoid saponins, akebonoic acid 28-O-β-d-glucopyranosyl-(1′′→6′-β-d-glucopyranosyl ester (1, akebonoic acid 28-O-(6′′-O-caffeoyl-β-d-glucopyranosyl-(1′′→6′-β-d-glucopyranosyl ester (Holboelliside A, 2 and 3β,20α,24-trihydroxy-29-norolean-12-en-28-oic acid 3-O-(6′-O-caffeoyl-β-d-glucopyranoside (Holboelliside B, 3 were isolated from the stems of Holboellia coriacea Diels, together with five known compounds, eupteleasaponin VIII (4, 3α-akebonoic acid (5, quinatic acid (6, 3β-hydroxy-30-norhederagenin (7 and quinatoside A (8. The structures of these compounds were determined on the basis of spectral and chemical evidence. Compounds 1–5 were evaluated for their inhibitory activity against three human tumors HepG2, HCT116 and SGC-7901 cell lines in vitro.
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MCGRANN, GRAHAM R D; STEED, ANDREW; BURT, CHRISTOPHER; GODDARD, RACHEL; LACHAUX, CLEA; BANSAL, ANURADHA; CORBITT, MARGARET; GORNIAK, KALINA; NICHOLSON, PAUL; BROWN, JAMES K M
2014-01-01
NAC proteins are plant transcription factors that are involved in tolerance to abiotic and biotic stresses, as well as in many developmental processes. Stress-responsive NAC1 (SNAC1) transcription factor is involved in drought tolerance in barley and rice, but has not been shown previously to have a role in disease resistance. Transgenic over-expression of HvSNAC1 in barley cv. Golden Promise reduced the severity of Ramularia leaf spot (RLS), caused by the fungus Ramularia collo-cygni, but ha...
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Feng, Wei; Jiang, Danfeng; Kee, Choon-Wee; Liu, Hongjun; Tan, Choon-Hong
2016-02-04
Hydroisoquinoline derivatives were prepared in moderate to good enantioselectivities via a bicyclic guanidine-catalyzed tandem isomerization intramolecular-Diels-Alder (IMDA) reaction of alkynes. With this synthetic method, the first enantioselective synthesis of (+)-alpha-yohimbine was completed in 9 steps from the IMDA products. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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It has been generally accepted that the Diels-Alder reaction mechanism is one of the major reaction mechanisms to produce dimers and polymers during heating process of vegetable oil. Soybean oil oxidized at 180 °C for 24 hrs with 1.45 surface area-to-volume ratio showed 36.1% polymer peak area in g...
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Li, Yingzi; Osuna, Sílvia; Garcia-Borràs, Marc; Qi, Xiaotian; Liu, Song; Houk, Kendall N; Lan, Yu
2016-08-26
Diels-Alder cycloaddition is one of the most powerful tools for the functionalization of single-walled carbon nanotubes (SWCNTs). Density functional theory at the B3-LYP level of theory has been used to investigate the reactivity of different-diameter SWCNTs (4-9,5) in Diels-Alder reactions with 1,3-butadiene; the reactivity was found to decrease with increasing SWCNT diameter. Distortion/interaction analysis along the whole reaction pathway was found to be a better way to explore the reactivity of this type of reaction. The difference in interaction energy along the reaction pathway is larger than that of the corresponding distortion energy. However, the distortion energy plots for these reactions show the same trend. Therefore, the formation of the transition state can be determined from the interaction energy. A lower interaction energy leads to an earlier transition state, which indicates a lower activation energy. The computational results also indicate that the original distortion of the SWCNTs leads to an increase in the reactivity of the SWCNTs. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Directory of Open Access Journals (Sweden)
Nils Klüver
Full Text Available Acetylcholinesterase (AChE inhibitors are widely used as pesticides and drugs. Their primary effect is the overstimulation of cholinergic receptors which results in an improper muscular function. During vertebrate embryonic development nerve activity and intracellular downstream events are critical for the regulation of muscle fiber formation. Whether AChE inhibitors and related neurotoxic compounds also provoke specific changes in gene transcription patterns during vertebrate development that allow them to establish a mechanistic link useful for identification of developmental toxicity pathways has, however, yet not been investigated. Therefore we examined the transcriptomic response of a known AChE inhibitor, the organophosphate azinphos-methyl (APM, in zebrafish embryos and compared the response with two non-AChE inhibiting unspecific control compounds, 1,4-dimethoxybenzene (DMB and 2,4-dinitrophenol (DNP. A highly specific cluster of APM induced gene transcripts was identified and a subset of strongly regulated genes was analyzed in more detail. The small heat shock protein hspb11 was found to be the most sensitive induced gene in response to AChE inhibitors. Comparison of expression in wildtype, ache and sop(fixe mutant embryos revealed that hspb11 expression was dependent on the nicotinic acetylcholine receptor (nAChR activity. Furthermore, modulators of intracellular calcium levels within the whole embryo led to a transcriptional up-regulation of hspb11 which suggests that elevated intracellular calcium levels may regulate the expression of this gene. During early zebrafish development, hspb11 was specifically expressed in muscle pioneer cells and Hspb11 morpholino-knockdown resulted in effects on slow muscle myosin organization. Our findings imply that a comparative toxicogenomic approach and functional analysis can lead to the identification of molecular mechanisms and specific marker genes for potential neurotoxic compounds.
