Miracle-dz/UniFAR-FTUs huggingface dataset:
RAPD analysis of genetic structure in four natural populations of Taxus baccata from southern Poland

Taxus baccata L. is an evergreen needle-leaved gymnosperm shrub or tree, growing up to 28 m high. The species is slow-growing and long-lived, reaching maturity only at ~70 years. It is extremely shade-tolerant but can withstand full exposure to the sun. Taxus is normally dioecious, rarely monoecious, and wind-pollinated (Thomas and Polwart, 2003). Its seeds, surrounded by a red fleshy arillus, are dispersed endozoochorously by birds or small mammals; clonal regeneration is important but is restricted mainly to polycormic propagation (Hulme, 1996; Thomas and Polwart, 2003; Hilfiker et al., 2004). English yew occurs all over Europe. In Scandinavia it grows up to 61°N latitude. The eastern limit of the range in Europe extends from the Gulf of Riga through the Białowieża Forest and down to the Carpathians. In the Alps it reaches 1100–1400 m a.s. l. , in the Carpathians 1660 m, in the Caucasus 1500 m and in the Middle East 2300 m. It also grows in North Africa (Bugała, 1975). The reason for Taxus baccata's decline has been analyzed in many papers (e.g., Bugała, 1975; Giertych, 2000). Some authors try to connect it with suspected low genetic diversity, but yew's high adaptability to different habitat conditions, and the production of numerous ornamental varieties, testifies rather to high genetic diversity (Bugała, 1975; Lewandowski et al., 1995). Until the 1980s, morphological markers were the only way to investigate variability (Elves and Henry, 1906; Pilger, 1916; Stecki and Bella, 1931; Krussmann, 1972; Kuświk, 1987). Significant progress in variability research took place with the discovery of molecular markers. For example, isoenzymatic markers have been used in research by Greer et al. (1993), Lewandowski et al. (1995), Wheeler et al. (1995), Hertel and Kohlstock (1996), Zhou et al. (1998), Rajewski et al. (1999) and Senneville et al. (2001). Today, DNA markers are more often used. They allow precise genome analysis, as they are mostly inherited in accordance with Mendelian genetics and are not subject to influences from the natural environment (Grzebelus, 1996). In the literature there is very little information about the genetic diversity of tree species that grow in low numbers and play a small role in generating forest ecosystems (Senneville et al., 2001). Most authors do research on tree species that are widespread and numerous (Hamrick et al., 1992).
Crop dominance exerts specific effects on foliage‐dwelling arthropods in Bacillus thuringiensis cotton

Shifts in crop composition in an agro‐ecosystem may have profound effects on plant‐associated arthropods. The widespread adoption of transgenic insect‐resistant cotton expressing insecticidal toxins Cry1A from Bacillus thuringiensis (Bt) has caused a dramatic shift in agricultural landscapes over the last 15 years, thus raising concerns about the potential impacts of Bt crops on nontarget organisms worldwide. The potential effect of crop composition shift as a result of the increasing acreage of Bt cotton on an arthropod community was assessed at three levels (0%, 75% and 100%) of Bt dominance in a 2‐year field trial in northern China. Three findings confirmed that the arthropod assemblage of a certain field was influenced by crop composition and its developmental stage: (i) the proportion of Bt cotton in the crop mixture consistently affected the abundance of pests, natural enemies and total arthropods; (ii) bootstrap methods demonstrated significant effects of Bt cotton on species richness, diversity and evenness; and (iii) non‐metric multidimensional scaling analysis showed that the arthropod community of a certain agricultural ecosystem varied with crop composition and plant developmental stage. The findings of the present study may have significant implications for cotton pest management with respect to transgenic Bt cotton, highlighting the potential of conservation biological control via the combination of an appropriate crop genetic ratio and timely chemical control.
Developmental stability in yellow dung flies (Scathophaga stercoraria): fluctuating asymmetry, heterozygosity and environmental stress

