Miracle-dz/UniFAR-FTUs huggingface dataset:
Satellite DNA sites in four species of the genus Astyanax (Teleostei, Characiformes)

Cytogenetic data about satellite DNA distribution in four Astyanax species (Characidae) from the Paraitinga river, Paraiba do Sul river basin, Brazil, are presented. In order to characterize the constitutive heterochromatin, C-banding, chromomycin A3 and DAPI fluorescence staining, as well as fluorescence in situ hybridization (FISH) with the satellite DNA As-51 probe were performed. A. scabripinnis and A. parahybae presented 2n = 50 and 2n = 48 chromosomes, respectively. The heterochromatin was located in the pericentromeric and terminal regions of many chromosomes, corresponding to GC-positive regions and to the As-51 satellite DNA in terminal regions. A. intermedius and A. giton, both with 2n = 50 chromosomes, showed little heterochromatin, mostly restricted to the terminal and pericentromeric regions of a few chromosomes. No GC-positive regions, neither any correspondence between the scarce heterochromatin of these species and the As-51 satellite DNA was observed. AT-positive blocks were not detected in any of the species studied. Based on these and other available data, the hypothesis that Astyanax represents a polyphyletic group is discussed.
The Composition of Mixed-Species Bird Flocks in Alto Quindío, Colombia

Abstract Mixed-species bird flocks are a prevalent characteristic of Andean avian communities. We describe the species composition of mixed-species bird flocks observed in a high mountain zone (3,000 to 3,450 m) of Quindío, central Andes, Colombia. The total number of species observed in mixed-species flocks was 42, and the mean number of species and individuals per flock were 5.1 and 11.5, respectively. Flock species composition was similar along the elevation gradient studied. Our observations suggest that five species (Margarornis squamiger, Iridisornis rufivertex, Conirostrum sitticolor, Mecocerculus stictopterus, and Diglossa cyanea) could be nuclear species in the flocks.
A new assessment of European forests carbon exchanges by eddy fluxes and artificial neural network spatialization

Recently flux tower data have become available for a variety of ecosystems under different climatic and edaphic conditions. Although Flux tower data represent point measurements with a footprint of typically 1 km × 1 km they can be used to validate models and to spatialize biospheric fluxes at regional and continental scales. In this paper we present a study where biospheric flux data collected in the EUROFLUX project were used to train a neural network simulator to provide spatial (1 km × 1 km) and temporal (weekly) estimates of carbon fluxes of European forests at continental scale. The novelty of the approach is that flux data were used to constrain and parameterize the neural network structure using a limited number of input driving variables. The overall European carbon uptake from this analysis was 0.47 Gt C yr−1 with distinctive differences between boreal and temperate regions. The length of the growing season is longer in the south of Europe (about 32 weeks), compared with north and central Europe, which have a similar length‐growing season (about 27 weeks). A peak in respiration was depicted in spring at continental scale as a coherent signal which parallel the construction respiration increase at the onset of the season as usually shown by leaf level measurements.
Assay of ascorbic phosphates and in-vitro availability assay of ascorbic mono- and polyphosphates.

A method was devised to assay ascorbic phosphate esters in biological materials by potassium bromoxide hydrolysis followed by determination of the liberated ascorbic acid. For the differential measurement of ascorbic acid and ascorbic phosphate, a spectrophotometric method was employed to screen out the interfering substances based on studies of absorbance curves of 2,4-dinitrophenyl hydrazine derivatives. A variety of vertebrate tissues were examined for phosphatase activity on ascorbic phosphate esters. The results suggest that pigeon kidney, rat liver and several tissues of fishes readily hydrolyse ascorbic monophosphate but not ascorbic polyphosphate. Hydrolysis of ascorbic monophosphate is completed by both phosphatases of intestine, kidney and liver acting at neutral pH and phosphatase of stomach acting at acid pH. Thus, ascorbic monophosphate has the potential to be a source of available vitamin C in vivo, and this explains its antiscorbutic activity in scurvy-prone animals.
Comparing pellet and stable isotope analyses of nestling Bonelli's Eagle Aquila fasciata diet