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Directory of Open Access Journals (Sweden)
Kathrin Davari
2017-04-01
Full Text Available Summary: Activation of immune cells results in rapid functional changes, but how such fast changes are accomplished remains enigmatic. By combining time courses of 4sU-seq, RNA-seq, ribosome profiling (RP, and RNA polymerase II (RNA Pol II ChIP-seq during T cell activation, we illustrate genome-wide temporal dynamics for ∼10,000 genes. This approach reveals not only immediate-early and posttranscriptionally regulated genes but also coupled changes in transcription and translation for >90% of genes. Recruitment, rather than release of paused RNA Pol II, primarily mediates transcriptional changes. This coincides with a genome-wide temporary slowdown in cotranscriptional splicing, even for polyadenylated mRNAs that are localized at the chromatin. Subsequent splicing optimization correlates with increasing Ser-2 phosphorylation of the RNA Pol II carboxy-terminal domain (CTD and activation of the positive transcription elongation factor (pTEFb. Thus, rapid de novo recruitment of RNA Pol II dictates the course of events during T cell activation, particularly transcription, splicing, and consequently translation. : Davari et al. visualize global changes in RNA Pol II binding, transcription, splicing, and translation. T cells change their functional program by rapid de novo recruitment of RNA Pol II and coupled changes in transcription and translation. This coincides with fluctuations in RNA Pol II phosphorylation and a temporary reduction in cotranscriptional splicing. Keywords: RNA Pol II, cotranscriptional splicing, T cell activation, ribosome profiling, 4sU, H3K36, Ser-5 RNA Pol II, Ser-2 RNA Pol II, immune response, immediate-early genes
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Shao, En-Si; Lin, Gui-Fang; Liu, Sijun; Ma, Xiao-Li; Chen, Ming-Feng; Lin, Li; Wu, Song-Qing; Sha, Li; Liu, Zhao-Xia; Hu, Xiao-Hua; Guan, Xiong; Zhang, Ling-Ling
2017-01-01
Tea production has been significantly impacted by the false-eye leafhopper, Empoasca vitis (Göthe), around Asia. To identify the key genes which are responsible for nutrition absorption, xenobiotic metabolism and immune response, the transcriptome of either alimentary tracts or bodies minus alimentary tract of E. vitis was sequenced and analyzed. Over 31 million reads were obtained from Illumina sequencing. De novo sequence assembly resulted in 52,182 unigenes with a mean size of 848nt. The assembled unigenes were then annotated using various databases. Transcripts of at least 566 digestion-, 224 detoxification-, and 288 immune-related putative genes in E. vitis were identified. In addition, relative expression of highly abundant transcripts was verified through quantitative real-time PCR. Results from this investigation provide genomic information about E. vitis, which will be helpful in further study of E. vitis biology and in the development of novel strategies to control this devastating pest. Copyright © 2016 Elsevier Inc. All rights reserved.
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Diel feeding rhythm of copepod size-fractions from Coliumo Bay, Central Chile
Directory of Open Access Journals (Sweden)
Danilo Calliari
2001-12-01
Full Text Available The feeding behaviour of the size fractionated copepod assemblage was studied over a diel cycle in Coliumo Bay. In this shallow environment the photic layer reached the bottom and salinity, temperature, and food availability were fairly homogeneous throughout the water column. All four size-fractions (250-500 ?m, 500-1000 ?m, 1000-2000 ?m, >2000 ?m showed a period of high feeding activity during the night and low feeding activity during the day. The persistence of nocturnal feeding in the presence of high food concentration over the 24-h cycle is interpreted as a predator avoidance strategy: empty guts by day make copepods less conspicuous to their visual daytime predators.