The genetic basis for developmental stability, the ability of an organism to withstand genetic and environmental disturbance of development, is poorly understood. Fluctuating asymmetry (FA: small random deviations from symmetry in paired, bilateral traits) is the most widely used measure of developmental stability, and evidence suggests FA is weakly and negatively associated with genome‐wide heterozygosity. We investigated the genetic basis of developmental stability in the yellow dung fly. Fly lines were inbred for 16 generations at which time they were homozygous at the phosphoglucomutase (PGM) loci and PGM appears to influence FA in at least one other taxon. After 16 generations of inbreeding, lines homozygous for different PGM alleles were crossed and levels of FA for four metric traits were compared in the inbred and crossed flies. We also compared FA levels in these flies with previously gathered data on wild‐type (second generation outcrossed) flies, and additionally looked at the effects of two environmental stresses (larval food limitation and increased temperature) on FA. There were no significant differences in any measure of FA, nor in mean FA, in any trait when inbred and crossed flies were compared. Comparison of FA in these and wild flies also revealed no significant differences. Food limitation had no influence on FA, whereas heat stress increased FA of naturally, but not sexually, selected traits. Our results do not show a negative relationship between heterozygosity and FA, but support the notion that FA levels are stress, trait and taxon specific.
The Effect of Standard Metabolic Rate on Egg Production in the Acridid Grasshopper, Xanthippus corallipes'

SYNOPSIS. Models of energy budgets often allocate energy between the broad categories of maintenance, growth, and reproduction. An important component of maintenance costs is standard metabolic rate, which is partially determined by body temperature. The relationship between thermoregulation, standard metabolism, and egg production was investigated in adult females of the acridid grasshopper Xanthippus corallipes from six populations along an elevation gradient. Individuals thermoregulate and maintain stable afternoon body temperatures which correlate negatively with elevation. Standard metabolic rates were calculated at each population's afternoon body temperature. These rates were then used to investigate the effect of variation in standard metabolic rate on egg production. Because of the pervasive effect of mass on standard metabolic rate and egg number, the variables were log-transformed. The effect of mass was removed by regression analyses, and residuals were calculated. An analysis of the residuals revealed that intermediate values of field standard metabolic rate correlate with high egg production, suggesting stabilizing selection on standard metabolic rate.
The involvement of marmesin and its interaction with GA3 and psoralens in parsley decay resistance

In parsley (Petroselinum crispum (Mill.) Mansf. ) with no decay prior to storage, the incidence rose to 12% after 1 month of storage at 1°C, and the concentration of +marmesin in leaves decreased from 32 to 4 μg g–1 fresh mass (FM). During that time, the concentration of psoralens increased from 8 to 41 μg g–1 FM. When parsley was treated with GA3 prior to storage, incidence of decay following 1 month of storage at 1°C was 3%, and the concentration of +marmesin was 21 μg g–1 FM. Concentrations of psoralens (psoralen, bergapten, and xanthotoxin) during that time reached 15 μg g–1 FM. Bioassays showed that +marmesin has much greater antifungal activity in vitro than psoralens.
Cross‐fertilizing aquatic and terrestrial research to understand predator risk effects

Research that conceptually transcends boundaries between aquatic and terrestrial ecosystems has a long history of increasing insight into ecology and evolution. To stimulate further cross‐fertilization between studies that focus on different ecosystems, we highlight several insights on risk effects—the costs of antipredator behavior—that have emerged in part because of combined advances in aquatic and terrestrial systems. Namely, risk effects (1) are not restricted to structured landscapes where antipredator behavior is easily measurable, (2) can be substantial even when prey experience very low predation rates, (3) are contingent on a three‐way interaction between the hunting mode of the predator, escape tactic of the prey, and features of the landscape/physical environment, and (4) can interact with direct predation (consumption) and resource availability (through its effects on prey energy state) to control consumer population size. We conclude by highlighting the value of exploring differences between aquatic and terrestrial risk effects and offering a prospectus for future studies of antipredator behavior and its ecological importance in both eco‐domains. WIREs Water 2014, 1:439–448. doi: 10.1002/wat2.1039
The influence of sward canopy structure on foraging decisions by grazing cattle. I. Patch selection

