bluuebunny/crossref_metadata_2025_split huggingface dataset:
Secretion of matrix metalloproteinase‐9 by the proinflammatory cytokine, IL‐1β: a role for the dual signalling pathways, Akt and Erk
Authors: Ruhul Amin A. R. M. , Senga Takeshi , Oo Myat Lin , Thant Aye Aye , Hamaguchi Michinari 
Published: June 2003

AbstractBackground: Matrix metalloproteinases including MMP‐9 mediate matrix destruction during chronic inflammatory diseases such as arthritis and atherosclerosis. MMP‐9 up‐regulation by inflammatory cytokines involve interactions between several transcription factors including activator protein‐1 and NFκB. The upstream regulatory pathways are less well understood.Results: To search for the mechanism of tissue destruction in the process of inflammatory disorders, we investigated the signalling pathway critical for the activation of MMP‐9 expression and secretion by IL‐1β. Treatment of Balb 3T3 cells with IL‐1β activated MMP‐9 transcription and subsequent secretion in a time‐ and dose‐dependent manner. Concomitantly, IL‐1β treatment of cells activated phosphorylation of Akt, Erk and p38. Treatment of cells with either LY294002, a PI3K inhibitor, or expression of a dominant negative form of Akt drastically suppressed the IL‐1β‐dependent secretion of MMP‐9. Pretreatment of cells with a MEK1 inhibitor, U0126, also strongly inhibited IL‐1β‐dependent secretion of MMP‐9. In contrast, pre‐treatment with a specific p38 kinase inhibitor, SB203580, had no effect on IL‐1β‐dependent secretion of MMP‐9. In addition, cells expressing constitutively active form of Akt or MEK1 showed no clear activation of MMP‐9 secretion, whereas these cells responded well to IL‐1β treatment. However, co‐transfection of cells with both active Akt and MEK1 was sufficient to induce MMP‐9 secretion without stimulation with IL‐1β.Conclusion: Taken together, our results suggest that IL‐1β stimulation of cells activates MMP‐9 secretion by the activation of the dual signalling pathways, the PI3K‐Akt and MEK1‐Erk and constitutive activation of these pathways were sufficient to induce MMP‐9 secretion.
Terminal deoxynucleotidyltransferase forms a ternary complex with a novel chromatin remodeling protein with 82 kDa and core histone
Authors: Fujita Kiyoko , Shimazaki Noriko , Ohta Yuko , Kubota Takashi , Ibe Shirou , Toji Shingo , Tamai Katsuyuki , Fujisaki Seiichiro , Hayano Takahide , Koiwai Osamu 
Published: June 2003

AbstractBackground: Terminal deoxynucleotidyltransferase (TdT) is a DNA polymerase that enhances the Ig and TcR gene diversity in the N region at the junctions of variable (V), diversity (D) and joining (J) segments in B‐ and T‐cells. TdT synthesizes the N region in concert with many proteins including DNA‐PKcs, Ku70 and Ku86. To elucidate the molecular mechanism of the N region synthesis, we first attempted to isolate the genes with products that directly interact with TdT.Results: Using a yeast two‐hybrid system, we isolated a cDNA clone encoding a novel nuclear protein that interacts with TdT. This protein was designated as TdT interacting factor 2 (TdIF2). The confined region of the C‐terminal in TdIF2 is involved in specific interaction with the entire C‐terminal in TdT. TdIF2 contains an acidic region comprised of 42 residues. TdIF2 was shown to bind specifically to a core histone by pull down assay using specific antibodies against TdIF2. When a TdT/TdIF2 complex was applied on to a DNA‐cellulose column, only TdT bound to the column while TdIF2 passed through. TdIF2 reduces the TdT activity to 46% of its maximum value in vitro assay system using activated DNA as primer.Conclusions: TdIF2 binds directly to TdT and core histone. Furthermore, TdT, TdIF2 and core histone form a ternary complex. TdIF2 liberates H2A/H2B from a core histone in correlation with PCNA. The enzymatic consequence of the TdIF2/TdT complex is the reduction of TdT activity in vitro. TdIF2 would function as a chromatin remodeling protein at the N region synthesis.
Soil N dynamics in relation to leaf litter quality and soil fertility in north‐western Patagonian forests
Authors: Satti Patricia , Mazzarino Maria Julia , Gobbi Miriam , Funes Florencia , Roselli Lucia , Fernandez Horacio 
Published: June 2003

