Miracle-dz/UniFAR-FTUs huggingface dataset:
Salinity response of transgenic potato genotypes expressing the oxalate oxidase gene

In vitro and in vivo responses of transgenic and non-transgenic potato (Solanum tuberosum L.) genotypes to salinity were investigated. A gene responsible for the production of oxalate oxidase enzyme, whose expression has been associated with plant stress tolerance, was used. Transgenic potato plants expressing the oxalate oxidase enzyme were produced using Agrobacterium-mediated transformation. The transgenic nature of the plants was verified by their antibiotic (kanamycin) resistance and then in vitro enzyme assays. Four independent transgenic genotypes obtained from 2 cultivars, Maris Bard and Desiree, were tested at 5 levels of NaCl (0%, 0.25%, 0.50%, 0.75% and 1.00% w/v) in vitro. The same genotypes were also tested at 3 levels of NaCl (0%, 0.50% and 0.75% w/v) under glasshouse conditions (in vivo). The results revealed that the growth of all genotypes was significantly inhibited by increasing salt treatments under both in vitro and in vivo conditions. Transgenic genotypes showed a relatively higher salinity tolerance than the non-transgenic genotypes in vitro. On the other hand, in the glasshouse, the results were less consistent but some transgenic genotypes showed superior tuber yield characteristics to the non-transgenics under salt stress.
Corticosterone in feathers is a long-term, integrated measure of avian stress physiology

1. Stress has pervasive consequences for the well-being of animals. Currently, understanding how individuals cope with stressors is typically accomplished via short-term quantification of blood glucocorticoids released after activation of the hypothalamic-pituitary-adrenal (HPA) axis. 2. We investigated whether the amount of corticosterone (CORT) deposited in growing feathers provides a long-term, integrated measure of HPA activity in birds using captive red-legged partridges Alectoris rufa as a model species. 3. We examined CORT levels in primary feathers induced to grow at the same time as stress series were performed with a capture and restraint protocol. Plasma CORT titres after stress-induced stimulation, but not baseline values, correlated with feather CORT. Feather levels showed the same pattern as plasma of decline across the breeding season, but more severely. 4. For females, CORT in naturally moulted flank feathers was highly and positively correlated with the number of eggs laid in the previous few months, but not clutch size of the following year. For males, the amount of black on a feather, known to be a social signal, was positively correlated with its CORT level. 5. The analysis of feather CORT is a novel methodology that allows for meaningful interpretations of how individuals respond to environmental perturbations and adjust to life-history stages. 6. The analysis of feather hormones has the unique advantages of allowing for experimentation and sampling at any time of the year with minimal investigator-induced impacts and artefacts, and shows the HPA activity of an individual with a flexible time frame from days to months depending on the length of time taken to grow the feather. As this technique can be applied to living or dead birds, or feathers picked up after moult, it provides the ultimate non-invasive physiological measure of considerable benefit in terms of animal welfare and sampling effort.
Home Range and Movement Patterns of Toucans: Implications for Seed Dispersal

Toucans (Ramphastidae) are highly frugivorous, widespread throughout the Neotropics, and travel long distances, thus likely providing dispersal for many tropical trees. Despite being large conspicuous members of the canopy and subcanopy bird community, their movement ecology has been little studied. To understand how these frugivores move through a lowland tropical forest, I tracked the movements of Ramphastos tucanus (White‐throated Toucan), Ramphastos vitellinus (Channel‐billed Toucan), and Pteroglossus pluricinctus (Many‐banded Araçari) in Yasuní National Park, Ecuador. The objectives of this study were to use radiotelemetry to estimate toucan home ranges, movement patterns, and potential seed dispersal distances. Using canopy nets, a total of 20 P. pluricinctus and three Ramphastos toucans were captured, radio‐tagged, and tracked over a 4‐yr period from 2001 to 2005. Average home range sizes were 191 and 86 ha for P. pluricinctus and Ramphastos toucans, respectively. The maximum travel distance in a single 30‐min tracking interval was 3665 m for P. pluricinctus and 3027 m for Ramphastos. Estimated dispersal distances of medium‐sized seeds ranged from 269 to 449 m. Large home range size and long‐distance movements indicate that toucans likely disperse seeds over a scale of hundreds of meters. This study is the first to estimate home range size of any toucan species in intact closed‐canopy forests.
Influence of dietary levels of soybean meal on the performance and gut histology of gilthead sea bream (Sparus aurata L.) and European sea bass (Dicentrarchus labrax L.)

