Miracle-dz/UniFAR-FTUs huggingface dataset:
Drivers of pollen limitation: macroecological interactions between breeding system, rarity, and diversity

Background: Plant species in biodiversity hotspots suffer more from pollen limitation than those in lower diversity regions, though this pattern is largely restricted to self-incompatible species. It is unknown whether higher pollen limitation is due to increased pollinator sharing or declines in pollinator abundance. Aims: Macroecological examinations of pollen limitation have been challenged by statistical confounds of phylogenetic non-independence and interrelationships between variables. Here, we perform phylogenetically corrected analyses of pollen limitation, examining an ensemble dataset of endemicity, abundance, species diversity, breeding system, floral symmetry, and pollinator richness. Methods: We apply model selection and path analysis to a large dataset of published studies of pollen limitation on 275 plant species distributed worldwide. Results: Plant diversity and breeding system were included in the best model. Even the best model explained only 13% of the among-species variation in pollen limitation, indicating a stochastic component in pollen receipt. Pollinator richness remained a consistent determinant of pollen limitation, influenced by floral symmetry and, to a lesser extent, plant diversity. Conclusions: Our results suggest that many traits examined thus far explain relatively little of the variation in pollen limitation, partly because their effects are subsumed by the roles played by breeding system and plant diversity.
Strawberry tree blight in Spain, a new disease caused by various Phytophthora species

During surveys for Phytophthora ramorum in garden centres in Majorca, Spain, 31 isolates of Phytophthora were recovered from potted strawberry trees (Arbutus unedo) showing leaf and twig blights. Many isolates of Phytophthora syringae and Phytophthora citrophthora as well as single isolates of P. ramorum, Phytophthora tropicalis and Phytophthora nicotianae were identified on morphological features and on the sequences of the internal transcribed spacer regions from ribosomal DNA genes. Phytophthora syringae was collected most frequently in late autumn and winter, whereas P. citrophthora was dominant during late summer and autumn. In vitro pathogenicity of P. syringae and P. citrophthora was compared with that of P. ramorum by inoculating intact detached leaves of A. unedo with zoospores and twigs with mycelial plugs. In addition, in vitro sporangial production was examined on inoculated excised leaves and on agar plugs at 12, 15 and 20°C. Phytophthora citrophthora produced the largest lesions both on leaves and on twigs at all temperatures. Phytophthora ramorum formed lesions comparable in size to those of P. syringae, but it significantly produced more sporangia on excised leaves and agar plugs. In a log inoculation assay, P. syringae caused large lesions in the inner bark, whereas those of P. ramorum were moderate. Strawberry tree blight has not yet been observed in natural ecosystems in the western Mediterranean areas. Possible biological and environmental limitations hindering disease spread in the wild are discussed.
The Nematode Caenorhabditis elegans

In 1965 Sydney Brenner chose the free-living nematode Caenorhabditis elegans as a promising model system for a concerted genetic, ultrastructural, and behavioral attack on the development and function of a simple nervous system. Since then, with the help of a growing number of investigators, knowledge about the biology of "the worm" has accumulated at a steadily accelerating pace to the extent that C. elegans is now probably the most completely understood metazoan in terms of anatomy, genetics, development, and behavior. The past few years have seen the completion of two major long-term projects that provide new insights into C. elegans development and lay important groundwork for future investigation: completion of the cell lineages of both sexes, from zygote to adult, and description of the complete anatomy at the level of electron microscope resolution, providing a complete "wiring diagram" of cell contacts in the animal. Recent years have also brought the first successes in molecularly cloning genes of developmental interest defined only by mutation, using transposon tagging as a generally applicable method for identification of the desired DNA sequences. Reintroduction of cloned DNA sequences into the genome has recently been accomplished. A physical map of the genome has been assembled with a combination of cosmid and YAC genes. This "Book of the Worm" serves as a reference source for C. elegans investigators as well as an introductory monograph for other biologists.
THE RHEOLOGY OF OIL‐IN‐WATER EMULSIONS

A microscope cell has been made to examine semi‐solid oil‐in‐water emulsions while flowing in a thin layer. Unautoclaved and autoclaved emulsions from cetyl alcohol, sodium lauryl sulphate, liquid paraffin with and without bentonite show differences in the dispersion of the globules. Those in the unautoclaved emulsions are mainly associated, “flocculated”, into loose clusters in which each globule is free to move independently of its neighbours. Composite masses of disperse phase, called agglomerates, are formed in emulsions prepared from a preformed “emulsifying wax” which are absent from emulsions formed by adding sodium lauryl sulphate to the aqueous phase. A compact type of floccule occurs in the autoclaved emulsions containing bentonite. The globules are surrounded by a hydrated layer of bentonite which restricts their movement and provides a mechanical barrier against deformation. Rigidity is supplied by association of the hydrated bentonite particles in a network to form a gel. The globules in the autoclaved emulsions without bentonite are readily deformed and show complete freedom of movement with no association into clusters.
Managing natural resources for their human values