SummaryWe examined the relationships among soil N dynamics, soil chemistry and leaf litter quality in 28 forest stands dominated by conifers, woody broad‐leaf deciduous species or broad‐leaf evergreens. Potential net N mineralization, net nitrification and microbial biomass N were used as indicators of soil N dynamics; pH, organic C, total N, exchangeable cations and extractable P as indicators of soil chemistry and N concentration, lignin concentration, C : N ratio and lignin : N ratio in senescent leaves as indicators of leaf litter quality. N dynamics were assessed in two consecutive years with contrasting precipitation.Net N mineralization was lower in stands of the three conifers and one of three broad‐leaf evergreen species than in stands of the other six broad‐leaf species (40–77 vs. 87–250 mg N kg−1after 16‐week incubations) and higher in the wetter year.The proportion of N nitrified was high beneath most species regardless of mineralization rates, soil N fertility and leaf litter quality, and was significantly higher for the wetter year. Ammonium was the predominant form of N in three sites affected by seasonal waterlogging and in two sites the predominant form changed from ammonium in the drier year to nitrate during the wetter year, probably due to differences in soil texture affecting soil moisture.Net N mineralization was linearly related to microbial biomass N, implying that the microbial activity per biomass unit was quite similar beneath all species. Constant microbial biomass during the wetter year suggested that as mineralization/nitrification increased, there was a higher potential risk of N losses.Although the litter lignin : N ratio allowed differentiation of soil N dynamics between broad‐leaf species and conifers, its constant value (23–28) in all broad‐leaf species made it a poor predictor of the differences found within this group. Across all sites and between broad‐leaf species, soil N dynamics were best explained by a combination of leaf litter lignin and soil chemistry indicators, particularly soil total N for net N mineralization and net nitrification, and soil organic C for microbial biomass N.
Spatial and temporal variation of biomass in a tropical forest: results from a large census plot in Panama
Authors: Chave Jérôme , Condit Richard , Lao Suzanne , Caspersen John P. , Foster Robin B. , Hubbell Stephen P. 
Published: June 2003

SummaryWe estimated the dry, living, above‐ground biomass (AGB) standing stock and its turnover in a 50‐hectare forest plot located in moist tropical forest on Barro Colorado Island, Panama. The estimates were obtained using inventory data collected every 5 years from 1985 to 2000, including measurements of all trees ≥ 1 cm diameter.Four different allometric regressions relating trunk diameter and height with AGB were compared. Based on the most consistent method, we estimated that the Barro Colorado forest holds 281 ± 20 Mg ha−1(1 Mg = 103kg) of AGB, lianas included. A third of the AGB is stored in trees larger than 70 cm in diameter.Stand‐level AGB increment (growth plus recruitment) was highest in the period 1985–90 (7.05 ± 0.32 Mg ha−1 year−1, mean ± 95% confidence limits based on samples of multiple hectares) and smallest in the period 1990–95 (5.25 ± 0.26 Mg ha−1 year−1), while AGB losses were similar during the three intervals (mean 5.43 ± 0.72 Mg ha−1year−1). This resulted in significant differences in AGB change (defined as increment minus loss) among census intervals; including branchfalls, the AGB of Barro Colorado Island increased in 1985–90 (+0.82 ± 0.84 Mg ha−1 year−1), decreased in 1990–95 (−0.69 ± 0.82 Mg ha−1 year−1), and increased again in 1995–2000 (+0.45 ± 0.70 Mg ha−1year−1). The 15‐year average was +0.20 Mg ha−1 year−1, but with a confidence interval that spanned zero (−0.68 to 0.63 Mg ha−1 year−1).Branchfalls and partial breakage of stems had a significant influence on the AGB changes. They contributed an average of 0.46 Mg ha−1 year−1to the AGB loss. About 5% of AGB increment was due to trees less than 10 cm in diameter.To test whether the AGB of tropical forests is increasing due to climate change, we propose that in each forest type, at least 10 hectares of forest be inventoried, and that measurements of the small classes (< 10 cm diameter) as well as large size classes be included. Biomass loss due to crown damage should also be estimated.
Temporal heterogeneity of soil moisture in grassland and forest
Authors: James Sarah E. , Pärtel Meelis , Wilson Scott D. , Peltzer Duane A. 
Published: June 2003

