Miracle-dz/UniFAR-FTUs huggingface dataset:
Role of NF-κB in the Antiproliferative Effect of Endothelin-1 and Tumor Necrosis Factor-α in Human Hepatic Stellate Cells

During chronic liver diseases, hepatic stellate cells (HSC) acquire an activated myofibroblast-like phenotype and proliferate and synthesize fibrosis components. Endothelin-1 (ET-1), which inhibited the growth of human myofibroblastic HSC, increased the formation of two NF-κB DNA binding complexes; this effect was also observed with tumor necrosis factor-α (TNF-α). The complexes were identified as the p50/p50 and p50/p65 NF-κB dimers. Activation of NF-κB was associated with the degradation of the inhibitory protein IκB-α; no IκB-β was detected. Activation of NF-κB and degradation of IκB-α were prevented by the NF-κB inhibitors sodium salicylate and MG-132. In addition to cyclooxygenase-1 (COX-1), COX-2 is also constitutively expressed in human HSC, and the use of dexamethasone and of SC-58125, a selective COX-2 inhibitor, revealed that COX-2 accounts for basal COX activity. Moreover, COX-2 mRNA and protein were up-regulated by ET-1 and TNF-α, whereas COX-1 was unaffected. Induction of COX-2 and stimulation of COX activity by ET-1 and TNF-α were prevented by sodium salicylate and MG-132, suggesting that activation of NF-κB by either factor is needed for stimulation of COX-2. Finally, SC-58125 and dexamethasone reduced the growth inhibitory effect of ET-1 and TNF-α, indicating that activation of COX-2 is required for inhibition of HSC proliferation. Taken together, our results suggest that NF-κB, by inducing COX-2 expression, may play an important role in the negative regulation of human myofibroblastic HSC proliferation.
Photosynthetic responses to submergence in mangrove seedlings

Flooding and salinity fluctuations are common in mangrove systems. Sometimes these events are long-lasting, persisting several months. With an increased frequency of heavy rainfalls and terrestrial run-off, subsequent floods have been associated with massive mangrove mortality and failure to regenerate in the region. Owing to climate change, these events are expected to be more common in the future. We investigated how three weeks of submergence in water of different salinities affected the photosynthetic rates in seedlings of three common mangroves: Bruguiera gymnorrhiza (L.) Lamk. ; Avicennia marina (Forssk.) Vierh. ; and Heritiera littoralis Dryand. We found that photosynthesis and survival rates declined with increasing salinity and submergence time for all species. Prolonged submergence caused a significant decline in photosynthetic rates (as electron transport rate – ETR) for B. gymnorrhiza (P = 0.021) and H. littoralis (P = 0.002), whereas significant effects of both salinity (P = 0.003) and submergence (P = 0.023) were observed between species. Maximum diurnal values of ETR declined in the order of A. marina > B. gymnorrhiza > H. littoralis. After submergence, survived seedlings were tended normally, watered twice a day with freshwater. Three seedlings of B. gymnorrhiza from freshwater and 33% seawater treatments and of A. marina from freshwater treatment displayed signs of recovery for the first 3–5 days, but after that they died. We conclude that submergence time and water salinity will affect the performance of mangrove areas, such that areas experiencing prolonged submergence with flooding dominated by saline water might be most severely impacted.
Tests of hypotheses on patterns of gall distribution along an altitudinal gradient

We investigated the distributional pattern of galling insects along an altitudinal gradient in southeastern Brazil. We sampled insects on 33,000 herbs, 3,520 shrubs, and 1,760 trees, at 44 sites across an elevational gradient of 700 m, in order to test four hypotheses: (a) harsh environment hypothesis that predicts higher galling species richness (GSR) in xeric than in mesic habitats; (b) altitudinal gradient hypothesis that predicts a negative correlation between GSR and altitude; (c) plant richness hypothesis that predicts a positive correlation between GSR and plant species richness (PSR); and (d) plant architecture hypothesis that predicts a positive correlation between GRS and the structural complexity of plants. Only hypothesis (a) was completely confirmed by our study; galling species richness was higher in xeric than in mesic habitats (Wilcoxon test = 5.5816, P < 0.0001). The altitudinal gradient negatively influenced galling richness in xeric habitats (for all plant categories, r2 = 0.83, F1,22 = 107.585, P < 0.0001), but there was no significant correlation between galling richness and altitude in mesic habitats (for all plant categories, F1,18 = 2.251, P > 0.05). The mean number of galling insects was higher on woody than on herbaceous plants, but did not differ between shrubs and trees, refuting the plant architecture hypothesis. The plant richness hypothesis was rejected because the correlation between GSR and PSR could have been influenced by the distribution of plant species along the altitudinal gradient.
Suppression of Heterodera glycines in soils from fields with long-term soybean monoculture

