Miracle-dz/UniFAR-FTUs huggingface dataset:
Phytomass and phenology of three alpine snowpatch species across a natural snowmelt gradient

Alpine snowpatch vegetation in Australia is restricted to high mountain areas and occurs in locations where winter snow persists longest into the summer. The timing of annual snowmelt is considered an important determinant of vegetation patterns in alpine areas because it affects the length of the growing season for plant species at landscape scales. There are few studies in Australia that have examined the effects of the date of snowmelt on the performance of plant species at small spatial scales. The phytomass and phenology of three common snowpatch species (Celmisia pugioniformis, Luzula acutifolia, Poa fawcettiae) was examined during one growing season across a natural snowmelt gradient to examine their response to time of snow release. Peak phytomass was significantly higher in early than late-melting zones for L. acutifolia and marginally higher there for C. pugioniformis. P. fawcettiae, however, produced higher mean peak phytomass in late- melting zones where soil was initially wetter in the growing season. Flower buds of L. acutifolia were evident as the snow melted, and flowering occurred at the same time in all areas of the snowpatch. The number of days from the date of snowmelt to the date of the first observed flower bud in C. pugioniformis and P. fawcettiae was 22-25 days shorter in late-melting areas than in early melting areas. For both of these species, flowering and subsequent seed set occurred simultaneously across the snowpatch regardless of the date of the initial snowmelt, suggesting that photoperiod controls flowering in these species. Our study suggests that the predicted declines in snow cover in Australia in coming decades may affect the phytomass of species that are currently constrained by late-lying snow. This, in turn, may affect their long-term patterns of distribution. If plants respond to photoperiod for flowering, as seems to be important here for C. pugioniformis and P. fawcettiae, it is unlikely that the periods following earlier than usual snowmelt will be fully utilised by these species. Any attempts at predicting or modelling future alpine plant distribution on the basis of warming scenarios may therefore need to account for photoperiod constraints on flowering as well changes in phytomass production.
RATP: a model for simulating the spatial distribution of radiation absorption, transpiration and photosynthesis within canopies: application to an isolated tree crown

The model RATP (radiation absorption, transpiration and photosynthesis) is presented. The model was designed to simulate the spatial distribution of radiation and leaf-gas exchanges within vegetation canopies as a function of canopy structure, canopy microclimate within the canopy and physical and physiological leaf properties. The model uses a three-dimensional (3D) representation of the canopy (i.e. an array of 3D cells, each characterized by a leaf area density). Radiation transfer is computed by a turbid medium analogy, transpiration by the leaf energy budget approach, and photosynthesis by the Farquhar model, each applied for sunlit and shaded leaves at the individual 3D cell-scale. The model typically operates at a 20‐30 min time step. The RATP model was applied to an isolated, 20-yearold walnut tree grown in the field. The spatial distribution of wind speed, stomatal response to environmental variables, and light acclimation of leaf photosynthetic properties were taken into account. Model outputs were compared with data acquired in the field. The model was shown to simulate satisfactorily the intracrown distribution of radiation regime, transpiration and photosynthetic rates, at shoot or branch scales.
Effects of glutamine on growth performance of weanling piglets

An experiment was conducted to investigate the effects of glutamine on growth performance of weanling piglets. Sixty piglets weaned at 21 days of age were randomly assigned to two groups (10 piglets per pen, 3 pens per group). The control group received a maize-soybean meal-based diet. The treatment group received a maize-soybean meal-based diet supplemented with 1.0% free -glutamine. Piglets were fed the diets for 20 days. Results showed that piglets fed the glutamine diet had lower diarrhoea ratio and shorter diarrhoea duration than those fed the control diet during 20 days after weaning. During the first ten days after weaning, pigs supplemented with glutamine had a 12.05% lower feed:gain ratio than those fed the control diet ( P 0.05) compared to the control. During the second ten days after weaning, serum urea nitrogen was reduced by 4.27% and serum concentrations of total protein increased by 18.70% in pigs supplemented with glutamine compared to the control (P > 0.05). There were no differences in albumin, T 3, T 4 and growth hormone.
OFFSPRING DESERTION BY DOUBLE-BROODED FEMALE BARN OWLS (TYTO ALBA)