AbstractThepresentstudywasperformedtodeterminetheef-fect of soybean meal (SBM) on the performance andguthistologyofgiltheadseabreamandEuropeanseabass. Three isonitrogenous and isolipidic extrudeddiets (crude protein, 470gkg 1 diet; crude fat,200g kg 1 diet) were formulated containing 0(0SBM), 180 (180SBM) and 300 (300SBM)gkg 1 diet SBM and tested on both species in two separateexperiments. Fish at an initial average weight ofaround18gwererandomlyallocatedto800Lsquaretanksconnectedtoaclosedrecirculatingsystem.Thetrialslasted80daysforseabreamand89daysforseabass. Fish were hand-fed to apparent satiation. In-creasing the level of SBM had no signi¢cant eiectsonthe speci¢cgrowth rate, feed intakeand feedcon-versionrateinboththespecies. Intheseabreamdis-tal intestine, lamina propria was moderately anddiiuselyexpanded in some ¢shduetoan increase incell in¢ltration represented by mononuclear cells,this ¢nding being more frequent in animals fed diet300SBM. No other morphological alterations in in-testinal folds, enterocytes or other in£ammationsigns were noticed in the sea bream distal intestineof any group. No histological diierences were foundinseabassinanyexperimentalgroup.Keywords: gilthead sea bream, European seabass, soybean meal, growth, gut histologyIntroductionCurrently, the importance of vegetable protein inaquaculture is well recognized by feed industry op-erators due to the growing pressure to ¢nd ¢sh meal(FM) substitutes in ¢sh diets. Among the diierentingredients, soybean meal (SBM) is one of the mostinterestingalternativeFMbecauseof theadvantagesof supply, price and protein and amino acid (AA)composition. On the other hand, the use of soybeanproducts may pose a series of problems that mayaiect palatability (Rackis 1974), protein digestibility(Glencross, Carter, Duijster, Evans, Dods, McCaierty,Hawkins, Maas & Sipsas 2004) and phosphorus bio-availability (Vielma, Makinen, Ekholm & Koskela2000), and may reduce feedutilization. Diierent ¢shspecieshaveshownvariablesensitivitytosoyantinu-tritional factors. In Atlantic salmon and rainbowtrout,SBMcausesimpairedgrowthandproteinutili-zation in addition to distinct morphological altera-tions in the intestine that become more pronouncedwith increasing dietary level (Krogdahl, Bakke-McKellep & Baeverfjord 2003). The morphologicalalterations are characterized by a widening of thelaminapropria,whichisin¢ltratedbyamixedpopula-tion of in£ammatory cells, and concurrent changesin enterocyte structure, including a decrease in oreven a loss of the supranuclear vacuoles present innormalenterocytes (Baeverfjord & Krogdahl1996), ashorteningof the microvilliand increased formation
Modelling the habitat requirement of riverine fish species at the European scale: sensitivity to temperature and precipitation and associated uncertainty

– Species distribution models (SDMs) have been widely used for different purposes such as studying species niche or forecasting the effects of global change on species distribution. Nevertheless, these models are often calibrated on datasets that only cover a fraction of the species’ realised niches, which could lead to unrealistic results. The aim of this study was to model the habitat requirements of 21 freshwater fish species that are native to Europe, using a dataset that accurately reflects their realised niches. Both temperature and precipitation were used as climatic factors to model the habitat requirements of the species, and the uncertainty associated with the fitted environment–occurrence relationships was examined. The results demonstrated the importance of accounting for these two climatic components when estimating the habitat requirements of riverine fish species and whether the uncertainty associated with model expectations varies with the species and the environmental factor considered. These results are discussed with regard to the known ecology of the 21 riverine fish species and within the perspective of climate change.
Population Studies in Predominantly Self-Pollinating Species. XIII. Intergenotypic Competition and Population Structure in Barley and Wheat