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Bloom, Chloe I; Graham, Christine M; Berry, Matthew P R; Rozakeas, Fotini; Redford, Paul S; Wang, Yuanyuan; Xu, Zhaohui; Wilkinson, Katalin A; Wilkinson, Robert J; Kendrick, Yvonne; Devouassoux, Gilles; Ferry, Tristan; Miyara, Makoto; Bouvry, Diane; Valeyre, Dominique; Dominique, Valeyre; Gorochov, Guy; Blankenship, Derek; Saadatian, Mitra; Vanhems, Phillip; Beynon, Huw; Vancheeswaran, Rama; Wickremasinghe, Melissa; Chaussabel, Damien; Banchereau, Jacques; Pascual, Virginia; Ho, Ling-Pei; Lipman, Marc; O'Garra, Anne
2013-01-01
New approaches to define factors underlying the immunopathogenesis of pulmonary diseases including sarcoidosis and tuberculosis are needed to develop new treatments and biomarkers. Comparing the blood transcriptional response of tuberculosis to other similar pulmonary diseases will advance knowledge of disease pathways and help distinguish diseases with similar clinical presentations. To determine the factors underlying the immunopathogenesis of the granulomatous diseases, sarcoidosis and tuberculosis, by comparing the blood transcriptional responses in these and other pulmonary diseases. We compared whole blood genome-wide transcriptional profiles in pulmonary sarcoidosis, pulmonary tuberculosis, to community acquired pneumonia and primary lung cancer and healthy controls, before and after treatment, and in purified leucocyte populations. An Interferon-inducible neutrophil-driven blood transcriptional signature was present in both sarcoidosis and tuberculosis, with a higher abundance and expression in tuberculosis. Heterogeneity of the sarcoidosis signature correlated significantly with disease activity. Transcriptional profiles in pneumonia and lung cancer revealed an over-abundance of inflammatory transcripts. After successful treatment the transcriptional activity in tuberculosis and pneumonia patients was significantly reduced. However the glucocorticoid-responsive sarcoidosis patients showed a significant increase in transcriptional activity. 144-blood transcripts were able to distinguish tuberculosis from other lung diseases and controls. Tuberculosis and sarcoidosis revealed similar blood transcriptional profiles, dominated by interferon-inducible transcripts, while pneumonia and lung cancer showed distinct signatures, dominated by inflammatory genes. There were also significant differences between tuberculosis and sarcoidosis in the degree of their transcriptional activity, the heterogeneity of their profiles and their transcriptional response to treatment.
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Directory of Open Access Journals (Sweden)
Emmanuelle C Leroy
Full Text Available Passive acoustic monitoring is an efficient way to provide insights on the ecology of large whales. This approach allows for long-term and species-specific monitoring over large areas. In this study, we examined six years (2010 to 2015 of continuous acoustic recordings at up to seven different locations in the Central and Southern Indian Basin to assess the peak periods of presence, seasonality and migration movements of Antarctic blue whales (Balaenoptera musculus intermedia. An automated method is used to detect the Antarctic blue whale stereotyped call, known as Z-call. Detection results are analyzed in terms of distribution, seasonal presence and diel pattern of emission at each site. Z-calls are detected year-round at each site, except for one located in the equatorial Indian Ocean, and display highly seasonal distribution. This seasonality is stable across years for every site, but varies between sites. Z-calls are mainly detected during autumn and spring at the subantarctic locations, suggesting that these sites are on the Antarctic blue whale migration routes, and mostly during winter at the subtropical sites. In addition to these seasonal trends, there is a significant diel pattern in Z-call emission, with more Z-calls in daytime than in nighttime. This diel pattern may be related to the blue whale feeding ecology.
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Transcriptional responses of olive flounder (Paralichthys olivaceus to low temperature.
Directory of Open Access Journals (Sweden)
Jinwei Hu
Full Text Available The olive flounder (Paralichthys olivaceus is an economically important flatfish in marine aquaculture with a broad thermal tolerance ranging from 14 to 23°C. Cold-tolerant flounder that can survive during the winter season at a temperature of less than 14°C might facilitate the understanding of the mechanisms underlying the response to cold stress. In this study, the transcriptional response of flounder to cold stress (0.7±0.05°C was characterized using RNA sequencing. Transcriptome sequencing was performed using the Illumina MiSeq platform for the cold-tolerant (CT group, which survived under the cold stress; the cold-sensitive (CS group, which could barely survive at the low temperature; and control group, which was not subjected to cold treatment. In all, 29,021 unigenes were generated. Compared with the unigene expression profile of the control group, 410 unigenes were up-regulated and 255 unigenes were down-regulated in the CT group, whereas 593 unigenes were up-regulated and 289 unigenes were down-regulated in the CS group. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses revealed that signal transduction, lipid metabolism, digestive system, and signaling molecules and interaction were the most highly enriched pathways for the genes that were differentially expressed under cold stress. All these pathways could be assigned to the following four biological functions for flounder that can survive under cold stress: signal response to cold stress, cell repair/regeneration, energy production, and cell membrane construction and fluidity.