Abstract Experiments were conducted in a greenhouse to evaluate soils for their degree of suppressiveness against the soybean cyst nematode, Heterodera glycines. The soils were collected in 2003 and 2004 from two fields with long-term soybean monoculture and one field with corn/soybean annual rotation. The soils were autoclaved, treated with formalin, or untreated. Both formalin and autoclave treatments removed suppressive factors and increased the nematode egg population density as compared with untreated soil. The mixture of 10% untreated soil with 90% treated soil resulted in similar nematode population densities as in the untreated soils collected from the two monoculture fields, indicating the suppressive factors were biological and can be transferred. The soils from the monoculture fields appeared to be more suppressive than the soil from the corn/soybean rotation. Hirsutella rhossiliensis was observed in all three soils, and parasitised a large percentage of second-stage juveniles of H. glycines in the monoculture soils in 2004. The fungus may be a major factor for the suppression of the nematode population, but in this study other biological factors cannot be ruled out.
Thiazolidinediones (PPARγ agonists) but not PPAR α agonists increase IRS‐2 gene expression in 3T3‐L1 and human adipocytes 1

Thiazolidinediones (TZD) improve insulin sensitivity in human as well as in different animal models of insulin resistance and Type 2 diabetes. However, no clear link to the insulin signaling events has been identified. Using differentiated 3T3‐L1 adipocytes, we found that TZD rapidly and markedly increased IRS‐2 gene expression. This effect was specific for PPARγ agonists and was not seen with PPARα agonists. It was rapidly induced (within 4 h) and maintained throughout the observation period of 48 h. It was also concentration dependent (EC50 ~50 nM) and not inhibited by cycloheximide, suggesting a direct effect on the IRS‐2 promoter. There was no evidence that TZD altered IRS‐2 mRNA stability, supporting that the increased mRNA levels were due to an increased gene transcription. IRS‐2 protein expression was increased ~30% after 48 h and ~50% after 96 h. No effects of TZD were seen on IRS‐1, PKB/Akt, or GLUT4 gene expression. TZD also increased IRS‐2 mRNA levels in cultured human adipose tissue. These data show the first direct link between TZD and a critical molecule in insulin's signaling cascade in both 3T3‐L1 and human adipocytes, and indicate a novel mode of action of these compounds. —Smith, U. , Gogg, S. , Johansson, A. , Olausson, T. , Rotter, V. , Svalstedt, B. Thiazolidinediones (PPARγ agonists) but not PPARa agonists increase IRS‐2 gene expression in 3T3‐L1 and human adipocytes. FASEB J. 15, 215–220 (2001)
New records of planktonic cyanobacteria in New Zealand freshwaters

Abstract New records of planktonic cyanobacteria in New Zealand freshwaters are reported. Identified for the first time were one genus, Sphaerocavum, represented by one species, and one species of Apha‐nocapsa, five species of Microcystis, and three of Anabaena. Microcystis panniformis has previously been recorded only from tropical or subtropical regions. Descriptions, drawings, and photographs of species are presented.
On gene pool divergence of the brown hare (Lepus europaeus, Pallas) in Vojvodina

Today it is widely accepted that a conservation of genetic diversity increases chances of animal survival. The aim of this study was investigation of gene pool divergence of the brown hare (Lepus europaeus) in Vojvodina. Allozymic diversity of 60 brown hares from different localities in Vojvodina was studied by polyacrylamide and starch gel electrophoresis at 31 putative structural gene loci. Only five loci: Idh-2, Pgd, Pgm, Es-1 and Es-D were polymorphic, possessing 2 to 6 different alleles. The value of average heterozygosity (Ho) was 0.0427, while polymorphism (P99%) was 8.4%. Nei's values of genetic distance (ranged from 0.000 to 0.029) and modified Roger's distance (ranged from 0.030 to 0.181) were calculated among hare populations. Apart from the relatively high values of heterozygosity and polymorphism, the nuclear gene pool diversity of brown hare population in Vojvodina based on allozyme variation is low and corresponds to the data obtained for the populations in Austria and Central Europe.
The soil chemical environment along a forest primary successional sequence on the Tanana River floodplain, interior Alaska

