Miracle-dz/UniFAR-FTUs huggingface dataset:
Species diversity in the third and fourth trophic levels: patterns and mechanisms

Etude des facteurs determinants pour la diversite des parasitoides de 285 insectes phytophages britanniques.Le niveau trophique,la niche de l'herbivore et l'architecture de la plante hote apparaissent comme des facteurs majeurs
Osteocytes Use Estrogen Receptor α to Respond to Strain but Their ERα Content Is Regulated by Estrogen

The role of mechanical strain and estrogen status in regulating ERα levels in bone cells was studied in female rats. OVX is associated with decreased ERα protein expression/osteocyte, whereas habitual strain and artificial loading has only a small but positive effect, except on the ulna's medial surface, where artificial loading stimulates reversal of resorption to formation.
Is structure or function a better measure of the effects of water abstraction on ecosystem integrity

Summary 1. Assessments of flow abstractions in streams often focus on changes to biological communities and in-stream physical characteristics, with little consideration for changes in ecosystem functioning. It is unclear whether functional indicators of ecosystem health may be useful for assessing the impacts of reduced discharge on small streams. 2. We used weirs and diversions to reduce stream discharge by over 89% in three small New Zealand streams (11–84 L s−1), ranging in water quality from pristine to moderately impaired. 3. We used both structural (benthic invertebrates) and functional (drifting invertebrates, leaf breakdown, coarse particulate organic matter (CPOM) retention and primary productivity) measures of ecosystem integrity to compare responses to water abstraction in before-after, control-impact designed experiments during summer 2005. 4. At the pristine site, the density of invertebrates, taxon richness, Macroinvertebrate Community Index (MCI), Quantitative MCI, percentage of Ephemeroptera, Plecoptera and Trichoptera individuals and percentage of filter-feeders decreased in response to reduced flows. Only taxon richness decreased at the mildly impaired stream, and reduced discharge had no effect on the invertebrate community at the stream with the lowest water quality. 5. We found that reduced discharge had little influence on the breakdown rate of willow leaves in mesh bags over 1 month. Primary productivity was also relatively insensitive to water abstraction. However, CPOM retention increased with decreased flows. Drift propensity of invertebrates increased at two sites but only within the first few days after flow reduction. 6. Structural measures of ecosystem integrity suggested that the impacts of water abstraction differed among streams of varying water quality, probably because of differences in the sensitivity of invertebrate assemblages in the three streams. In contrast, the three functional measures tested were generally less sensitive to water abstraction impacts, although understanding how stream ecosystems respond to water abstraction clearly requires that both are considered.
Comparison of Southern Appalachian high‐elevation outcrop plant communities with their Northern Appalachian counterparts

Abstract. Southern Appalachian high‐elevation outcrops harbour six regionally rare Northern Appalachian taxa usually considered relicts of a Pleistocene alpine flora. For five of the six taxa, minimum elevation in the south was 367–1113 m higher than in the north. While habitats compared between the two regions share only 9% of their total flora, individual plots had up to 70% of their species occurring in the opposite region. The northern affinity of southern outcrops increased with elevation, slope steepness, soil Cu, B and SO4 and decreased with potential solar radiation and soil Na. As a result, communities above 1600 m on felsic bedrock, and above 1350 m on mafic bedrock, were most northern in composition. Northern affinity of southern outcrops also increased with latitude, which may partly result from closer geographic proximity to past communities that provided progenitors for the current northern flora. Northern treeless habitats increased in southern affinity with increased slope steepness, perennial seepage, vegetation height, shade, soil pH, Al, Mn, Na and decreased elevation and organic matter. As a result, northern outcrop communities below treeline were most similar to those on southern outcrops. This suggests that southern outcrop vegetation may be more similar to Pleistocene outcrop vegetation than to Pleistocene alpine vegetation. Partial constrained ordination showed that while compositional differences between the Northern and Southern Appalachian habitats were largely explained by environmental differences, there was a significant component of residual variation explained by north or south position that was unrelated to environment. These residual compositional differences may result from historical influences on community structure involving stochastic extinction and colonization processes.
Relationship between post‐fire regeneration and leaf economics spectrum in Mediterranean woody species