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Fast Hetero-Diels-Alder Reactions Using 4-Phenyl-1,2,4-Triazoline-3,5-Dione (PTAD) as the Dienophile
Celius, Tevye C.
2010-01-01
A hetero-Diels-Alder reaction that proceeds rapidly and only requires a simple filtration to purify the product is presented. The dienophile, 4-phenyl-1,2,4-triazoline-3,5-dione (PTAD), is prepared by the heterogeneous oxidation of 4-phenylurazole by the bromenium ion, Br[superscript +], generated in situ by the oxidation of potassium bromide by…
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Transcriptional responses of Treponema denticola to other oral bacterial species.
Directory of Open Access Journals (Sweden)
Juni Sarkar
presented here provide an in-depth understanding of the transcriptional responses triggered by contact-dependent interactions between microorganisms inhabiting the periodontal pocket.
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Directory of Open Access Journals (Sweden)
Karthikeyan Selvarasu
2017-10-01
Full Text Available Cancer is a complex and progressive multi-step disorder that results from the transformation of normal cells to malignant derivatives. Several oncogenic signaling pathways are involved in this transformation. PPARG (Peroxisome proliferator-activated receptor gamma mediated transcription and signaling is involved in few cancers. We have investigated the PPARG in gastric tumors. The objective of the present study was to investigate the PPARG mediated transcriptional response in gastric tumors. Gene-set based and pathway focused gene-set enrichment analysis of available PPARG signatures in gastric tumor mRNA profiles shows that PPARG mediated transcription is highly activated in intestinal sub-type of gastric tumors. Further, we have derived the PPARG associated genes in gastric cancer and their expression was identified for the association with the better survival of the patients. Analysis of the PPARG associated genes reveals their involvement in mitotic cell cycle process, chromosome organization and nuclear division. Towards identifying the association with other oncogenic signaling process, E2F regulated genes were found associated with PPARG mediated transcription. The current results reveal the possible stratification of gastric tumors based on the PPARG gene expression and the possible development of PPARG targeted gastric cancer therapeutics. The identified PPARG regulated genes were identified to be targetable by pioglitazone and rosiglitazone. The identification of PPARG genes also in the normal stomach tissues reveal the possible involvement of these genes in the normal physiology of stomach and needs to be investigated.
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Cha, Seung Bin; Lee, Won Jung; Shin, Min Kyoung; Jung, Myung Hwan; Shin, Seung Won; Yoo, An Na; Kim, Jong Wan; Yoo, Han Sang
2013-06-27
Brucella abortus is an intracellular zoonotic pathogen which causes undulant fever, endocarditis, arthritis and osteomyelitis in human and abortion and infertility in cattle. This bacterium is able to invade and replicate in host macrophage instead of getting removed by this defense mechanism. Therefore, understanding the interaction between virulence of the bacteria and the host cell is important to control brucellosis. Previously, we generated internalization defective mutants and analyzed the envelope proteins. The present study was undertaken to evaluate the changes in early transcriptional responses between wild type and internalization defective mutants infected mouse macrophage, RAW 264.7. Both of the wild type and mutant infected macrophages showed increased expression levels in proinflammatory cytokines, chemokines, apoptosis and G-protein coupled receptors (Gpr84, Gpr109a and Adora2b) while the genes related with small GTPase which mediate intracellular trafficking was decreased. Moreover, cytohesin 1 interacting protein (Cytip) and genes related to ubiquitination (Arrdc3 and Fbxo21) were down-regulated, suggesting the survival strategy of this bacterium. However, we could not detect any significant changes in the mutant infected groups compared to the wild type infected group. In summary, it was very difficult to clarify the alterations in host cellular transcription in response to infection with internalization defective mutants. However, we found several novel gene changes related to the GPCR system, ubiquitin-proteosome system, and growth arrest and DNA damages in response to B. abortus infection. These findings may contribute to a better understanding of the molecular mechanisms underlying host-pathogen interactions and need to be studied further.