Interactions between various genotypes were studied in four varieties of barley, four varieties of wheat, and eight barley genotypes which had survived up to 18 generations of mutual selection in a heterogeneous population. The results showed that first-order interactions between genotypes from the heterogeneous barley population were much larger than those between the varieties of wheat and barley. Natural selection therefore appears to preserve genotypes which interact synergistically. Deterministic and stochastic simulations predicted fixation of the variety with the highest pure-stand reproductive value in populations of the wheat and barley varieties. However, they predicted the development of stable multigenotypic associations in populations formed from the eight genotypes isolated from the heterogeneous barley population. The effect of random variation in the reproductive values was to decrease the time to fixation when there was no stable nontrivial equilibrium; however, when such an equilibrium existed, stochastic variation increased genetic diversity. The significance of intergenotypic interactions in maintaining genetic diversity was discussed.
Reduction in last male sperm precedence caused by competitive assault on a mating male in Gastrophysa viridula, a highly polygamous leaf beetle

A possibly novel aspect of direct male-male competition found in the dock beetle, Gatrophysa viridula is addressed. In this beetle, intra-sexual competitive tactics include persistent interruption and breaking of rival matings but with no subsequent takeover of the freed females. This situation creates a question about the ultimate value of male assaults, especially about their influence on the sperm precedence of both attacking and attacked males. Sperm precedence (progeny sired) of both undisturbed and attacked males was estimated by the irradiated male method. Sperm precedence of the last copulating, undisturbed male (Plast) was estimated as 0.45 (± 0.37 SD), provided ejaculation competitiveness of both irradiated and control males was equal. Comparison of sperm precedence resulting from undisturbed and assailant-disturbed copulation, revealed a 30% negative influence of competitor intrusion on the sperm priority of a mating male. This effect persists throughout the next 7 days with an average of 8.7 egg batches laid per female during this period. Two suspected genetic pay-offs of these energy and time-consuming assault tactics are considered. The first is related to the release of an extra individual to the pool of sexually available females. The second possibility is based on the promotion of the attacker's sperm already present within a female. According to a theoretical estimation, an attack on a mating male would contribute to the protection of the attacker's paternity from the next deposited batch in (1) 3.1, (2) 1.7 and (1) 1.0 eggs on average, if the attacking male had been, respectively, (1) the one who first copulated with that same female before the males attacked (2) the one before last (3) the second before last to copulate with the mating female (provided that there is stable sperm priority and limited migrations of beetles).
Effects of iron excess on cell viability and mitogen-activated protein kinase activation in rice roots

Iron is an essential micronutrient for normal growth and development of plants. However, at high concentrations, iron can become toxic to plants. Very little information is known about the molecular mechanism responsible for the regulation of plant growth by excess iron. The aim of this study was to investigate the signal transduction pathway activated by increasing concentrations (0.5, 1.0, and 2.5 mm) of iron. We showed that iron elicited a remarkable myelin basic protein (MBP) kinase activity. By Western blot and immunoprecipitation analysis, we suggested that iron-activated 42-kDa MBP kinase is a mitogen-activated protein kinase (MAPK). Cell death in rice roots due to iron toxicity was investigated using inhibitors of signal molecules known to regulate programmed cell death in plants. Phenylarsine oxide (PAO) and sodium orthovanadate, known inhibitors of tyrosine phosphatase, reduced iron-induced root cell death, but cantharidin and endothall two-serine/threonine phosphatase inhibitor enhanced iron-induced root cell death. Moreover, our results revealed that H+-ATPase might participate in iron-induced cell death. These results suggested that the MAPK, reactive oxygen species, protein phosphatase, and H+-ATPase might function in the plant iron-triggered signaling pathway in rice roots.
Sex-Ratio Variation in Marsupials