Summary

Differences between growth forms in the spatial heterogeneity of associated soil resources, such as water, are well‐documented. We tested for differences in the temporal heterogeneity of soil moisture between natural grassland, shrubland and Populus tremuloides forest at the northern edge of the Great Plains.
Weekly measurements of soil moisture over a year, and daily measurements during a growing season, both showed significant interactions between habitat and time. Soils under grassland and shrubs were wettest at the start of the growing season but driest at the end.
The coefficient of variation of soil moisture content over time during the growing season was significantly higher in grassland than in forest. Similar results were found for whole‐year measurements, and at two depths beneath the soil surface (10 and 30 cm).
We found little interception of rainfall in any vegetation type. The net effect of vegetation on soil moisture during a drying period, however, was significantly greater in grassland than in forest, suggesting that differences in the temporal heterogeneity of soil moisture content are related to resource uptake.
Effects of life‐state on detectability in a demographic study of the terrestrial orchid Cleistes bifaria
Authors: Kéry Marc , Gregg Katharine B. 
Published: June 2003

Summary

Most plant demographic studies follow marked individuals in permanent plots. Plots tend to be small, so detectability is assumed to be one for every individual. However, detectability could be affected by factors such as plant traits, time, space, observer, previous detection, biotic interactions, and especially by life‐state.
We used a double‐observer survey and closed population capture–recapture modelling to estimate state‐specific detectability of the orchid Cleistes bifaria in a long‐term study plot of 41.2 m2. Based on AICc model selection, detectability was different for each life‐state and for tagged vs. previously untagged plants. There were no differences in detectability between the two observers.
Detectability estimates (SE) for one‐leaf vegetative, two‐leaf vegetative, and flowering/fruiting states correlated with mean size of these states and were 0.76 (0.05), 0.92 (0.06), and 1 (0.00), respectively, for previously tagged plants, and 0.84 (0.08), 0.75 (0.22), and 0 (0.00), respectively, for previously untagged plants. (We had insufficient data to obtain a satisfactory estimate of previously untagged flowering plants).
Our estimates are for a medium‐sized plant in a small and intensively surveyed plot. It is possible that detectability is even lower for larger plots and smaller plants or smaller life‐states (e.g. seedlings) and that detectabilities < 1 are widespread in plant demographic studies.
State‐dependent detectabilities are especially worrying since they will lead to a size‐ or state‐biased sample from the study plot. Failure to incorporate detectability into demographic estimation methods introduces a bias into most estimates of population parameters such as fecundity, recruitment, mortality, and transition rates between life‐states. We illustrate this by a simple example using a matrix model, where a hypothetical population was stable but, due to imperfect detection, wrongly projected to be declining at a rate of 8% per year.
Almost all plant demographic studies are based on models for discrete states. State and size are important predictors both for demographic rates and detectability. We suggest that even in studies based on small plots, state‐ or size‐specific detectability should be estimated at least at some point to avoid biased inference about the dynamics of the population sampled.
Ecological aspects of seed desiccation sensitivity
Authors: Tweddle John C. , Dickie John B. , Baskin Carol C. , Baskin Jerry M. 
Published: June 2003

Summary

The ability of seeds to survive desiccation is an important functional trait and is an integral part of plant regeneration ecology. Despite this, the topic has received relatively little attention from ecologists. In this study, we examine the relationships between seed desiccation tolerance and two important aspects of plant regeneration ecology: habitat and dormancy. This is done by comparative analysis of a data set of 886 tree and shrub species from 93 families.
The proportion of species displaying desiccation sensitive seeds declines as the habitat becomes drier, and possibly also cooler, although the latter observation requires cautious interpretation. Desiccation sensitivity is most common in moist, relatively aseasonal vegetation zones, but is infrequent in, though not absent from arid and highly seasonal habitats.
The highest frequency of desiccation sensitivity occurs in non‐pioneer evergreen rain forest trees, although 48% of the species examined have desiccation tolerant seeds. In contrast, all pioneer taxa within the data set have drying tolerant seeds.
Desiccation sensitivity is more frequent in seeds that are non‐dormant on shedding (c. 31%), than dormant (c. 9%). Highest frequencies of drying tolerance occur in seeds with physical or combinational dormancy, at 99% and 100%, respectively.
Although there is an association between non‐dormancy and desiccation sensitivity in both tropical and temperate zones, the relationship does not appear to be causal.
Working from the hypothesis that seed desiccation sensitivity represents a derived state in extant species, we use the results to investigate and discuss possible ecological trade‐offs and associated fitness advantages. These may explain the hypothesized repeated loss of this trait. The frequent association between large seed size and desiccation sensitivity is also considered.
Mire development across the fen–bog transition on the Teifi floodplain at Tregaron Bog, Ceredigion, Wales, and a comparison with 13 other raised bogs
Authors: Hughes P. D. M. , Barber K. E. 
Published: June 2003