Summary 1Recent work has identified global-scale relationships between key leaf traits (leaf economics spectrum). However, it is important to determine whether this approach can be applied at local scale with smaller subsets of species facing similar environments. Since fire is a key process in Mediterranean shrubland dynamics we analyze whether fire-related life-history traits influence the pattern of correlation between the leaf economic spectrum and leaf moisture traits. 2Using structural equation modelling and exploratory path analysis, we developed alternative models to test how interspecific leaf traits are related to the seasonal variation of water content (leaves and shoots) and to the type of post-fire regeneration of Mediterranean woody species. 3This study demonstrates that for these species seasonal variation in water content and fuel moisture would be better predicted by the presence or absence of a trait describing post-fire seedling establishment than by the leaf economic spectrum traits. However, leaf dry matter content (LDMC) is influenced by both the leaf economic spectrum and the post-fire regenerative type. 4Seeder species (those that recruit via seeds immediately after fire) present lower LDMC and higher relative seasonal variation of relative water content (RWCrsv) than non-seeders. We hypothesize that since seeder species mostly evolved under the Mediterranean climate, they developed a particular strategy of drought tolerance (without causing an effect to the relation between the volume occupied by cytoplasm relative to the volume occupied by cell walls), which is the cause of the observed relation between LDMC and RWCrsv. 5This study suggests that the leaves of Mediterranean woody species would follow the general leaf economics spectrum (Wright et al. 2004) but that specific selective forces, such as disturbance regime, acting at regional scale also play a relevant role to explain leaf traits related to water content.
The role of proline dehydrogenase and Δ1-pyrroline-5-carboxylate dehydrogenase in the regulation of proline homeostasis in Gracilaria tenuistipitata (Gigartinales, Rhodophyta) exposed to high temperature

Abstract The role of proline dehydrogenase (PDH; EC 1.4.3.1) and Δ1-pyrroline-5-carboxylate dehydrogenase (P5CDH; EC 1.5.1.12) in the regulation of proline homeostasis was investigated in Gracilaria tenuistipitata var. liui Zhang et Xia exposed to elevated temperature (35°C). On exposure to 35°C, proline accumulated accompanied by a decrease in the specific activity of PDH. During recovery to 25°C, the levels of proline that accumulated at 35°C (4 d) decreased within 1 d, and concomitantly the specific activity of PDH recovered. The changes in PDH activity were inversely related to the changes in proline levels. However, the specific activity of P5CDH remained unchanged when exposed to 35°C or during recovery to 25°C. The apparent Km (for proline) value of partially purified PDH for 35°C-treated thalli was about fourfold that of 25°C-treated thalli, whereas the apparent Vmax value was similar in 25°C- and 35°C-treated thalli. The apparent Km (for pyrroline-5-carboxylate) value of partially purified P5CDH .
Antioxidant Activity of the Phycoerythrobilin Compound Formed from a Dried Korean Purple Laver (Porphyra sp.) during in Vitro Digestion

To evaluate the accessibility and function of phycoerythrin (a purple-pigment protein) found in purple laver (Porphyra sp.), antioxidant activity of the phycoerythrobilin compound (chromophore of the pigment protein) formed from the dried Korean purple lavers was determined by in vitro digestion. Results suggest that the apoprotein of phycoerythrin is readily digested to release the phycoerythrobilin compound during the gastrointestinal digestion process of mammals. The peroxy radical scavenging capacity was 2.7-fold greater in the phycoerythrobilin compound than in the purple laver extracts. The various therapeutic activities of phycoerythrin appear to be associated with the phycoerythrobilin compound released during mammalian gastrointestinal digestion.
Laccase Production and One-electron Oxidation Activity in Wood Degradation by the Soft-rot Deuteromycete Graphium sp

The mechanism of wood degradation by the soft-rot deuteromycete, Graphium sp. , was investigated. One-electron oxidation activity, assayed by ethylene generation from 2-keto-4-thiomethylbutyric acid (KTBA), and phenol oxidase activity were measured in intact cultures and in Sephadex G-50 fractions from the acetone-precipitated extracellular media, with glucose or wood as the carbon source for the cultures. Both the one-electron oxidation activity and the phenol oxidase activity were higher in wood cultures than in glucose cultures. Most of the phenol oxidase activity in wood cultures appeared to derive from laccase. Most of the ethylene generation from KTBA was attributed to hydroxyl radicals, produced by a lowmolecular-weight substance in the extracellular media. This substance was composed of peptides, carbohydrates, and Fe (II), and catalyzed redox reactions between O2 and unidentified electron donors, to produce hydroxyl radicals via H2O2. It is suggested that hydroxyl radicals may produce new phenolic substructures on the lignin polymer, making it susceptible to attack by laccase. Thus, both one-electron oxidation activity and laccase activity are important in wood degradation by Graphium sp.
The role of nitric oxide in priming-induced low-temperature tolerance in two genotypes of tomato