Diet analyses are central to the study of avian trophic ecology, and stable isotope analyses have made an increasing contribution in the last two decades. Few isotopic studies have assessed the diet of raptor species, which are more frequently analysed by conventional diet methods such as pellet analysis. In this study, we compare prey consumption estimates of nestling Bonelli’s Eagles Aquila fasciata from conventional pellet analysis (in terms of items and biomass) and stable isotopic mixing models (SIAR) using d 13 C, d 15 N and d 34 S of feathers. The pellet analysis showed that European Rabbits Oryctolagus cuniculus, pigeons (mainly Common Wood Pigeons Columba palumbus and Domestic Pigeons Columba livia dom.), Red-legged Partridges Alectoris rufa, passerines, Yellowlegged Gulls Larus michahellis and Eurasian Red Squirrels Sciurus vulgaris were the main prey, so they were selected for diet reconstructions in SIAR. At the population level, mean prey consumption estimates were similar for pellets (both items and biomass) and SIAR. At the territory level, the weighted kappa statistic showed good ordinal scale agreement in main prey consumption between items or biomass and SIAR. Although the intraclass correlation coefficient showed poor method agreement when considering all prey in the same analysis, the intraclass correlation coefficients for each prey category showed significant agreement between pellets and SIAR when estimating the consumption of Rabbits, pigeons and Gulls, with lower agreement for passerines and Squirrels. Lastly, there was poor method agreement for estimates of Partridges. Our results suggest an overall agreement between the pellet analysis and SIAR when estimating nestling Bonelli’s Eagle diet at both the population and, to a lesser extent, the territory level, supporting the usefulness of isotopic mixing models when identifying the terrestrial and marine components of raptor diets.
Phosphorus and Amylose Branching in Rice Starch Granules

Phosphorus content of rice starch granules prepared by DoBS extraction of milled rice protein was lowest and was mainly 6-phosphoglucose for 2 waxy rices. For 6 nonwaxy rices it was highest and predominantly phospholipid P based on choline content. Defatting with water-saturated butanol reduced both choline and P content of nonwaxy rice starch. Once recrystallized amylose of 7 rices had 72–84% β-amylolysis limit, DP 532–793 glucose units per reducing end, CL 101–157 glucose units per nonreducing end and 3.4–7.5 branches/molecule. Phosphor und Amyloseverzweigung in Reisstarkekornern. Der Phosphorgehalt von Reisstarkekornern, die durch Natrium-Dodecyl-Benzolsulfonat-Extraktion (DoBS) des gemahlenen Reisproteins vorbehandelt wurden, war am niedrigsten und lag bei 2 wachsigen Reissorten uberwiegend in Form von Glucose-6-phosphat vor. Bei 6 nicht-wachsigen Reissorten war er am hochsten und basierte als Phosphorlipid-Phosphor vorwiegend auf dem Cholingehalt. Die Entfettung mit wassergesattigtem Butanol verminderte sowohl den Cholin-als auch den Phosphorgehalt der nicht-wachsigen Reisstarke. Die einmal rekristallisierten Amylosen von sieben Reissorten hatten β-Amylolysegrenzen von 72–84%, Polymerisationsgrade (DP) von 532–793 Glucoseeinheiten je reduzierendem Ende, mittlere Kettenlangen (CL) von 101–157 Glucoseeinheiten je nicht-reduzierendem Ende und 3,4–7,5 Verzweigungen je Molekul.
The MMTV-PyVT Transgenic Mouse as a Multistage Model for Mammary Carcinoma and the Efficacy of Antineoplastic Treatment