Patch selection by grazing dairy cows in response to simultaneous variation in combinations of sward structural characteristics was examined in three experiments in which four mature dairy cows were offered a choice of patches (typically 0.9 m × 0.9 m) of perennial ryegrass (Lolium perenne) presented in a linear arrangement. Treatments involved combinations of variations in sward height, stubble height and/or depth of regrowth, prepared by preliminary cutting treatments. They were arranged in balanced sets of four to nine treatments, which were arranged in linear sequences of eighteen to twenty-seven patches. Within experiments, sequences were balanced across replicate sets of patches, which were grazed separately by individual cows. The number of bites removed and the residence time for each patch were highly correlated in all three experiments, and the results are reported using number of bites per patch as an estimator of foraging behaviour. In the first experiment, with vegetative swards, cows preferentially selected the tallest swards. When swards comprising reproductive stem were offered in Experiment 2, cows selectively grazed short-stubble swards rather than tall-stubble swards, although both offered a similar depth of regrowth. Cows did not exhibit preference for swards comprising the greatest quantity of leaf mass, indicating that the spatial distribution of plant components assumed greater importance. In the third experiment, the number of bites removed increased with increasing depth of regrowth, and was negatively correlated with sward height. The three patch-appraisal cues investigated were broadly ranked in order of importance as (i) depth of regrowth, (ii) sward maturity and (iii) sward height. There was no evidence, at least at a short temporal scale, that patch behaviour was influenced by conditions in adjacent patches, suggesting that the cows assessed grazing opportunities on a patch-by-patch basis.
Mistletoe macroecology: spatial patterns in species diversity and host use across Australia

Mistletoes are parasitic plants, the spatial distributions of which are poorly understood on macroecological scales. Because of their highly unusual life history, investigating mistletoe macroecology may provide new insight into broad-scale patterns in species distributions. We collated data on the spatial distribution and host use of 65 species of Loranthaceous mistletoes across the continent of Australia, and tested two predictions. First, we predicted mistletoe diversity would be unrelated to productivity (i.e. evapotranspiration and precipitation), as the parasitic lifestyle might relax environmental constraints on their distributions. Second, we predicted that mistletoe host ranges (number of infected host species) would increase in areas with more potential host species. The basis of this prediction is that greater host generality is likely to evolve in regions with greater host diversity because of greater unpredictability in encounter rates with particular host species. Conversely, in regions with fewer potential hosts, randomly dispersing mistletoe propagules are likely to repeatedly encounter particular host species, thus favouring the evolution of host specialization. The results were generally consistent with these predictions. Mistletoe diversity across Australia was weakly associated with environmental conditions, whereas mistletoe host ranges increased significantly with total plant diversity. Macroecological patterns in mistletoes are unusual. In contrast to non-parasitic plants, mistletoe diversity is poorly correlated with productivity. Host ranges varied predictably across Australia, providing the first quantitative support for the hypothesis that mistletoes in diverse regions tend to be host generalists, whereas mistletoes in depauperate regions tend to be host specialists. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 106, 459‐468. ADDITIONAL KEYWORDS: diversity gradients ‐ host‐parasite interactions ‐ Loranthaceae ‐ mistletoes ‐ parasitism.
The Emergence of Antibiotics Resistance and Utilization of Probiotics for Poultry Production