Species composition and structure are important properties that can influence the extent to which people value a natural element. Hence these two properties can provide a means to directly manage natural elements to meet values-based goals. With this principle in mind, we studied soil seed bank assembly in two wetland vegetation elements recognized for their science/education, opportunity and system benefit values. Because seed banks drive the composition and structure associated with a vegetation element, which in turn influence human value satisfaction, variance partitioning modeling was used to determine which combination of filters best described patterns in the seed bank beta diversity. A combination of abiotic (soil permeability and soil salinity) and spatial filters with several interactions were the best descriptors of beta diversity, particularly for one vegetation element (wetland 1). Within the remaining vegetation element (wetland 2), a much greater diversity of weed species was observed. Base.
Cascading thresholds to heteroclinicity in an ecosystem model

Using a model of three consumer/resource pairs coupled in an ecosystem model, previous work has demonstrated a particular dynamical behavior in which a switch from a chaotic attractor to a heteroclinic cycle is the underlying mechanism that causes extinction of some components of the system. The complex bifurcation sequence from chaos to heteroclinic cycle in this model is described using numerical methods. Evidence is presented suggesting a structure of nested manifolds that gradually reverse stabilities as the bifurcation parameter changes.
Factors affecting purse seine catches: an observer-based analysis

A total of 72 fi shing trips were carried out by fi shery scientists onboard a purse seiner in the Pagasitikos Gulf (Greece) in an attempt to identify factors affecting total and individual species’ catches. As trawling is completely banned in the study area, purse seining is the main fi shing method. It was found that month, water depth and fi shing area affected total and Trachurus spp. catches of the purse seine fi shery, with month and water depth alone explaining 77.8% and 6.4% respectively of the total variation of the data. Signifi cant interactions observed indicate that the fl uctuations in total catches differed by month and fi shing area as well as fi shing area and water depth. Fishing area and water depth interaction were found to affect Trachurus spp. catches signifi cantly. Results also suggested that generalized linear modelling of the purse seine catches can be used to obtain representative abundance indices by reducing the observed variability. Fishery scientists’ onboard observations alongside fi sh market recordings during the same period confi rmed that each fi sher has developed an individual decision-making fi shing process. Fisher’s trip choice behaviour was found to be modulated by several factors, such as distance of fi shing grounds from the port, market demands (both in terms of species and market prices), weather conditions, alternative fi shing strategies, previously gathered information, economic pressure and personal skills. These fi ndings are discussed in the light of the need to incorporate additional quantitative information to stock abundance estimates if improved fi sheries management scenarios are to be advanced.
Spatial and temporal variation of bird dawn chorus and successive acoustic morning activity in a Mediterranean landscape

Ecoacoustic techniques using multiple acoustic sensors and two metrics of the acoustic community – the acoustic complexity index (ACI) and the chorus ratio (CR) – were successfully used to describe and characterize the morning acoustic activity of birds according to three equal temporal intervals during spring 2013: Dawn Chorus, Post Chorus 1, and Post Chorus 2.The metrics were applied across five Italian Mediterranean locations (Valenza, Madonna dei Colli, Monte Curto, Virolo, Croce di Tergagliana) that differed by land-cover typologies. Results from the ACI metrics showed a peak during the Dawn Chorus and a visible lull close to sunrise between Dawn Chorus and Post Chorus 1.The lull was evident in all localities except Valenza, where singing activity was relatively constant across the successive morning intervals. Temperature and vegetation structure were confirmed as important factors associated with morning acoustic activities. Vegetation evenness and temperature across the season was negatively correlated with ACI, whereas CR was positively correlated with temperature and vegetation diversity. Of the 33 species of birds identified during the maximum dawn chorus activity, Blackcap, Blackbird, European Robin, and Great Tit were acoustically dominant and their activity was significantly higher before sunrise except for Blackcap, whose acoustic activity showed no significant differences across time intervals. The dawn chorus is one of the most conspicuous behaviours of birds, engendering much speculation but no definitive, univocal explanations. The ecoacoustic approach opens a new perspective for investigating this complex phenomenon.
Model Animals for Space Experiments - Species Flown in the Past and Candidate Animals for the Future Experiments