Animal models are commonly used to analyze the mechanism of carcinogenesis as well as the development and screening of potent drugs. Although numerous animal models of breast cancer have been used in research, few display multiple stages of tumorigenesis. The transgenic strain FVB/N-Tg(MMTV-PyVT) 634 Mul/J (also known as PyVT) was established to determine the effect of mammary gland-specific expression of the polyomavirus middle T antigen. Here the PyVT model with three distinct stages of tumor development (Pre, Early, and Late stages) was used as a model system for measuring tumor growth, tumor burden, and metastasis of mammary carcinomas. Additionally the expression profile of the molecular markers, survivin and Ki-67, was determined. Three antineoplastic compounds were tested over a 14-day period to determine their efficacy at attenuating tumor growth at each stage of development. Interestingly cisplatin and paclitaxel were determined to be ineffective anticancer drugs, while tamoxifen significantly reduced tumor growth in the Pre and Early stages of tumor formation.
Effect of hydroperiod on seed-bank composition in semipermanent prairie wetlands

Bottom samples were collected from two semipermanent prairie wetlands to determine if known hydroperiod differences were reflected in seed-bank composition. Samples were also taken a 2nd year in one wetland to assess between-year variation. Seed density and composition were determined by counting and identifying seedlings that emerged from samples placed in a greenhouse. Most seed-bank characteristics were statistically indistinguishable between wetlands, including floristic composition and total seed density. A significant difference occurred, however, in the relative importance of mudflat annuals and emergents. The mudflat group was much more abundant in the wetland with the shorter hydroperiod (82 vs. 51%). More frequent exposure of the substrate probably yielded greater seed production. Also, a longer hydroperiod depressed seed density in the open water zone (open water zone, 1309 seeds/m2; two emergent zones, 2840 and 9893 seeds/m2). A seed-bank assay may detect subtle hydroperiod differences among w.
Geographic Variation Analysis of Dipodomys ordii Using Nonmetric Cranial Traits

Geographic variation in 18 nonmetric cranial traits was assessed for 11 populations of Dipodomys ordii from Oklahoma, Texas, and New Mexico. Frequencies of all traits were examined for sex, size, and side dependencies in a geographically restricted sample of 272 crania. Two traits were significantly affected by sex, two by cranial size, and two exhibited different frequencies on the left side of the skull than on the right. Relatively few within-individual and among-population intertrait correlations were found. The distance measure used in testing for interpopulation trait frequency differences was the Mean Measure of Divergence (MMD), as modified by Green and Suchey (1976). Nonmetric multidimensional scalings of distance matrices derived from each of four trait subsets and a principal components analysis based on one subset gave similar results. The 11 samples were displayed in three-dimensional summaries approximately as expected on the basis of their geographic distribution. Because nonmetric traits may be adaptively neutral, frequency differences between populations may result from genetic drift. Nonmetric traits are clearly of value in studies of geographic variation in Dipodomys . I follow Sjovold (1977) in suggesting that consideration be given to each trait with regard to how strongly it is influenced by dependencies (e.g., sex and size) that may confound interpretation of results.
Population genetic structure and genetic variability of the marbled sole Pleuronectes yokohamae on the coast of Gyeongsangnam-do, Korea

Abstract This study uses the mitochondrial DNA control region to identify the genetic diversity and population structure of the marbled soles (Pleuronectes yokohamae) that inhabit Jinhae Bay and Yokji Island in the nearby sea and the adjacent waters of Namhae, Hansan Island, and Jaran Bay. Direct sequencing of the PCR products revealed 379 bp sequences with 83 variable nucleotide sites, defining a total of 91 haplotypes. The haplotype diversity was high, ranging from 0.917 ± 0.031 to 0.983 ± 0.008, and nucleotide diversity ranged from 0.015 ± 0.008 to 0.024 ± 0.012. In addition, 48 haplotypes (52.7%) were unique. Pairwise F ST values were very low, with the maximum value occurring between PYH (Hansan Island) and PJI (Jinhae Bay) (F ST = 0.011). Therefore, no significant genetic differentiation was evident between any pair of sampling localities.
Comparative proteomic analysis of Orobanche and Phelipanche species inferred from seed proteins