Summary

A literature comparison of 14 radiocarbon‐dated macrofossil records of raised peat bog initiation indicates that there is a relationship between the prevailing climate and the character of the first ombrotrophic vegetation communities at peatland sites in Britain and Ireland.
All that is required for ombrotrophy is the separation of the mire growing surface from the influence of surface and subsurface waters. This could occur via vertical accumulation of the peat mass or a lowering of the water table. The establishment of bog species can be rapid once isolation occurs.
Peatlands may become ombrotrophic in a variety of water table conditions and climatic regimes. There are at least two distinctive routes to ombrotrophy, via a ‘dry‐pioneer oligotrophic community’ or via a ‘wet‐pioneer oligotrophic community’.
Tregaron South‐east Bog does not fit the pattern suggested by the literature comparison. The Fen–Bog Transition (FBT) occurred in a period of increased effective precipitation but the first ombrotrophic community was indicative of relatively dry, ‘hummocky’ bog and a deep or unstable water table.
The transitional poor fen communities at Tregaron South‐east Bog were short‐lived. Sphagnum palustre mire lasted for 90 years compared to 300 years at Bolton Fell Moss in Cumbria, and the FBT was synchronous across much of the bog.
The Tregaron peatland complex has a long history of water table fluctuations as shown by the stratigraphy of the marginal peats.
Channel incision in the River Teifi could have contributed to the development of ‘dry hummock’ pioneer bog in the humid climatic conditions at 7300 cal. BP, by reducing the level of lagg streams.
The effects of spatial pattern of nutrient supply on the early stages of growth in plant populations
Authors: Day K. J. , Hutchings M. J. , John E. A. 
Published: June 2003

Summary

We report an experimental study of the effects of pattern of nutrient supply on the early stages of growth in populations of Cardamine hirsuta. Populations were grown with nutrients provided in one of four spatial patterns (three heterogeneous and one homogeneous). In the three heterogeneous treatments, nutrient‐rich and nutrient‐poor substrate patches of different sizes were set up in chequerboard patterns, with patches of each type accounting in total for half of the substrate, both by volume and area. All treatments provided the same total quantity of nutrients.
After 31 days of growth, populations in the heterogeneous treatments had produced significantly more root, shoot and total biomass than those in homogeneous conditions. The coefficient of variation in shoot sizes, and the variation in root biomass per unit of substrate, were also significantly greater in populations growing under heterogeneous conditions. In the heterogeneous treatments significantly more than 50% of the biomass was located in nutrient‐rich patches, and this proportion increased significantly as patch size increased.
In heterogeneous treatments, yield of plant parts from nutrient‐rich locations was significantly greater than that of plant parts in nutrient‐poor locations. It was also significantly greater than that recovered from equivalent locations in the homogeneous treatment.
We conclude that the spatial configuration of nutrients significantly affects plant population yield, the spatial distribution of population biomass, and plant size hierarchy during the early stages of population growth, even when total nutrient supply is held constant. We predict that these early effects of heterogeneity will continue to have impacts, not only on size structure, but also on the spatial pattern of mortality and the overall level of mortality, at later stages of population growth.
Effects of water level, shade and time on germination and growth of freshwater marsh plants along a simulated successional gradient
Authors: Kellogg Chev H. , Bridgham Scott D. , Leicht Stacey A. 
Published: June 2003