Nearly 50 multicelluar animal species have ever been flown on the near earth orbit or further. Animals used in space experiments range from Primates to Cnidaria. Widely used laboratory animals on the ground, such as rats and fruit flies, are frequently flown species. Mice, however, seem less popular in space experiments, probably because of their relatively poor resistance to the stressful space environment. To keep rodents onboard the space craft in a health state requires tremendous efforts. Moreover, the use of rodents onboard the International Space Station (ISS) has become extremely difficult, due to the cancellation of the Centrifuge facility. Rearing fish in space, on the other hand, is easier than to keep rodents, since their waste excretions are borne by the water flow and can be effectively removed by filtering. Fish are suitable model for the studies on development, radiation effects and vestibular functions. Among fish, Medaka (Oryzias latipes) will be the most useful species for space experiments, with the inventory of inbred and mutant strains, their genome sequence data, and the established gene knockout technologies. Medaka together with established small laboratory animals, such as C. elegans, are most promising species for the experiments onboard the ISS. Other unique groups of animals in space experiment are those inhabit in the arid area. These animals, such as Mongolian Gerbil (Meriones unguiculatus), generally require few drinking water and produce little amount of waste. This enables flight hardware being simpler. Although the lack of their genome sequence data is a big drawback, they are useful for space experiments, especially for those utilizing recoverable capsule satellites.
Transport system for citric acid in Proteus vulgaris.

Strains of Proteus vulgaris utilized only citric acid among the tricarboxylic acids. Citric acid uptake in P. vulgaris IFO 3045 was mediated by a single transport system induced by citrate, isocitrate or cis-aconitate and possessed a weak affinity to isocitric acid. This citric acid transport system corresponds to the system of Salmonella typhimurium or Serratia marce-scens, which is induced by citrate, isocitrate or cis-aconitate and transports citric and isocitric acids.
Characterization of the molecular environment of the protein tyrosine phosphatase PTP-BL

Recently, one of the PDZ domains in the cytosolic protein tyrosine phosphatase Fasassociated phosphatase-1 (FAP-1)/PTP-BAS was shown to interact with the Cterminal tS-L-V peptide of the human Fas receptor (Sato, T., Irie, S., Kitada, S., and Reed, J.C. (1995) S c ie n c e 268, 411-415), suggesting a role for protein (de)phosphorylation in Fas signaling. To investigate whether this interaction is conserved in mouse, we performed yeast two-hybrid interaction experiments and transfection studies in mouse T cell lines. For the corresponding PDZ motif in the mouse homologue of FAP-1/PTP-BAS, PTP-BL, only an interaction with human but not with mouse Fas could be detected. Presence of the tS-L-V motif proper, which is unique for human Fas, rather than the structural context of its C-terminus, apparently explains the initially observed binding. To test for functional conservation of any indirect involvement of PTP-BL in Fas-mediated signaling, we generated T lymphoma cell lines stably expressing mouse or human Fas receptor with and without PTP-BL. No inhibitory effect of PTP-BL was observed upon triggering apoptosis using mouse or human Fas-activating antibodies. Together with the markedly different tissue expression patterns for PTP-BL and Fas receptor, our findings suggest that protein tyrosine phosphatase PTP-BL does not play a key role in the Fas-mediated death pathway. Introduction Many signaling pathways depend upon the reversible assembly of protein complexes to evoke temporally and spatially distinct effects. Small modular protein domains like Src homology 2 (SH2) and SH3 domains and phosphotyrosine-binding (PTB) domains, were found to play an important role in signal transduction cascades (Cohen et al., 1995; Lemmon et al., 1996; Pawson, 1995). Recently, it has become clear that PDZ motifs have a
Genetic Variation and Population Structure of Arabidopsis lyrata ssp. lyrata (Brassicaceae) along the Eastern Seaboard of North America

Abstract Arabidopsis lyrata ssp. lyrata is widespread but edaphically restricted, which suggests that the dispersal ability and level of genetic exchange among populations might be limited. We assessed levels of genetic diversity and population differentiation within and among six A. lyrata ssp. lyrata populations from along the eastern seaboard of the United States by examining variation at nine microsatellite loci among 233 individuals. These data were also evaluated to assess any relationship between geographic and genetic distance and correlation of genetic diversity with population size. Measures of genetic diversity across all 9 microsatellite loci were high in most populations. Genetic diversity, as measured by number of alleles, was generally higher in the Maryland and New York populations, as compared with the southern most sampled populations in Virginia. Genetic differentiation among regions was highly significant and large (FST = 0.47). This was supported by several analyses, suggesting that there is little gene flow among the regions sampled. There was a strong positive correlation between geographic and genetic distance, which is indicative of the pattern of isolation-by-distance. Population size correlated with the number of alleles within populations, supporting population genetic theory that larger populations harbor greater genetic diversity. Wright's FST and genetic structure analysis also provided evidence of genetic partitioning at small (<100 m) geographic distances between two areas sampled within one locality. These results indicate that the largest proportion of variation was explained by within population differences and may have implications for the conservation of this widespread but fragmented taxon.
Size and Timing of Metamorphosis in Complex Life Cycles: Time Constraints and Variation