Abstract In double-brooded species, the sex that contributes less to breeding success may desert offspring before the end of the rearing period to start a new breeding attempt with another partner. I evaluated that prediction in the Barn Owl (Tyto alba), a species in which the male feeds the brood on average twice as often as the female. Among birds that produced a second brood, 46% of females and 4% of males deserted their offspring before completion of parental duties to remate with another partner at a distance of 1 to 10 km. Offspring desertion did not appear to incur a reproductive cost to the deserter, because deserting females at the first nest produced a similar number of offspring as nondeserting ones. In most cases, the new mate of deserting females had not been previously captured in the study area, and hence had probably not previously bred that season. Although the second clutch of deserting females was larger and produced two weeks earlier than that of nondeserting females, their nesting success did not differ.
COI barcoding of Hydroides: a road from impossible to difficult

Abstract. A fragment of the cytochrome c oxidase subunit I (COI) gene has been used increasingly for species identification and discovery in eukaryotes. However, amplifying COI has proven difficult, or even impossible, in some taxa due to non-homology between the universal primers and the target DNA region. Among the most problematic animal groups is Serpulidae (Annelida). These sedentary marine animals live in self-secreted calcareous tubes and many of them, especially of the genus Hydroides, are economically important reef-builders, foulers, and biological invaders. We developed novel taxon-specific primers for amplifying COI from Hydroides, and for the first time generated 460-bp COI sequences from 11 of 14 species attempted. Average Kimura-2-parameter interspecific sequence distance (26.2%) was >60 times greater than the average intraspecific distance (0.43%), indicating that the COI gene is effective for species delimitation in Hydroides. Although applicability of the new primers for a wide range of serpulids needs to be tested, barcoding of Hydroides is now on its way from impossible to difficult. We anticipate that COI barcoding will provide a modern species identification tool and, combined with other molecular markers, yield important insights in phylogeny and evolutionary ecology of this large and important genus.
Wild Turkey Movements During Flooding After Opening of the Morganza Spillway, Louisiana

Abstract The opening of the Morganza Spillway in Louisiana on 18 May 2011 to relieve historic flooding along the lower Mississippi river subsequently inundated thousands of acres of bottomland forest in the Atchafalaya basin. Since 2001, we have conducted Meleagris gallopavo silvestris (Eastern Wild Turkey) population ecology research on the Sherburne Wildlife Management Area, located approximately 30 km south of the Morganza spillway. In expectation of the Morganza spillway opening, between 11 and 14 May, we captured and fitted 5 (1 M, 4 F) adult Eastern Wild Turkeys with µGPS transmitters to monitor turkey response to basin flooding. By 19 May 2011, our study area was inundated with >3 m of flood waters, and remained completely inundated until 11 June 2011. Via radio-telemetry, we confirmed one female was depredated immediately before flood waters inundated our study site, and one female survived and reached dry ground created by receding water on 16 June. A second female lived 21 days and made circuitous movements within the tree canopy before dying, and the lone male died after 31 days. Movements of the second female through the canopy during flooding suggested a deliberate search for topographically higher areas within her range. Our findings suggest that rapid, widespread flooding conditions created by opening of the Morganza spillway likely negatively affected Wild Turkey populations across the Atchafalaya basin through direct reductions in survival. Further research is needed to assess how flood mitigation efforts affect Wild Turkey populations in floodplains along the Mississippi River and other alluvial floodplains.
Host plant variation in plant‐mediated indirect effects: moth boring‐induced susceptibility of willows to a specialist leaf beetle

Abstract 1. We examined the plant‐mediated indirect effects of the stem‐boring moth Endoclita excrescens (Lepidoptera: Hepialidae) on the leaf beetle Plagiodera versicolora (Coleoptera: Chrysomelidae) in three willow species, Salix gilgiana, S. eriocarpa, and S. serissaefolia.
Assessing genetic diversity of Pakistani citrus varieties using microsatellite markers.

Ten microsatellite markers i.e. Expressed Sequence Tag Simple Sequence Repeat (EST-SSR) markers were used to develop finger print profiles of sixteen Citrus cultivars. The DNA fingerprints were used to characterize the samples and detection of different level of polymorphisms. The total alleles identified were 64 with an average of 6.4 alleles / locus. Two markers i.e. TAA33 and BQ624307 gave minimum number of alleles (4) while one marker naming TAA41 detected the maximum alleles (11) and hence was the most polymorphic marker. The highest no. of alleles were observed in Tahiti lime where ten markers resulted in a total of 24 alleles. The lowest number of alleles was detected in two cultivars namely Meiwa and Eustis lime with 13 alleles each. To show the genetic relationship among varieties, the genetic dissimilarity values calculated by Ward’s minimum variance method were used to develop a dendrogram with DARwin software package v. 5.0. 158. Kew words: diversity; genetic markers; phylo-genetic relationship; microsatellites
Site factor on nutritional content of Arundinaria alpina and Oxytenanthera abyssinica bamboo shoots in Ethiopia