Alkaline soils exist under forest vegetation on the Tanana River floodplain of interior Alaska. The objectives of this study were to describe the soil chemical properties and to examine controls on these chemical properties along a forest primary-successional sequence. Soil saturation pastes were prepared from duplicate sites along the successional sequence representing bare alluvium (stage I), open willow (stage III), poplar–alder (stage V), and white spruce (stage VIII). Calcium, Mg, SO4, and ions responsible for alkalinity were the dominant solutes in the saturation extracts. Soil horizons were generally calcareous (CaCO3) and therefore alkaline (pH > 7.0) across the successional sequence. The CaCO3-containing soil horizons were saturated to supersaturated with respect to calcite. Many soil horizons in the plots of stages III and V from one site were saturated with respect to gypsum (CaSO4•2H2O), whereas other stages and sites were generally undersaturated. Phosphate availability in CaCO3-containing so.
The diet of Pacific gulls (Larus pacificus) breeding at Seal Island in northern Bass Strait

Abstract. The endemic Pacific gull (Larus pacificus) is Australia’s largest larid, and though little is currently known of its foraging ecology, its size and wide distribution suggest that it may play an important role within the marine environment. In the present study, regurgitate pellets collected from Seal Island in northern Bass Strait were used to compare intra- and interannual trends in diet composition. The main taxa identified in pellets were the common diving-petrel (Pelecanoides urinatrix), leatherjacket species (Family Monacanthidae), short-tailed shearwater (Puffinus tenuirostris) and mirror bush (Coprosma repens). Analysis of similarity (ANOSIM) identified no significant differences in numerical abundance of the dominant prey species between years, suggesting that the prey base in this region is temporally consistent or that the gulls consume low enough numbers to be unaffected by fluctuation in prey populations. Diving-petrels were consumed in consistently high numbers, suggesting the gulls may be an important predator of this species, or that the gulls are particularly skilled at foraging for them.
The ATP Synthase γ Subunit.

A role in coupling proton transport to catalysis of ATP synthesis has been demonstrated for the Escherichia coli F0F1 ATP synthase γ subunit. Previously, functional interactions between the terminal regions that were important for coupling were shown by finding several mutations in the carboxyl-terminal region of the γ subunit (involving residues at positions 242 and 269-280) that restored efficient coupling to the mutation, γMet-23 → Lys (Nakamoto, R. K., Maeda, M., and Futai, M. (1993) J. Biol. Chem. 268, 867-872). In this study, we used suppressor mutagenesis to establish that the terminal regions can be separated into three interacting segments. Second-site mutations that cause pseudo reversion of the primary mutations, γGln-269 → Glu or γThr-273 → Val, map to an amino-terminal segment with changes at residues 18, 34, and 35, and to a segment near the carboxyl terminus with changes at residues 236, 238, 242, and 246. Each second-site mutation suppressed the effects of both γGln-269 → Glu and γThr-273 → Val, and restored efficient coupling to enzyme complexes containing either of the primary mutations. Mapping of these residues in the recently reported x-ray crystallographic structure of the F1 complex (Abrahams, J. P., Leslie, A. G., Lutter, R., and Walker, J. E.(1994) Nature 370, 621-628), reveals that the second-site mutations do not directly interact with γGln-269 and γThr-273 and that the effect of suppression occurs at a distance. We propose that the three γ subunit segments defined by suppressor mutagenesis, residues γ18-35, γ236-246, and γ269-280, constitute a domain that is critical for both catalytic function and energy coupling.
Poliovirus RNA-dependent RNA Polymerase (3Dpol)