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Rong, Zi-Qiang; Wang, Min; Chow, Chi Hao Eugene; Zhao, Yu
2016-07-04
Highly efficient and diastereodivergent aza-Diels-Alder reactions have been developed to access either diastereomeric series of benzofuran-fused δ-lactams and dihydropyridines in nearly perfect stereoselectivity (d.r. >20:1, >99 % ee for all examples). The complementarity of N-heterocyclic carbene and chiral amine as the catalyst was demonstrated for the first time, together with an excellent level of catalytic efficiency (1 mol % loading). © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Ji, Jing; Zheng, Lingyu; Yue, Jianyun; Yao, Xiamei; Chang, Ermei; Xie, Tiantian; Deng, Nan; Chen, Lanzhen; Huang, Yuwen; Jiang, Zeping; Shi, Shengqing
2017-01-01
Glutamate decarboxylase (GAD), as a key enzyme in the γ -aminobutyric acid (GABA) shunt, catalyzes the decarboxylation of L-glutamate to form GABA. This pathway has attracted much interest because of its roles in carbon and nitrogen metabolism, stress responses, and signaling in higher plants. The aim of this study was to isolate and characterize genes encoding GADs from Caragana intermedia , an important nitrogen-fixing leguminous shrub. Two full-length cDNAs encoding GADs (designated as CiGAD1 and CiGAD2 ) were isolated and characterized. Multiple alignment and phylogenetic analyses were conducted to evaluate their structures and identities to each other and to homologs in other plants. Tissue expression analyses were conducted to evaluate their transcriptional responses to stress (NaCl, ZnSO 4 , CdCl 2 , high/low temperature, and dehydration) and exogenous abscisic acid. The CiGAD s contained the conserved PLP domain and calmodulin (CaM)-binding domain in the C-terminal region. The phylogenetic analysis showed that they were more closely related to the GADs of soybean, another legume, than to GADs of other model plants. According to Southern blotting analysis, CiGAD1 had one copy and CiGAD2 -related genes were present as two copies in C. intermedia . In the tissue expression analyses, there were much higher transcript levels of CiGAD2 than CiGAD1 in bark, suggesting that CiGAD2 might play a role in secondary growth of woody plants. Several stress treatments (NaCl, ZnSO 4 , CdCl 2 , high/low temperature, and dehydration) significantly increased the transcript levels of both CiGAD s, except for CiGAD2 under Cd stress. The CiGAD1 transcript levels strongly increased in response to Zn stress (74.3-fold increase in roots) and heat stress (218.1-fold increase in leaves). The transcript levels of both CiGAD s significantly increased as GABA accumulated during a 24-h salt treatment. Abscisic acid was involved in regulating the expression of these two CiGAD s under salt
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Directory of Open Access Journals (Sweden)
Mujeeb A. Sultan
2016-09-01
Full Text Available A theoretical study of the regioselectivity of the Diels-Alder reaction between 1,8-dichloroanthracene and acrolein is performed using DFT at the B3LYP/6-31G(d,p level of theory. The FMO analysis, global and local reactivity indices confirmed the reported experimental results. Potential energy surface analysis showed that the cycloadditions (CAs favor the formation of the anti product. These results are in good agreement with the reported results obtained experimentally where the anti is the major product.
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Brulíková, Lucie; Harrison, Aidan; Miller, Marvin J; Hlaváč, Jan
2016-01-01
The hetero-Diels-Alder reaction between a nitroso dienophile and a conjugated diene to give the 3,6-dihydro-2 H -1,2-oxazine scaffold is useful for the synthesis of many biologically interesting molecules due to the diverse opportunities created by subsequent transformations of the resulting 1,2-oxazine ring. This review discusses the rationale for the observed regio- and stereoselectivity and the methods developed in recent years used to control and improve the stereo- and regioselectivity for the synthesis of 1,2-oxazine scaffolds.
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Spectacular Rate Enhancement of the Diels-Alder Reaction at the Ionic Liquid/n-Hexane Interface.
Beniwal, Vijay; Manna, Arpan; Kumar, Anil
2016-07-04
The use of the ionic liquid/n-hexane interface as a new class of reaction medium for the Diels-Alder reaction gives large rate enhancements of the order of 10(6) to 10(8) times and high stereoselectivity, as compared to homogeneous media. The rate enhancement is attributed to the H-bonding abilities and polarities of the ionic liquids, whereas the hydrophobicity of ionic liquids was considered to be the factor in controlling stereoselectivity. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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George, Kelly A; Archer, Melanie S; Toop, Tes
2015-01-01
This study explored the molecular mechanisms potentially underlying blow fly nocturnal oviposition. A behavioral study revealed that Calliphora vicina (Robineau-Desvoidy) (Diptera: Calliphoridae) possesses a diel rhythm of oviposition in light under 12:12 light/dark conditions. Reversal to 12:12 dark/light resulted in oviposition behavior changing to align with the adjusted regime in most females, but four of 59 experimental females lacked a diel rhythm of oviposition (were arrhythmic). Real-time PCR was used to monitor the molecular expression levels of known circadian genes per and tim in C. vicina to determine whether gene expression and behavior correlated. As with behavior, reversing light/dark conditions changed rhythmic gene expression to align with an adjusted light regime. This suggests that although it is unlikely that C. vicina will colonize dead bodies at night, arrhythmic females and oviposition in the dark was demonstrated. © 2014 American Academy of Forensic Sciences.