Abstract The present study was conducted to evaluate the contribution of nitric oxide (NO) to the priming effects on seed germination, seedling vigour and low-temperature tolerance of two tomato cultivars (Solanum lycopersicum, cv. Cherry and Falcato) under four different constant temperatures (10, 15, 20 and 25°C). Treatments included priming in a polyethylene glycol 6000 (PEG 6000) solution (osmopriming) or presoaking in sodium nitroprusside (SNP) solution, a donor of NO, for 24 h at 25°C. Suboptimal temperatures reduced seed germination and subsequent seedling growth, as well as amylase activity, in both cultivars, but Falcato was more sensitive to low temperature than Cherry. Both osmopriming and SNP treatments enhanced germination capacity, germination index, seedling root and shoot length, α- and β-amylase activities and sugar content under suboptimal temperatures, especially in Falcato. We observed similarities between the modes of action of the two priming treatments. Both treatments increased seed NO content, whereas their positive effects on germination and subsequent seedling growth under low-temperature stress was reversed by the addition of methylene blue (MB), a scavenger of NO. This is the first report that suggests that positive effects of priming are most likely mediated through NO signalling.
Inheritance of Low Linolenic Acid Content in Zero-Erucic Acid Ethiopian Mustard

Zero-erucic acid Ethiopian mustard (Brassica carinata A. Braun) seed oil has very high linolenic acid content (210 g kg –1 ), which confers low oxidative stability to the oil. The line AB4 with low linolenic acid content ( 23 g kg –1 ) ratio, which suggested segregation of alleles at three independent loci. The three-gene model was confi rmed in the analysis of linolenic acid content in F 2:3 families. Nine out of 341 F 2:3 families had stable low linolenic acid content, which fi tted the 1:63 ratio observed in
Cellulose and xylan degrading enzymes of the plant pathogenic fungus, Fusarium oxysporum SUF850.

Strains producing higher levels of cellulolytic enzymes were selected from among 520 strains of plant pathogenic fungi, Fusarium species, and F. oxysporum strain SUF850 was found to be the best producer. When strain SUF850 was cultured using one of three polysaccharides, Avicel, carboxy- methyl cellulose (CMC) or xylan, as a carbon source, the culture filtrate contained degrading activi- ties toward all three substrates, i.e., irrespective of the carbon source used. From the culture filtrate of Avicel-grown cells, four distinct enzymes were purified to homogeneity, as judged on SDS-PAGE. They were designated as CMCase I, CMCase II, /Miitrophenyl-β-d-cellobiosidase and xylanase, and the characteristics of the individual enzymes were examined and compared.
THE ENDOPHYTIC FUNGAL COMMUNITY IN LEAVES OF A COASTAL REDWOOD POPULATION-DIVERSITY AND SPATIAL PATTERNS

SUMMARY Leaf endophytic fungi were isolated from 1 to 12-yr-old leaves of mature trees and basal sprouts of coastal redwood [Sequoia sempervirens (D. Don ex Lamb.) Endl. ] in a redwood forest in Central California. Almost all samples yielded at least one species. The two most frequent species were Pleuroplaconema sp. and Cryptosporiopsis abietina Petrak. Among isolated taxa are endophytic generalists, species previously known as pathogens and a possible specialist. Species composition in leaves of progressing age in single branches revealed a patchy pattern of leaf colonization without an obvious sequence of succession. Changes in diversity and equitability in the endophytic community with leaf age are linked with differential distribution of some species in young versus old leaves and the increase in species richness in 4- and 5-yr-old leaves. The endophytic communities from leaves of trees and sprouts were generally similar, but with important differences in species richness and in distribution of Pleuroplaconema sp. and Pestalotiopsis funerea (Desm.) Stey. Principal component analysis based on endophytic frequency also indicated closeness of trees and sprouts as groups, but clearly separated each tree from its sprout. Differential susceptibility between trees and sprouts to endophytic infection is suggested on the basis of their endophytic communities.
Soil allelochemical residue effects of nemafric-BL and nemarioc-AL phytonematicides on soil health, growth of sweet sorghum and Meloidogyne species