Orobanche and Phelipanche species are root parasitic plants some of which infect important crops, causing extensive damage. In an attempt to unravel molecular systematic in these genera using protein markers, we established the protein profile of twelve species by two-dimensional gel electrophoresis (2-DE). Proteins were detected by Sypro Ruby staining and the gel images were digitalised and analysed. The 2-DE maps contained from 30 to 140 protein spots for the analysed species. A virtual master gel was built with spots present in all species and revealing the presence of 260 protein spots. Only one protein was monomorphic, while 143 were unique to a single species. Proteins were scored for the presence or absence of homologous spots to create a binary matrix. Phylogenetic analysis was carried out using maximum parsimony and distance method. The trees obtained were rooted using Cistanche phelypaea as an out-group. Both analyses showed Orobanche as a monophyletic group. AMOVA analysis revealed phenotypic diversity between species within genera, as well as a considerable level of variation between genera. This is a first step to help in the phylogenetic classification of parasitic plants by means of proteomics.
Vegetation Similarity and Avifaunal Food Value of Restored and Natural Marshes in Northern New York

Measuring the success of wetland restoration efforts requires an assessment of the wetland plant community as it changes following restoration. But analyses of restored wetlands often include plant community data from only one time period. We studied the development of plant communities at 13 restored marshes in northern New York for 4 years, including 1 year prior to restoration and 3 years afterwards. Restored wetlands ranged in size from 0.23 to 1.70 ha. Four reference wetlands of similar basin morphology, soil type, and size (0.29–0.48 ha) that occurred naturally in the same area were studied as comparisons. Dike construction to restore hydrology disturbed the existing vegetation in some parts of the restored sites, and vegetation was monitored in both disturbed and undisturbed areas. Undisturbed areas within the restored sites, which were dominated by upland field grasses before restoration, developed wetland plant communities with lower wetland index values but comparable numbers of wetland plant species than the reference wetlands, and they lagged behind the reference sites in terms of total wetland plant cover. There were significantly more plant species valuable as food sources for wetland birds, and a significantly higher percent cover of these species, at the undisturbed areas of the restored sites than at the reference wetlands. Areas of the restored sites that were disturbed by dike construction, however, often developed dense, monospecific cattail stands. In general, the plant communities at restored sites became increasingly similar to those at the reference wetlands over time, but higher numbers of herbaceous plants developed at the restored sites, including food plants for waterfowl, rails, and songbirds. Differences in shrub cover will probably lessen as natural recolonization increases shrub cover at the restored sites. Natural recolonization appears to be an effective technique for restoring wetlands on abandoned agricultural fields with established plant cover, but it is less successful in areas where soil has been exposed by construction activity.
Recent advances in the discovery and development of stilbenes and lactones in anticancer therapy

The stilbene and lactone moieties are important components of a number of compounds that have potential therapeutic roles in many areas including anticancer therapy. Since the significance of these moieties were recognised, a myriad of structurally-related or different analogues have been studied and tested against various pharmacological modalities that may provide novel targets in therapies, for example in conditions where insufficient apoptosis leads to the formation of cancer. Recently, there have been a number of studies directed at the search for novel anticancer compounds incorporating stilbene and/or lactone moieties. The particular aim of this review is to focus on, and summarise, selected patents from 1999 – 2003 on stilbenes and lactones with anticancer properties.
Data transformation and standardization in the multivariate analysis of river water quality

Multivariate approaches are being increasingly applied to aquatic studies; however, their ecological relevance has not been adequately addressed. This paper examines the effects of data transformation and standardization on principal-components analysis (PCA) of river water quality. Two currently popular methods, log(x + 1) and standardizing to 0 mean and 1 variance, were evaluated. The choice of the data-handling methods substantially affected the analytic output. However, both methods tested were found to be flawed, with the major problem being disregard for the biological/ecotoxicological significance of water-quality variables and their ranges. We developed a new standardization model, which incorporates water quality standards into data standardization. This provides a mechanism to improve the biological relevance of multivariate analysis. The new model-based PCA yields an assessment of water quality that is more ecologically meaningful than any others tested. We discuss the ecological implications o.
Levels of dispersal and tail loss in an Australian gecko (Gehyra variegata) are associated with differences in forest structure