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Directory of Open Access Journals (Sweden)
Hamzehloueian Mahshid
2014-01-01
Full Text Available The present study reports a systematic computational analysis of the two possible pathways, fused and bridged, for an intramolecular hetero Diels-Alder (IMHDA and an intramolecular 1,3-dipolar cycloaddition (IMDCA of 2-vinyloxybenzaldehyde derivatives. The potential energy surface analysis for both reactions is in agreement with experimental observations. The activation energies associated with the two regioisomeric channels in IMHDA reaction show that the bridged product is favored, although in IMDCA, the most stable TS results the fused product. The global electronic properties of fragments within each molecule were studied to discuss the reactivity patterns and charge transfer direction in the intramolecular processes. The asynchronicity of the bond formation and aromaticity of the optimized TSs in the Diels-Alder reaction as well as cycloaddition reaction were evaluated. Finally, 1H NMR chemical shifts of the possible regioisomers have been calculated using the GIAO method which of the most stable products are in agreement with the experimental data in the both reaction.
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DNA damage-inducible transcripts in mammalian cells
International Nuclear Information System (INIS)
Fornace, A.J. Jr.; Alamo, I. Jr.; Hollander, M.C.
1988-01-01
Hybridization subtraction at low ratios of RNA to cDNA was used to enrich for the cDNA of transcripts increased in Chinese hamster cells after UV irradiation. Forty-nine different cDNA clones were isolated. Most coded for nonabundant transcripts rapidly induced 2- to 10-fold after UV irradiation. Only 2 of the 20 cDNA clones sequenced matched known sequences (metallothionein I and II). The predicted amino acid sequence of one cDNA had two localized areas of homology with the rat helix-destabilizing protein. These areas of homology were at the two DNA-binding sites of this nucleic acid single-strand-binding protein. The induced transcripts were separated into two general classes. Class I transcripts were induced by UV radiation and not by the alkylating agent methyl methanesulfonate. Class II transcripts were induced by UV radiation and by methyl methanesulfonate. Many class II transcripts were induced also by H2O2 and various alkylating agents but not by heat shock, phorbol 12-tetradecanoate 13-acetate, or DNA-damaging agents which do not produce high levels of base damage. Since many of the cDNA clones coded for transcripts which were induced rapidly and only by certain types of DNA-damaging agents, their induction is likely a specific response to such damage rather than a general response to cell injury
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Wier, Andrew M; Nyholm, Spencer V; Mandel, Mark J; Massengo-Tiassé, R Prisca; Schaefer, Amy L; Koroleva, Irina; Splinter-Bondurant, Sandra; Brown, Bartley; Manzella, Liliana; Snir, Einat; Almabrazi, Hakeem; Scheetz, Todd E; Bonaldo, Maria de Fatima; Casavant, Thomas L; Soares, M Bento; Cronan, John E; Reed, Jennifer L; Ruby, Edward G; McFall-Ngai, Margaret J
2010-02-02
Mechanisms for controlling symbiont populations are critical for maintaining the associations that exist between a host and its microbial partners. We describe here the transcriptional, metabolic, and ultrastructural characteristics of a diel rhythm that occurs in the symbiosis between the squid Euprymna scolopes and the luminous bacterium Vibrio fischeri. The rhythm is driven by the host's expulsion from its light-emitting organ of most of the symbiont population each day at dawn. The transcriptomes of both the host epithelium that supports the symbionts and the symbiont population itself were characterized and compared at four times over this daily cycle. The greatest fluctuation in gene expression of both partners occurred as the day began. Most notable was an up-regulation in the host of >50 cytoskeleton-related genes just before dawn and their subsequent down-regulation within 6 h. Examination of the epithelium by TEM revealed a corresponding restructuring, characterized by effacement and blebbing of its apical surface. After the dawn expulsion, the epithelium reestablished its polarity, and the residual symbionts began growing, repopulating the light organ. Analysis of the symbiont transcriptome suggested that the bacteria respond to the effacement by up-regulating genes associated with anaerobic respiration of glycerol; supporting this finding, lipid analysis of the symbionts' membranes indicated a direct incorporation of host-derived fatty acids. After 12 h, the metabolic signature of the symbiont population shifted to one characteristic of chitin fermentation, which continued until the following dawn. Thus, the persistent maintenance of the squid-vibrio symbiosis is tied to a dynamic diel rhythm that involves both partners.