The objective of this study was to characterise some of the nutritional values of the two bamboo species grown and consumed in western parts of Ethiopia. The bamboo shoots of each the two species were collected from each of the three sites and analyzed for their nutritional and mineral composition. The average moisture content of the bamboo shoots was more than 90% for both species but the fat content as determined on dry weight basis indicated a significant variation ranging from 0.6 to 2.2% for Oxytenanthera abyssinica and from 0.6 to 1.5% forArundinaria alpina. Highland bamboo (A. alpina) shoots characterized with high nitrogen content (5.40%) implying that they may have high content of protein, but the lowland bamboo (O. abyssinica) was low in nitrogen content (3.10%). The average ash contents of the highland bamboo shoots collected from Tekur Incheny, Enjibara and Masha site were 14.20, 15.50 and 17.20%, respectively. The average nutrient elements in the shoots of O. abyssinica were in the order of K>N>P>Ca>Mg, whereas in A. alpina bamboo shoots observed to have slight variation in the arrangement of these elements with the order of K>N>P> Mg > Ca. Key words: Arundinaria alpina, Oxytenanthera abyssinica, bamboo shoots, mineral elements, nutrients.
Coral bleaching, reef fish community phase shifts and the resilience of coral reefs

The 1998 global coral bleaching event was the largest recorded historical disturbance of coral reefs and resulted in extensive habitat loss. Annual censuses of reef fish community structure over a 12‐year period spanning the bleaching event revealed a marked phase shift from a prebleach to postbleach assemblage. Surprisingly, we found that the bleaching event had no detectable effect on the abundance, diversity or species richness of a local cryptobenthic reef fish community. Furthermore, there is no evidence of regeneration even after 5–35 generations of these short‐lived species. These results have significant implications for our understanding of the response of coral reef ecosystems to global warming and highlight the importance of selecting appropriate criteria for evaluating reef resilience.
Abundance of invertebrate prey for birds on organic and conventional arable farms in the Netherlands

As a result of agricultural intensification, populations of farmland birds have been in steep decline for several decades. Reduction in food abundance has been mentioned as one factor behind these declines. Extensive farm management, such as use of organic methods, is expected to provide more food for birds. In this study we compared invertebrate prey abundance for birds during the breeding season between organic and conventional arable farms. We made comparisons for three different groups of birds: (1) birds feeding on soil-living invertebrates (earthworms), (2) birds feeding on ground-dwelling invertebrates and (3) birds feeding on aerial invertebrates. Invertebrate abundance was compared between organic and conventional farms, crop and non-crop habitats, and between crop and non-crop habitats under the same farm management. On organic sites, earthworm abundance was 2–4 times higher than on conventional sites, but no differences were found between crop types. Total abundance of ground-dwelling invertebrates did not differ between organic and conventional sites, but positive effects were found for several individual taxonomic groups, such as carabid beetles and spiders. On organic farms, invertebrate abundance was higher in carrots, cereals and onions compared to other crops; on conventional farms this was true for onions. When compared with most crops, ground-dwelling invertebrate abundance was low in uncropped field margins and on ditch banks. On organic farms, aerial invertebrate abundance was approximately 70% higher than on conventional farms. On cereal fields, aerial invertebrates were especially abundant
Development of Effective Seed Decontamination Technology to Inactivate Pathogens on Mung Bean Seeds and Its Practical Application in Japan

The majority of seed sprout-related outbreaks has been associated with Escherichia coli O157:H7 and Salmonella. Therefore, it is necessary to find an effective method to inactivate possible pathogenic bacterial populations on the seeds prior to sprouting. In general, sanitizing is more effective in reducing contamination on seeds than on sprouts. A successful seed decontamination treatment must inactivate microbial pathogens while preserving seed viability, germination, and vigor. Seeds vary in sensitivity to antimicrobial agents and other treatments, which determine how well they germinate and grow after treatment. In addition, a treatment that is effective for one type of seed may not be applicable to all types of seeds. Seeds vary in surface features, which may influence how well an antimicrobial agent can access and inactivate pathogens on or in the seed. The use of a number of physical, non-thermal processing technologies, alone or in combination with antimicrobial chemicals, could be useful for seed decontamination. Until now, hot water treatment at 85°C for 40 seconds followed by cooling in cold water for 30 sec and soaking in chlorine water was found effective in inactivating pathogens while preserving seed viability, germination, and vigor. Therefore, hot water treatment could be an effective seed decontamination method for mung bean seeds intended for sprout production.
In silico prediction and characterization of three-dimensional structure of Actin-1 of Arabidopsis thaliana