A field trial was initiated to investigate the post-treatment effects of soil allelochemical residue (SAR) of nemafric-BL and nemarioc-AL phytonematicides on soil health, growth of sweet sorghum (Sorghum bicolor) and population densities of Meloidogyne species. SAR conditions were created in tomato (Solanum lycopersicum) trials, with treatments comprising untreated control, nemafric-BL 3%, nemafric-BL 6%, nemarioc-AL 3% and nemarioc-AL 6%, which were applied at empirically established intervals for a 56-day crop cycle. Soil preparation was followed by a 30-day fallow to allow for microbial decomposition of root remnants. Sweet sorghum seeds were sown on spots where tomato plants grew and soil samples were collected for determining the soil health status at two-leaf stage. At 80 days after sowing, SAR effects improved soil health and contributed 8% in total treatment variation (TTV) of chlorophyll and sugar contents each in sweet sorghum, with nemarioc-AL 3 and 6% phytonematicides stimulating improvement of the two variables. Nemafric-BL SAR effects had no effect on growth of sweet sorghum. In contrast, SAR effects contributed 76 and 39% in TTV of nematode population densities in root and soil, respectively. SAR effects of nemafric-BL and nemarioc-AL inhibited nematode numbers by 67–97% and 64–80%, respectively. In conclusion, SAR effects on soil health, plant growth and nematode population densities were desirable, suggesting that the two products were each still active in the soil.
Feeback between Plants and Their Soil Communities in an Old Field Community

The nature of the interaction between plants ant their soil community was investigated by testing for differential responses of four old—field perennial plant species to inocula derived from soil communities that had been grown with ("cultured by") one of these four plant species. The differentiation of the soil communities was evident in measurements of plant survival, phenology, growth, and root—shoot ratios. Effects on survival and growth suggest negative feedbacks between these species and the soil communities that they culture. Survival rates of Krigia dandelion were significantly reduced when grown with their own" soil community. Considered as a whole, the three other species (all grasses) had significantly lower growth and root—shoot ratios when grown with soil communities started with their own inocula compared to soil communities started with the inocula of other species. However, the significance of this effect on growth rate and root—shoot ratios was due primarily to the pairwise comparison of Anthoxanthum odoratum and Danthonia spicata and of Anthoxanthum and Panicum sphaerocarpon, respectively. Pairwise comparisons of Danthonia and Panicum do not suggest differential responses to each other's soils in growth rate or root—shoot ratios nor do soil communities appear to affect the relative competitive ability of these two species. While the components of the soil community responsible for these effects have not been identified, similar although less pronounced patterns were observed in experiments using inocula consisting of washed live root segments as compared to experiments using whole soil as inoculum, suggesting that root pathogens are one important agent.
Interaction between p85 and Rab5 in the presences and absence of phosphorylated PDGFR peptide

ii ACKNOWLEDGEMENTS iii TABLE OF CONTENTS v LIST OF FIGURES viii LIST OF ABBREVIATIONS x 1.0 INTRODUCTION 1 1.1 Signal Transduction Pathways 1 1.2 Receptor Tyrosine Kinases 2 1.3 Phosphatidylinositol 3'-kinase (PI3K) 5 1.4 Endocytosis 8 1.5 Rab Proteins 9 1.5. 1 p85 is a Rab5GAP 15 1.5. 2 Tau Proteins Have a Rab5GAP Activity 16 1.6 Protein-Protein Interactions 20 1.7 Surface Plasmon Resonance 21 2.0 HYPOTHESIS AND OBJECTIVES 24 2.1 Hypothesis 24 2.2 Objectives 24 3.0 MATERIALS AND METHODS 26 3.1 Reagents and Supplies 26 3.2 Methods 26 3.2.1 Bacterial Strains and Growth Media 26 3.2.2 Eukaryotic Cell Lines and Growth Media 27 3.2. 3 Purification of GST-Fusion Proteins 28 3.2. 3.1 Ion Exchange Chromatography 29 3.2. 3.2 Dynamic Light Scattering 29 3.2. 4 Purification of His6-tagged Proteins 30
Redescription of Elthusa emarginata (Bleeker, 1857) (Crustacea, Isopoda, Cymothoidae), type species of the genus Elthusa Schioedte & Meinert, 1884