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Uncovering transcriptional regulation of metabolism by using metabolic network topology
DEFF Research Database (Denmark)
Patil, Kiran Raosaheb; Nielsen, Jens
2005-01-01
in the metabolic network that follow a common transcriptional response. Thus, the algorithm enables identification of so-called reporter metabolites (metabolites around which the most significant transcriptional changes occur) and a set of connected genes with significant and coordinated response to genetic......Cellular response to genetic and environmental perturbations is often reflected and/or mediated through changes in the metabolism, because the latter plays a key role in providing Gibbs free energy and precursors for biosynthesis. Such metabolic changes are often exerted through transcriptional...... therefore developed an algorithm that is based on hypothesis-driven data analysis to uncover the transcriptional regulatory architecture of metabolic networks. By using information on the metabolic network topology from genome-scale metabolic reconstruction, we show that it is possible to reveal patterns...
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A computational study of the Diels Alder reactions involving acenes: reactivity and aromaticity
Cheng, Mei-Fun; Li, Wai-Kee
2003-01-01
Ab initio and DFT methods have been used to study the Diels-Alder reactivity and the aromaticity of four linear acenes, namely, naphthalene, anthracene, tetracene and pentacene. In total, eight additional pathways between ethylene and four acenes have been studied and all of them are concerted and exothermic reactions. It is found that the most reactive sites on the acenes are the center ring's meso-carbons. Also, reactivity decreases along the series pentacene > tetracene > anthracene > naphthalene. In addition, the NICS results indicate that the most reactive rings in the acenes are those with the highest aromaticity. These results are consistent with those of other theoretical studies and experiments.
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Dynamic analysis of stochastic transcription cycles.
Directory of Open Access Journals (Sweden)
Claire V Harper
2011-04-01
Full Text Available In individual mammalian cells the expression of some genes such as prolactin is highly variable over time and has been suggested to occur in stochastic pulses. To investigate the origins of this behavior and to understand its functional relevance, we quantitatively analyzed this variability using new mathematical tools that allowed us to reconstruct dynamic transcription rates of different reporter genes controlled by identical promoters in the same living cell. Quantitative microscopic analysis of two reporter genes, firefly luciferase and destabilized EGFP, was used to analyze the dynamics of prolactin promoter-directed gene expression in living individual clonal and primary pituitary cells over periods of up to 25 h. We quantified the time-dependence and cyclicity of the transcription pulses and estimated the length and variation of active and inactive transcription phases. We showed an average cycle period of approximately 11 h and demonstrated that while the measured time distribution of active phases agreed with commonly accepted models of transcription, the inactive phases were differently distributed and showed strong memory, with a refractory period of transcriptional inactivation close to 3 h. Cycles in transcription occurred at two distinct prolactin-promoter controlled reporter genes in the same individual clonal or primary cells. However, the timing of the cycles was independent and out-of-phase. For the first time, we have analyzed transcription dynamics from two equivalent loci in real-time in single cells. In unstimulated conditions, cells showed independent transcription dynamics at each locus. A key result from these analyses was the evidence for a minimum refractory period in the inactive-phase of transcription. The response to acute signals and the result of manipulation of histone acetylation was consistent with the hypothesis that this refractory period corresponded to a phase of chromatin remodeling which significantly
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DEFF Research Database (Denmark)
Putaala, H; Barrangou, R; Leyer, G J
2010-01-01
a comparative analysis of the global in vitro transcriptional response of human intestinal epithelial cells to Lactobacillus acidophilus NCFM™, Lactobacillus salivarius Ls-33, Bifidobacterium animalis subsp. lactis 420, and enterohaemorrhagic Escherichia coli O157:H7 (EHEC). Interestingly, L. salivarius Ls-33...
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Yang, Limin
2014-08-01
A facile N-heterocyclic carbene catalytic enantioselective aza-Diels-Alder reaction of oxodiazenes with α-chloroaldehydes as dienophile precursors is reported, with excellent enantioselectivity (ee > 99%) and excellent yield (up to 93%). DFT study showed that cis-TSa, formed from a top face approach of oxodiazene to cis-IIa, is the most favorable transition state and is consistent with the experimental observations. © 2014 American Chemical Society.