The worldwide increase in the use of antibiotics in farm animals, especially for poultry production to treat and prevent bacterial infections and as growth promoters in feeds has increased microbial resistance to antibiotics. Recent scientific evidences show that resistance to antibiotics is not only due to the ability of bacterial population to survive the effect of inhibitory concentration of antimicrobial agents, but may also arise from several pathways which include the transmissibility of acquired resistance to their progeny and across to other unrelated bacteria species through extra chromosomal DNA fragment called the plasmid which provide a slew of different resistances. The emergence and dissemination of resistant bacterial strains like Campylobacter sp, Escherichia coli and Enterococcus sp. from poultry products to consumer put humans at risk to new strains of bacteria that resist antibiotic treatment. Resistant bacteria thwart antibiotics by interfering with their mode of action via a range of effectors’ mechanisms, including synthesis of inactivating enzymes, cell wall and ribosomal alteration, and modified membrane carrier systems. These mechanisms are specific to the type of resistance developed. Because of the growing global concerns that resistance bacteria can pass from animals to humans, there is an increase in public and governmental interest in combating out imprudent usage of antibiotics in animal husbandry. Improvement in the hygienic practices of handling raw poultry products and adequate heat treatment to eliminate the possibility of antibiotic resistant bacteria surviving which play a role in preventing the spread. More attention should be focused on alternative approach involving the use of probiotic microorganisms that can similarly enhance poultry productivity and produce safe edible products.
Letter to the Glyco-Forum: Cholera toxin B subunit binding does not correlate with GM1 expression: a study using mouse embryonic neural precursor cells

Gangliosides, sialic acid-containing glycosphingolipids, are ubiquitously expressed in all eukaryotic cells and are primarily localized in the plasma membrane. Cholera toxin B subunit (Ctxb), a component of a heat-labile enterotoxin produced by Vibrio cholerae, has been frequently used as a probe to detect GM1 ganglioside because of its high affinity for this glycolipid. In this study, we evaluated the reactivity of Ctxb and the expression of GM1 in mouse embryonic neuroepithelial cells (NECs). Analysis of Ctxb reactivity of NECs based on flow cytometry revealed that about 80% of the cells are Ctxb positive. A detailed biochemical analysis, however, indicated that GM1 was expressed in NECs in barely detectable quantities. Thus, it was thought that reactivity of Ctxb in the NECs could arise from high-affinity interaction with GM1. Because Ctxb is commonly used as a reagent for flow cytometry and GM1 cell staining, we recommend that using this reagent alone would be inconclusive and that biochemical analysis of GM1 should also be performed to avoid overestimation of GM1 expression and/or mischaracterization of the ganglioside species.
Shoots, roots and ectomycorrhiza formation of pine seedlings at elevated atmospheric carbon dioxide

The effect of elevated atmospheric CO 2 concentration on the growth of shoots, roots, mycorrhizas and extraradical mycorrhizal mycelia of pine (Pinus silvestris L.) was examined. Two and a half-month-old seedlings were inoculated axenically with the mycorrhizal fungus Pisolithus tinctorius (Pers.) by a method allowing rapid mycorrhiza formation in Petri dishes. The plants were then cultivated for 3 months in growth chambers with daily concentrations of 350 and 600 μmol mol -1 CO 2 during the day. Whereas plants harvested after 1 and 2 months did not differ appreciably between ambient and increased CO 2 concentrations, after 3 months they developed a considerably higher root biomass (+57%) at elevated CO 2 , but did not increase significantly in root length. The mycorrhizal fungus Pisolithus tinctorius, which depended entirely on the plant assimilates in the model system, grew much faster at increased CO 2 : 3 times more mycorrhizal root clusters were formed and the extraradical mycelium produced had twice the biomass at elevated as at ambient CO 2 . No difference in shoot biomass was found between the two treatments after 91d. However, since the total water consumption of seedlings was similar in the two treatments, the water use efficiency was appreciably higher for the seedlings at increased CO 2 because of the higher belowground biomass.
Production of lipase and biomass by Staphylococcus simulans grown on sardinella (Sardinella aurita) hydrolysates and peptone