Abstract Elthusa emarginata (Bleeker, 1857) (Crustacea, Isopoda, Cymothoidae), type species of the genus Elthusa Schioedte & Meinert, 1884, is redescribed according to the specimen observed by Schioedte & Meinert (1884) extant in the National Museum of Natural History in Paris, here designated as lectotype, and from some additional specimens collected in Indonesia on goatfishes belonging to the genus Parupeneus (Perciformes, Mullidae). This study allows an updating of the diagnosis of the genus Elthusa.
Biomolecular Databases

During the past two decades, computerized biomolecular databases have rapidly expanded and have been prominently integrated into laboratory work in biological sciences. This article offers an exploratory look at the potential significance of these databases as novel tools for scientific communication. The article develops the concept of a science communication regime—a sociotechnical system that constitutes a particular means of scientific communication, such as the scientific journal. This concept is then used to examine biomolecular databases and their potential implications for scientific institutions and practices. The field of genome research provides empirical examples, and the discussion explores the potential significance of these new forms of electronic communication.
Hyphomicrobium indicum sp. nov. (Hyphomicrobiaceae Douglas)

ABSTRACT During the eighth cruise of the R/V Anton Bruun, as part of the International Indian Ocean Expedition a bacterium was isolated from bottom mud at a depth of 400 meters. The extreme pleomorphism of this organism commended it for detailed study. It was subsequently named Hyphomicrobium indicum and a comparative study with other Hyphomicrobium sp. undertaken.
Cloning, sequencing, and mapping of an α-actinin gene from the nematode Caenorhabditis elegans

The dense-bodies in the body wall muscle of the nematode Caenorhabditis elegans function to anchor the actin thin filaments to the adjacent sarcolemma. One of the major components of the dense-bodies is the actin-binding protein alpha-actinin. To facilitate a genetic analysis of alpha-actinin, we have cloned a cDNA encoding the nematode protein, identified its position on the nematode physical map, and developed a unique PCR based approach to test the position of the cloned gene relative to known genetic deletions. The peptide sequence deduced from the cDNA shows that, apart from a few exceptional regions, the nematode protein shows strong similarity to other known alpha-actinins. Its position on the genetic map shows that none of the known muscle affecting mutations identified in C. elegans are in this alpha-actinin gene. This gene has been given the name atn-1 (alpha-actinin-1).
Activity of Enzymes Related to H2O2 Generation and Metabolism in Leaf Apoplastic Fraction of Tomato Leaves Infected with Botrytis cinerea

Hydrogen peroxide generation rates of uninfected and infected leaves of two tomato (Lycopersicon esculentum) cultivars showing differential susceptibility to Botrytis cinerea were determined. The superoxide anion, hydroxyl radical, ascorbate contents and changes in NADH peroxidase, superoxide dismutase (SOD), ascorbate peroxidase (APX) and catalase (CAT) activities in the apoplast fraction were analysed. Infected leaves had an increased hydrogen peroxide level. It was greater and generally occurred earlier in plants of the less susceptible cv. Perkoz than in those of the more susceptible cv. Corindo. Induction of nitrotetrazolium blue reducing activity and SOD levels in apoplast were higher in cv. Perkoz 24 h after inoculation. In the controls, NADH peroxidase activity in apoplast was higher in the more susceptible cv. Corindo, but after infection it increased faster and to a higher level in the less susceptible cv. Perkoz. NADH oxidation was inhibited by only 15% by a specific inhibitor DPI (diphenylene-iodonium) but was completely inhibited by KCN and NaN 3 . Similar increases in APX activity after 48 h and a small increase in catalase activities were observed in both cultivars soon after infection. These results indicate that resistance of tomato plants to infection by the necrotrophic fungus B. cinerea may result from early stimulation of hydrogen peroxide and superoxide radical generations by NADH peroxidase and SOD in apoplastic space, and they confirm the important role of their enhanced production in apoplastic spaces of plants.