Corridors of natural habitat are often sought to maintain dispersal and gene flow among habitat patches. However, structural changes in natural habitat over space and time may influence connectivity. Here we investigate whether differences in forest structure and the frequency of potential retreat sites is associated with the genetic structure of a tree-dwelling Australian gecko (Gehyra variegata). We sampled 113 adult geckos from multiple state forest and adjacent reserve locations within the Pilliga forest, New South Wales, Australia. Individuals were genotyped at 14 microsatellite loci and levels of dispersal were inferred by the degree of genetic structuring observed in state forest and reserve. A greater proportion of dead trees and tree debris (features that are used as retreat sites by G. variegata) were present within the state forests than in the reserve locations (P < 0.05). This reduction in frequency of retreat sites in reserves was associated with significantly less genetic structuring of G. variegata, implying higher levels of dispersal. Tail loss was also significantly higher in G. variegata sampled in reserves than in the state forests. We conclude that dispersal characteristics in G. variegata are associated with structural changes to natural habitat and that this may influence rates of predation.
PATTERNS AND CONTROLS OF PRIMARY PRODUCTION IN THE PATAGONIAN STEPPE: A REMOTE SENSING APPROACH†

We took advantage of regional gradients to study the spatial relationships between aboveground net primary production (ANPP) and climate in the Patagonian steppe of South America. We explored the same relationships through time, considering the natural variations of ANPP and climate for 11 yr. Based on NOAA/AVHRR satellite normalized difference vegetation index (NDVI) data, we evaluated the effects of climate on annual and seasonal ANPP across regional gradients of precipitation (100-500 mm/yr) and tem- perature (218-98C of annual mean). We studied ANPP climatic controls through time at four sites using NDVI and meteorological data. We used annual NDVI integral as a surrogate of annual ANPP. Annual NDVI integral increased linearly along regional gradients of precipitation, and its annual variability de- creased exponentially. Annual NDVI integral was, in most cases, unrelated to precipitation through time. We described the seasonality of ANPP using four variables derived from seasonal NDVI curves: the dates of growing season start and end, the date of maximum NDVI, and the length of the growing season. The growing season started later toward the cold extreme of the regional temperature gradients and, within a given site through time, during the coldest years. The dates of maximum NDVI and end of the growing season occurred later toward the humid or cold extremes of the regional gradients, whereas the length of the growing season was positively affected by precipitation and temperature along these gradients. These variables were not associated with climate through time. The response of the start of the growing season to temperature was greater in time, following the natural climatic fluctuations, than in space, accompanying regional temperature gradients. This difference probably resulted because the time required for shifts in community composition and plant adaptation is longer than one year. Climatic determinants of ANPP shifted from precipitation alone to precipitation plus temperature when the temporal scale of analysis changed from annual to seasonal. Our results indicate the feasibility of forecasting forage availability a few months prior to the beginning of the growing season, but not during the whole year. Longer term data sets and manipulative experiments are required to forecast annual ANPP and predict its response to climate change.
Daytime variation in T‐cell‐mediated immunity of Eurasian kestrel Falco tinnunculus nestlings

Host-parasite interactions are central in evolutionary and behavioural ecology. In the last few years, skin injections of the mitogen Phytohaemagglutinin (PHA) have become one of the most important and widely used in-vivo assays of immune function in birds. However, there are no studies of the circadian variation suggesting that care should be taken interpreting results when using this technique. This 3-year study assessed PHA responses as a function of daylight time in 310 Eurasian kestrel Falco tinnunculus nestlings at 24 days of age in Central Spain. I found that T-cell-mediated immunity was positively related to nestling mass and varied among years. Controlling for these variables, I also found that T-cell-mediated immunity decreased with the hour of sampling, and that this pattern was consistent between years. In addition, I found that at the end of the day only, T-cell-mediated immunity decreased with brood size. Parasites seem not to be behind this pattern, but I suggest that the cumulative effect of sibling competition during the day might explain the decrease of cellular immunity with the hour of sampling. Thus, I strongly recommend that future studies of cellular immunity should control for this potential source of variation when nestling self-maintenance is evaluated by the PHA-induced skin-swelling response.