Complex life cycles are characterized by niche shifts at the time of metamorphosis. Current models predict optimal sizes for metamorphosis based on maximizing growth, minimizing mortality, or some balance of these goals. These models predict optimal sizes that are independent of the time of metamorphosis. Reproduction and other major events in the life history of organisms are often constrained to seasons, and the state (e.g., mass) of the organism at that time is related to fitness. Therefore, an organism's state as well as the time that that state is achieved are central variables in these time—constrained life histories. We extend earlier theory to include explicit time constraints in three, hypothetical, complex life cycles. Dynamic optimization models are constructed to determine optimal time and mass trajectories for niche shifts. First, we consider the habitat shift at emergence in mayflies, where reproduction terminates a growth period in the first habitat and is constrained to a season. Second, we consider the habitat shift at metamorphosis in amphibians, where reproduction terminates a growth phase in the second habitat and reproduction is constrained to a single point in time. Third, we combine the first two effects to allow an extended period of reproduction in amphibians. Here optimal time and mass trajectories are determined for two niche shifts–the shift from aquatic to terrestrial habitat and the shift from a growth phase to a reproductive phase. We present analytical theory that allows both quantitative and qualitative predictions. Problem constructions and solutions are presented graphically to aid intuition in interpreting our results and extending the framework to other parameter values and other life—history examples. The general conclusion is that time constraints on complex life histories lead to optimal sizes for niche shifts that vary with time. In time—constrained life histories, any variation in the state of individuals at some time prior to reproduction will be preserved to some degree at reproduction. Therefore, in time—constrained life histories, we expect optimal switches in habitat use or life history stage to depend not only on state but also on the time that state is achieved.
Cloning and Expression of Bacteriophage T4 Lysozyme Gene (Gene e) in Escherichia coli via PCR Amplification

Lysozyme (EC 3.2.1.17) is an enzyme that catalyzes the hydrolysis of b(1-->4) glycosidic bonds between N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM), which are present in peptidoglycan heteropolymers of the prokaryotic cell wall. The purpose of this study was the cloning and expression of the bacteriophage T4 lysozyme gene (gene e) via PCR amplification in Escherichia coli using the pUC18 and pRS416 vectors. PCR amplification is carried out by using the primers having Bam HI recognition sites at their 5' ends. After digesting the vectors and PCR product with Bam HI endonuclease, two recombinant plasmids were constructed by ligation reaction and named pUC18L and pRS416L respectively. Recombinant E. coli cells harboring these plasmids expressed the gene e, that is, they secreted the active T4 lysozyme (called lysozyme E) into the culture medium. At the same time it was observed that E. coli clones producing lysozyme E were grown in L and LB medium without lysis, but burst out easily in a hypotonic environment such as distilled water or 10 mM Tris-HCl pH 8.0. It is suggested that the cell wall of E. coli may be weakened by the action of the lysozyme E, but the osmotic pressure balanced by the NaCl concentration in the medium may protect the damaged cells from lysis. These results show that any E. coli plasmid vectors bearing gene e may facilitate the isolation of plasmid or chromosomal DNA without using cell wall and cell membrane disruptive agents such as EDTA, lysozyme and SDS. For this purpose, pUC18L (E. coli) and pRS416L (E. coli - Saccharomyces cerevisiae shuttle vector) are constructed as prototype vectors.
Synchronous and high frequency germination of interior spruce somatic embryos following partial drying at high relative humidity

The germination of mature somatic embryos of interior spruce was limited by the low frequency of root emergence. In addition, development was abnormal, since elongation and greening of the hypocotyl and cotyledons preceded root emergence by 1–2 weeks. Pretreatment of the embryos on water-saturated Kim-paks increased the frequency of root emergence but did not alter the abnormal pattern of germination. Somatic embryos do not survive desiccation at room humidity, but partial drying at high humidity promoted germination up to 90%. Furthermore, this treatment decreased the time required for root emergence such that elongation of the root and hypocotyl–cotyledon was synchronized over a period of 5–6 days. This germination closely resembled that of excised zygotic embryos. Drying over a range of humidities indicated that humidities of 81% and lower were lethal to the embryos, whereas germination was enhanced following treatment at humidities greater than 95% relative to untreated controls. The best germination .