Summary

We examined the effect of soil organic content (1.4, 3.6, 7.2% soil C), water level (+2, −1, −4 cm from soil surface) and duration (13 or 33 days) on 10 species that varied in abundance during succession in freshwater marshes. We also determined the effect of shade (0, 40, 80% shade) and soil organic content (1.4 and 7.2% soil C) on germination of six species over 62 days with water 0.5 cm below the soil surface.
Water level consistently affected species germination on both dates. Above‐ground biomass was generally higher with increasing organic content of soil, but shade had little effect on germination or height.
The hydrologic zone in which species were found in the field was a good indicator of the response of germination to hydrology. Both early successional species and species widespread across the successional gradient show similar germination on all organic contents, while later successional species appear to germinate best at higher organic contents.
Successional changes in soils are capable of affecting plant community development, independent of disturbance.
Multiple pathways for woody plant establishment on floodplains at local to regional scales
Authors: Cooper David J. , Andersen Douglas C. , Chimner Rodney A. 
Published: June 2003

Summary

The structure and functioning of riverine ecosystems is dependent upon regional setting and the interplay of hydrologic regime and geomorphologic processes. We used a retrospective analysis to study recruitment along broad, alluvial valley segments (parks) and canyon segments of the unregulated Yampa River and the regulated Green River in the upper Colorado River basin, USA. We precisely aged 811 individuals of Populus deltoides ssp. wislizenii (native) and Tamarix ramosissima (exotic) from 182 wooded patches and determined the elevation and character of the germination surface for each. We used logistic regression to relate recruitment events (presence or absence of cohort) to five flow and two weather parameters.
Woody plant establishment occurred via multiple pathways at patch, reach and segment scales. Recruitment occurred through establishment on (1) vertically accreting bars in the unregulated alluvial valley, (2) high alluvial floodplain surfaces during rare large flood events, (3) vertically accreting channel margin deposits in canyon pools and eddies, (4) vertically accreting intermittent/abandoned channels, (5) low elevation gravel bars and debris fans in canyons during multi‐year droughts, and (6) bars and channels formed prior to flow regulation on the dammed river during controlled flood events.
The Yampa River's peak flow was rarely included in models estimating the likelihood that recruitment would occur in any year. Flow variability and the interannual pattern of flows, rather than individual large floods, control most establishment.
Regulation of the Green River flow since 1962 has had different effects on woody vegetation recruitment in canyons and valleys. The current regime mimics drought in a canyon setting, accelerating Tamarix invasion whereas in valleys the ongoing geomorphic adjustment of the channel, combined with reduced flow variability, has nearly eliminated Populus establishment.
A single year's flow or a particular pattern of flows over a sequence of years, whether natural or man‐made, produces different recruitment opportunities in alluvial and canyon reaches, in diverse landforms within a particular river reach, and for Populus and Tamarix. The design of flows to restore riparian ecosystems must consider these multiple pathways and adjust the seasonal timing, magnitude and interannual frequency of flows to match the desired outcome.
Numerical studies of optical switching and optical bistability phenomena of nano‐ or meso‐size spheres
Authors: Okamoto T. , Haraguchi M. , Fukui M. 
Published: June 2003

SummaryWe propose the use of numerical calculations of the optical response of nonlinear Kerr‐spheres, modifying the Mie theory. As a numerical example, we use a CuCl sphere coated with a Kerr‐nonlinear sphere, taking into account the excitation of the Z3‐exciton. The results clearly show that optical bistable and/or optical switching devices can be realized on a nano‐ and meso‐size scale when the real part of the dielectric constant of CuCl is negative.
Upconversion fluorescence imaging of erbium‐doped fluoride glass particles by apertureless SNOM
Authors: Fragola A. , Aigouy L. , De Wilde Y. , Mortier M. 
Published: June 2003

AbstractWe have imaged fluorescent erbium‐doped fluoride glass particles by apertureless scanning near‐field optical microscopy. The optical excitation has been performed at λ = 780 nm whereas fluorescence emission has been collected around λ = 550 nm. This process, called upconversion by energy transfer, involves two erbium ions and is not linear. Besides an improvement of the lateral resolution, we have observed on some particles that the fluorescence is not homogeneously distributed, but is rather localized in some zones brighter than others. By making tip approach curves, we have also observed that the amount of fluorescence intensity scattered by the tip is increasing when the tip is approaching the sample surface.