Detailed studies of the kinetics and mechanism of nucleotide incorporation catalyzed by the RNA-dependent RNA polymerase from poliovirus, 3Dpol, have been limited by the inability to assemble elongation complexes that permit activity to be monitored by extension of end-labeled primers. We have solved this problem by employing a short, symmetrical, heteropolymeric RNA primer-template that we refer to as “sym/sub. ” Formation of 3Dpol-sym/sub complexes is slow owing to a slow rate of association (0.1 μm −1 s−1) of 3Dpol and sym/sub and a slow isomerization (0.076 s−1) of the 3Dpol-sym/sub complex that is a prerequisite for catalytic competence of this complex. Complex assembly is stoichiometric under conditions in which competing reactions, such as enzyme inactivation, are eliminated. Inactivation of 3Dpol occurs at a maximal rate of 0.051 s−1 at 22 °C in reaction buffer lacking nucleotide. At this temperature, ATP protects 3Dpol against inactivation with aK 0.5 of 37 μm. Once formed, 3Dpol-sym/sub elongation complexes are stable (t 1 2 = 2 h at 22 °C) and appear to contain only a single polymerase monomer. In the presence of Mg2+, AMP, 2′-dAMP, and 3′-dAMP are incorporated into sym/sub by 3Dpol at rates of 72, 0.6, and 1 s−1, respectively. After incorporation of AMP, 3Dpol-sym/sub product complexes have a half-life of 8 h at 22 °C. The stability of 3Dpol-sym/sub complexes is temperature-dependent. At 30 °C, there is a 2–8-fold decrease in complex stability. Complex dissociation is the rate-limiting step for primer utilization. 3Dpoldissociates from the end of template at a rate 10-fold faster than from internal positions. The sym/sub system will facilitate mechanistic analysis of 3Dpol and permit a direct kinetic and thermodynamic comparison of the RNA-dependent RNA polymerase to the other classes of nucleic acid polymerases.
Implications of soil substrate and land use for properties of fen soils in North-East Germany Part II: Aspects of structure in the peat soil landscape

Abstract The aim of the study was to investigate the effects of peat soil substrate governed by the hydrological type of mire, land use and state of anthropogenic changes on the fen soil structure in terms of the water retention curve, soil aggregates and topsoil strength. Our hypothesis was that morphological parameters of the peat soil landscape, like peat thickness and water table, are correlated with functional parameters of internal soil structure like water retention or cone resistance. These parameters were measured along several transects in fens of the Rhin-Havelluch and the Uckermark region. Results confirmed our hypothesis. The peat thickness was cross-correlated with the state of anthropogenic soil changes and soil structure. The type of land use (grassland, forest) had significant implications for the moisture status and structure in terms of density, strength, pore size distribution and aggregate sizes of topsoils.
Inherent Growth Capacity and Social Costs of Bluegill and Hybrids of Bluegill and Green Sunfish: Which Fish Really Grows Faster?

Abstract There is interest in knowing whether the bluegill Lepomis macrochirus or a hybrid of bluegill and green sunfish L. cyanellus (F1: male bluegill × female green sunfish; hereafter called B × G hybrids) can be grown faster to food market size (225–340 g). The predominant view is that the hybrid grows faster. In this study, the inherent growth capacities (IGCs) of age-1 bluegills and B × G hybrids were determined over four successive 25-d periods (May–August 2000) by holding them individually at 22°C and feeding them to apparent satiation three times daily. The hybrid's IGC was greater during period 1 but fell to only 33% of the bluegill's over the three subsequent periods; the consumption and gross growth efficiency (GGE) of the hybrid showed similar declining patterns. The growth-in-weight trajectory of bluegills crossed above that of the hybrids at about 30 g. Gonadosomatic index values suggested that hybrid growth rates declined below those of the bluegill because the former invested more energy .
Invasion of broad‐leaf tree species into a larch plantation: seasonal light environment, photosynthesis and nitrogen allocation

We have studied how tree seedlings with differing leaf phenological traits change their nitrogen allocation in seasonally changing light environments. Specifically, we have investigated seasonal changes in maximum leaf photosynthetic rates in situ, and changes in nitrogen, chlorophyll and ribulose-1,5-bisphosphate carboxylase oxygenase (Rubisco) content. We have also estimated nitrogen allocation characteristics from leaf nitrogen to photosynthetic proteins, light-harvesting protein and other proteins in four successional tree species growing in a larch plantation. The gap phase species, Magnolia hyporeuca Siebold et Zucc. , displays higher photosynthetic rates to compensate for the short leafy period and allocates more nitrogen to Rubisco. In contrast, tree species that grow at the forest floor, Prunus ssiori F. Schmidt and Carpinus cordata Blume, use the leafless period of the canopy trees to change their allocation of nitrogen from Rubisco to chlorophyll in line with canopy closure. Quercus mongolica Fischer ex Ledeb. var. crispula (Blume) Ohashi is a mid-successional tree species, and maintains a high photosynthetic rate in September because it allocates more nitrogen to Rubisco. We conclude that phenological differences in tree seedlings are clearly reflected in the nitrogen allocation pattern at gaps and at the forest floor in larch plantations.
Red spruce stands downwind from a coal-burning power generator: tree-ring analysis