Fish protein hydrolysates from low cost fish species (Sardinella aurita) were prepared and tested as carbon and nitrogen sources for microbial growth and lipase production by Staphylococcus simulans. When cultivated in media containing Whole Sardinella Hydrolysate (WSH) or Meat Sardinella Hydrolysate (MSH), lipase production was significantly low, 5 and 10 U/ml, respectively. However, lipase production was strongly enhanced when partially defatted sardinella hydrolysate was used and highest lipase production was obtained with Partially Defatted Meat sardinella Hydrolysate (PDMSH) (55 U/ml), higher than that obtained with tryptone as nitrogen source. Peptone from sardinella was also prepared and compared with a tryptone from casein and other fish peptones. The results revealed that sardinella peptone is a good substrate for the growth of S. simulans.
Effects of water velocity on phosphate uptake in coral reef-hat communities

To determine a Stanton number (Stm, a dimensionless number giving the ratio of uptake rate to the rate of advection of the substance past the uptake surface) for a reef-flat community without the effects of wave surge, we placed communities of reef organisms in the bottom of a flume, 9.3 m long and 0.35 m wide. Water was pumped over the experimental communities at 13 different surface flow velocities, ranging between 2.3 and 58 cm s‒1. Rate of phosphate (P) uptake at each velocity was measured by raising the ambient P concentration to ∼2 µM and measuring the rate of decrease in P concentration. Stm for P uptake in the flume was significantly greater than estimates of Stm derived from engineering studies of mass and heat transfer. This result confirms the finding of anomalously high mass transfer based on field data. Rates of P uptake increased as water velocity increased. The log of the first-order rate coefficient for P uptake was directly proportional to the log of velocity with a slope of ∼0.76. These results indicate that the rate of P uptake into reef benthos is controlled by diffusive boundary layers near the surfaces of organisms and that the surface geometry is such that improved transfer in comparison with engineering surfaces is obtained.
Generalized food-deceptive orchid species flower earlier and occur at lower altitudes than rewarding ones

Aims Food-deceptive pollination, in which plants do not offer any food reward to their pollinators, is common within the Orchidaceae. As food-deceptive orchids are poorer competitors for pollinator visitation than rewarding orchids, their occurrence in a given habitat may be more constrained than that of rewarding orchids. In particular, the success of deceptive orchids strongly relies on several biotic factors such as interactions with co-flowering rewarding species and pollinators, which may vary with altitude and over time. Our study compares generalized food-deceptive (i.e. excluding sexually deceptive) and rewarding orchids to test whether (i) deceptive orchids flower earlier compared to their rewarding counterparts and whether (ii) the relative occurrence of deceptive orchids decreases with increasing altitude. Methods To compare the flowering phenology of rewarding and deceptive orchids, we analysed data compiled from the literature at the species level over the occidental Palaearctic area. Since flowering phenology can be constrained by the latitudinal distribution of the species and by their phylogenetic relationships, we accounted for these factors in our analysis. To compare the altitudinal distribution of rewarding and deceptive orchids, we used field observations made over the entire Swiss territory and over two Swiss mountain ranges. Important Findings We found that deceptive orchid species start flowering earlier than rewarding orchids do, which is in accordance with the hypotheses of exploitation of naive pollinators and/or avoidance of competition with rewarding co-occurring species. Also, the relative frequency of deceptive orchids decreases with altitude, suggesting that deception may be less profitable at high compared to low altitude.
Amino acid composition of some woodland arthropods and its implications for breeding tits and other passerines

Several studies on Parids have noted a peak in the provisioning of spiders to nestlings in the early stages of development. It has been suggested that spider proteins are rich in the sulphur-containing amino acid (SAA) cysteine and that increased provisioning may serve to provide extra cysteine during rapid feather growth. Amino acid analyses were conducted on samples of arthropod groups known to feature in the diet of breeding tits. Cysteine and methionine (both SAA) levels were slightly higher in aranaea protein than in that of other arthropods. However, we argue that the increased level of SAA found in aranaea is insufficient to drive the observed diet selection and that the timing of peak aranaea provisioning does not support the feather growth hypothesis. Instead, we propose that observed patterns of provisioning are due to high levels of taurine present in aranaea and that taurine may be an essential nutrient during a critical stage of chick development.