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Seasonal and diel variation in xylem CO2 concentration and sap pH in sub-Mediterranean oak stems.
Salomón, Roberto; Valbuena-Carabaña, María; Teskey, Robert; McGuire, Mary Anne; Aubrey, Doug; González-Doncel, Inés; Gil, Luis; Rodríguez-Calcerrada, Jesús
2016-04-01
Since a substantial portion of respired CO2 remains within the stem, diel and seasonal trends in stem CO2 concentration ([CO2]) are of major interest in plant respiration and carbon budget research. However, continuous long-term stem [CO2] studies are scarce, and generally absent in Mediterranean climates. In this study, stem [CO2] was monitored every 15min together with stem and air temperature, sap flow, and soil water storage during a growing season in 16 stems of Quercus pyrenaica to elucidate the main drivers of stem [CO2] at different temporal scales. Fluctuations in sap pH were also assessed during two growing seasons to evaluate potential errors in estimates of the concentration of CO2 dissolved in xylem sap ([CO2*]) calculated using Henry's law. Stem temperature was the best predictor of stem [CO2] and explained more than 90% and 50% of the variability in stem [CO2] at diel and seasonal scales, respectively. Under dry conditions, soil water storage was the main driver of stem [CO2]. Likewise, the first rains after summer drought caused intense stem [CO2] pulses, suggesting enhanced stem and root respiration and increased resistance to radial CO2 diffusion. Sap flow played a secondary role in controlling stem [CO2] variations. We observed night-time sap pH acidification and progressive seasonal alkalinization. Thus, if the annual mean value of sap pH (measured at midday) was assumed to be constant, night-time sap [CO2*] was substantially overestimated (40%), and spring and autumn sap [CO2*] were misestimated by 25%. This work highlights that diel and seasonal variations in temperature, tree water availability, and sap pH substantially affect xylem [CO2] and sap [CO2*]. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.
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Kulakovskiy, Ivan V.
2011-08-18
Motivation: Modern experimental methods provide substantial information on protein-DNA recognition. Studying arrangements of transcription factor binding sites (TFBSs) of interacting transcription factors (TFs) advances understanding of the transcription regulatory code. Results: We constructed binding motifs for TFs forming a complex with HIF-1α at the erythropoietin 3\\'-enhancer. Corresponding TFBSs were predicted in the segments around transcription start sites (TSSs) of all human genes. Using the genome-wide set of regulatory regions, we observed several strongly preferred distances between hypoxia-responsive element (HRE) and binding sites of a particular cofactor protein. The set of preferred distances was called as a preferred pair distance template (PPDT). PPDT dramatically depended on the TF and orientation of its binding sites relative to HRE. PPDT evaluated from the genome-wide set of regulatory sequences was used to detect significant PPDT-consistent binding site pairs in regulatory regions of hypoxia-responsive genes. We believe PPDT can help to reveal the layout of eukaryotic regulatory segments. © The Author 2011. Published by Oxford University Press. All rights reserved.
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pH modulates the binding of early growth response protein 1 transcription factor to DNA.
Mikles, David C; Bhat, Vikas; Schuchardt, Brett J; Deegan, Brian J; Seldeen, Kenneth L; McDonald, Caleb B; Farooq, Amjad
2013-08-01
The transcription factor early growth response protein (EGR)1 orchestrates a plethora of signaling cascades involved in cellular homeostasis, and its downregulation has been implicated in the development of prostate cancer. Herein, using a battery of biophysical tools, we show that the binding of EGR1 to DNA is tightly regulated by solution pH. Importantly, the binding affinity undergoes an enhancement of more than an order of magnitude with an increase in pH from 5 to 8, implying that the deprotonation of an ionizable residue accounts for such behavior. This ionizable residue is identified as His382 by virtue of the fact that its replacement by nonionizable residues abolishes the pH dependence of the binding of EGR1 to DNA. Notably, His382 inserts into the major groove of DNA, and stabilizes the EGR1-DNA interaction via both hydrogen bonding and van der Waals contacts. Remarkably, His382 is mainly conserved across other members of the EGR family, implying that histidine protonation-deprotonation may serve as a molecular switch for modulating the protein-DNA interactions that are central to this family of transcription factors. Collectively, our findings reveal an unexpected but a key step in the molecular recognition of the EGR family of transcription factors, and suggest that they may act as sensors of pH within the intracellular environment. © 2013 FEBS.