Tree rings of red spruce (Picearubens Sarg.) in uneven-aged forest stands downwind of an SO2, source (a coal-burning power generator) were analyzed in terms of spatial and temporal trends for bole increments and elemental concentrations (Al, Ca, Mg, K, P, Mn, Zn, Fe, Ni, Cu, Cr) in xylem. Five-year core segments were pooled with respect to distance from emission source, time of wood formation, and tree age (young trees 35 years). Soil analysis was done for all stands (total of 28) by soil layer (forest floor, A and B horizons) for pH, exchangeable K, Ca, Mg, Al, and oxalate-extractable Al and Fe. Also analyzed was the snowpack at each stand at three sampling dates in February and March 1986. The snow data for pH, Ca, Mg, K, and SO4 were highly variable, with some of the variability presumably related to fallout of fly ash. The soil data were also variable, but revealed a gain of water-soluble and bicarbonate-extractable SO4, and a loss of exchangeable Mg with increasing proximity to .
Influence of Winter Annual Weed Management and Crop Rotation on Soybean Cyst Nematode (Heterodera Glycines) and Winter Annual Weeds

Abstract Certain winter annual weeds have been documented as alternative hosts to soybean cyst nematode (SCN), and infestations of such species have become common in no-till production fields in the Midwest. This research was conducted to determine the influence of herbicide- and cover-crop-based winter annual weed management systems and crop rotation on winter annual weed growth and seed production, SCN population density, and crop yield. Two crop rotations (continuous soybean and soybean-corn) and six winter annual weed management systems (a nontreated control, fall and spring herbicide applications, spring-applied herbicide, fall-applied herbicide, fall-seeded annual ryegrass, and fall-seeded winter wheat) were evaluated in no-tillage systems from fall 2003 to 2006 at West Lafayette, IN and Vincennes, IN. Fall or spring herbicide treatments generally resulted in lower winter annual weed densities than cover crops. Densities of henbit and purple deadnettle increased over years in the cover crop systems but remained constant in the herbicide systems. Averaged over sites and years, winter annual weed densities were nearly 45% lower in the spring than the fall due to winter mortality. Corn yield was reduced by the cover crops at West Lafayette but not Vincennes. Winter annual weed management system had no influence on soybean yield. SCN population density was reduced by including corn in the crop sequence but was not influenced by winter annual weed management. The density of weedy host species of SCN in the experimental area was relatively low (less than 75 plants m−2) compared to densities that can be observed in production fields. The results of these experiments suggest that inclusion of corn into a cropping sequence is a much more valuable SCN management tool than winter annual weed management. In addition, control of winter annual weeds, specifically for SCN management, may not be warranted in fields with low weed density. Nomenclature: Soybean cyst nematode, Heterodera glycines Ichinohe; corn, Zea mays L. ; soybean, Glycine max (L.) Merr; wheat, Triticum aestivum L.
PREDICTION OF LONG‐DISTANCE DISPERSAL USING GRAVITY MODELS: ZEBRA MUSSEL INVASION OF INLAND LAKES

Gravity models are commonly used by geographers to predict migration and interaction between populations and regions. Even though rarely used by ecologists, gravity models allow estimation of long-distance dispersal between discrete points in heterogeneous landscapes. We developed a production-constrained gravity model to forecast zebra mussel (Dreissena polymorpha) dispersal into inland lakes of Illinois, Indiana, Michigan, and Wisconsin (USA) based on the site and location of lakes and the number and location of boats within 364 counties. A deterministic form of this model was used to estimate best-fit parameters for distance coefficient, Great Lakes boat-ramp attractiveness, and colonization cutoff threshold. A stochastic model thus developed from these parameters allows for random changes in colonization likelihood. The results of our model are highly correlated with the actual pattern of colonized lakes in southern Michigan and southeastern Wisconsin at the end of 1997. Areas of central Wisconsin and.