Many marsupials produce sex ratios biased towards male or female young. In several cases these changes are comfortably accommodated in the existing theory of sex allocation. Local resource competition and the Trivers-Willard hypothesis have been usefully applied to several data sets, and preliminary experimental work has supported the main tenets of theory. By contrast, several data sets lack explanation, and provide challenges to theoreticians. The high frequency of bias in marsupials does not result from data-dredging, as bias is usually reported in descriptive accounts of marsupial reproduction, without recourse to any theoretical or mechanistic explanations. It is not possible to distinguish whether the marsupial mode of reproduction is well suited to manipulate sex allocation, or whether it facilitates measurement of biased sex allocation. As for most eutherians and birds, the mechanism of prenatal sex allocation is unknown for any marsupial. However, the current interest in sex-determining mechanisms in marsupials suggests a profitable avenue for collaboration between geneticists, physiologists and evolutionary ecologists.
Variation in sperm swimming behaviour and its effect on fertilization success in the serpulid polychaete Galeolaria caespitosa

Summary Established models of fertilization kinetics in free-spawning marine invertebrates predict that fertilization success is dependent upon sperm swimming velocity. Despite the prevalence of these models, there are very few published tests of this assumption. To test this, the effects of sperm swimming characteristics on fertilization success were studied in Galeolaria caespitosa (Polychaeta, Serpulidae). Both sperm activity (% motility) and sperm swimming velocities were highly variable within this species. Sperm were motile for up to 6–7 h after activation; however, mean motility, swimming velocity and fertilization success decreased after 4 h. Eggs of G. caespitosa were fertilizable up to 10 h after spawning; however, the number of embryos resulting from fertilization by fresh sperm also decreased after 4 h. Sperm motility and velocity were not affected by water-soluble egg extracts. When gamete concentration, contact time, and age were held constant, fertilization success in G. caespitosa remained highly variable. Some of this variability was attributable to observed variability in sperm motility and velocity. Fertilization success was positively related to sperm velocity (P = 0.014), but there was no correlation between percent sperm motility and fertilization success (P = 0.85). Cross-fertilization experiments indicated that individual egg fertilizability and male-female compatibility also play an important role in determining the fertilization success and thus may obscure any effects of sperm motility.
Phylogeography of spiny mice (genus Acomys, Rodentia: Muridae) from the south‐western margin of the Sahara with taxonomic implications

The present study aims to depict the overall pattern of Acomys history in south-western Sahara. We tested the specific predictions that: (1) several mitochondrial clades can be identified and that they coincide with the described species; (2) successive phases of desert expansion and contraction during the last 3 Myr have resulted in several phases of demographic expansion and population fragmentation in Acomys; and (3) isolation-by-distance occurs. The extent of phylogeographic patterns and molecular genetic diversity (cytochrome b gene and D-loop) were addressed in a survey of 90 individuals of Acomys from 38 localities. Our phylogeographical analyses show a strong genetic structure within western Saharan Acomys, with several phylogroups displaying non-overlapping geographic distributions. Restricted gene flow with isolation-by-distance was recorded and a signal of population expansion was detected within several clades. We suggest that during arid or semi-arid paleoclimatic periods, when large sandy areas were present, Acomys was restricted to rocky massifs, whereas, in more humid periods, when savannah and/or steppe habitat prevailed, this species was able to disperse and to survive outside rocky areas because food resources were abundant. Based on a comprehensive sampling and the use of an integrative approach (i.e. combining cytogenetic, molecular and morphological data), we firmly propose that Acomys airensis should be considered as a junior synonym of Acomys chudeaui. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 98, 29-46.
Pseudomonas pseudoalcaligenes subsp. citrulli subsp. nov.

Ten nonfluorescent Pseudomonas strains isolated from water-soaked lesions on cotyledons of plants of five Citrullus lanatus (watermelon) plant introductions were characterized and compared phenotypically with 22 other pseudomonads. The strains were distinguished phenotypically from other known plant pathogenic pseudomonads. The watermelon bacterium was aerobic. Cells were rod-shaped, gram negative, and motile by means of a single polar flagellum. They were nonfluorescent and grew at 41°C but not at 4°C. Oxidase production and the 2-ketogluconate reaction were positive. The 10 strains utilized β-alanine, L-leucine, D-serine, n-propanal, ethanol, ethanolamine, citrate, and fructose for growth. No growth occurred with sucrose or glucose. Their deoxyribonucleic acid base composition was 66 ± 1 mol% guanine plus cytosine. The bacterium is phenotypically similar to P. pseudoalcaligenes but differs from it in being pathogenic to watermelon, Cucumis melo (cantaloupe), Cucumis satiwus (cucumber), and Cucurbita pepo (squash). The name P. pseudoalcaligenes subsp. citrulli is proposed for the new subspecies, of which strain C-42 (= ATCC 29625) is the type strain.
Molecular sex-typing in shorebirds: a review of an essential method for research in evolution, ecology and conservation

Knowing the correct sex of individuals is essential both for research in evolutionary ecology and for practical conservation. Recent molecular advances have produced cheap, quick and reliable methods for sexing birds including chicks, juveniles, immatures and adults. Shorebird researchers have not yet fully utilised these advances. Here we provide an overview of work in this area to date with two objectives: (i) to review the major applications of molecular sexing and findings of shorebird research so far, and (ii) to provide an essential guide on how to carry out molecular sexing using current methods whilst avoiding methodological pitfalls. We encourage shorebird researchers to make better use of molecular sex-typing techniques in studies of conservation, migration, foraging ecology and breeding behaviour.
Population Variation in Fossil Graptolites: a Quantitative Study Based on Single Species Assemblages

There are several different types of variation in populations of fossil organisms. These include intra-specific (population) variation, evolutionary variation (specimens on a slab accumulating over thousands of years), and preservational variation. An understanding of the extent and type of variation present in a population is fundamental to biological and paleontological studies. This study examines several populations of fossil graptolites from which population variation can be studied without the influence of the other types, and includes several types of morphometric analyses to examine population variation in several species of fossil graptolites. These analyses include isolating three dimensionally preserved specimens from limestone, and then photographing, digitizing, and measuring the specimens. Statistical measures such as standard deviation, coefficient of variance, modal distribution, and an index of dispersion (a similar test to the coefficient of variation, specifically meant for measuring count-based data sets as opposed to continuous data sets) will be used. We expect to gain an understanding of the range of biological variation in a number of morphologic characters in these taxa.
Individual variation in response to simulated territorial challenge among territory-holding song sparrows

Lack (1946) suggested that male songbirds exhibit consistent individual differences in the vigor or manner in which they defend their territories against intrusion. The causes and consequences of such individual variation have not been incorporated into models of territoriality, however, because of a lack of experimental data confirming Lack's suggestion. In this paper, we test the possibility that male song sparrows Melospiza melodia who are successful territory holders differ consistently in the vigor with which they defend their territory, by conducting repeated song playback trials with the same set of territory-holding subjects across a breeding season. We found only relatively weak seasonal trends in responsiveness: the amount birds sang in response to playback increased significantly across the breeding season and responsiveness was generally lower when a male's social mate was egg laying. By contrast, we found extensive variation among males in how closely they approached a simulated territorial intrusion. These individual differences remained significantly consistent across four rounds of playback trials that spanned the breeding season as determined by Kendall's coefficient of concordance. Our results confirm that some individual song sparrows are consistently more vigorous than others in territory defense, at least in one conspicuous aspect of their behavior, and suggest that further work is needed to understand the nature and consequences of variation in patterns of defense among successful territory holders.