Abstract Actin-1 is a ubiquitous protein belonging to the reproductive class of Actin family in Arabidopsis thaliana. Thisprotein is involved in the formation of filaments that are major components of the cytoskeleton. Despite the im-portance of this protein, very little information is availa ble regarding its structure and function in plants. In thisstudy, analysis of the protein sequence was done an d comparative model of Actin-1 was constructed (UNIPROTID: P0CJ46) from Arabidopsis thaliana using the crystal structure of Dictyostelium discoideum actin (PDB ID:1NLV-A) as template employing Modelle r version 9.9. The stable structure was generated by 5 nanosecond mole-cular dynamics simulation steps usin g GROMOS43A1 96 force field that characterized its structural and dynamicfeature. The biochemical function of the final simulated structure was also investigated using PROFUNC. Themolecular simulation study suggested that the modeled Acti n-1 protein retain its stable conformation in aqueoussolution. The predicted binding sites in the modeled Actin- 1 protein are very informative for further protein-ligandinteraction study.
Insect hydrocarbons: analysis, structures and functions 1

Hydrocarbons are excellent markers for insects, as they are permanent and abundant components of their cuticle. They are present in the epicuticle, which is the most external layer of this cuticle, and they are very simple molecules, containing only carbon and hydrogen. They are linear or branched, saturated or unsaturated and contain 20 to 50 carbons. A highly sensitive method for their characterization is gas chromatography (GC) with capillary columns and various detectors, including mass spectrometry which gives structural information directly. Various biological aspects of these molecules are discussed in relation to species specificity, population polymorphism and physiological variations, and are illustrated by examples mainly from Diptera. In addition to their role in the protection of the animal, hydrocarbons actively participate in stimulation of sexual behaviour and recognition of castes and colonies for social insects. Field applications have been designed to control these insects.
Responses of reactive oxygen metabolism and quality in mango fruit to exogenous oxalic acid or salicylic acid under chilling temperature stress

After being immersed in water, oxalic acid (OA) or salicylic acid (SA) aqueous solutions, mango (Mangifera indica L. cv. Zill) fruit were stored at 14°C or at 5°C with shelf life to determine the effects of exogenous OA or SA on reactive oxygen metabolism, quality and chilling injury (CI) of the fruit. Mango CI could be reduced by OA and SA treatments. Compared with that in control, accompanied with alleviated CI at shelf life, fruit treated with OA or SA had significantly higher reduction states of ascorbate and glutathione. Moreover, the treated fruit showed lower superoxide anion content, higher hydrogen peroxide content, lower lipoxygenase (EC 1.13.11.12) activity and higher activities of superoxide dismutase (EC 1.15.1.1), catalase (EC 1.11.1.6), guaiacol peroxidase (EC 1.11.1.7), ascorbate peroxidase (EC 1.11.1.11) and glutathione reductase (EC 1.6.4.2). In addition, fruit firmness, total soluble solids and titratable acidity content were not obviously affected by OA and SA treatments. It was suggested that the effect of OA or SA on mango CI probably attributed to more reducing status of ascorbate and glutathione, less O2− accumulation and more H2O2 accumulation.
Feeding, Thermoregulation, and Offspring Viability in Gravid Garter Snakes (Thamnophis sirtalis): What Makes Laboratory Results Believable?

Abstract Animals held in the unnatural surroundings of the laboratory sometimes may exhibit unusual behavior, making experimental results difficult to interpret unless the natural history of the species is well understood. Some well-studied species, such as the garter snake Thamnophis sirtalis, which usually seem to adapt well to captivity, are therefore commonly used in laboratory experiments and assumed to function normally. However, this assumption may sometimes be unfounded. In this study, captive gravid T. sirtalis showed reduced feeding behavior, similar to free-ranging gravid snakes from the same population but showed very different thermoregulatory behavior, choosing low temperatures instead of high. By contrast, gravid congeners, Thamnophis elegans, showed similar feeding and thermoregulatory behavior in captivity and in the field. Choice of lower temperature by gravid T. sirtalis apparently led to extended periods of parturition for individual females and a high incidence of dead young in litters. Other studies of T. sirtalis in captivity also have yielded fairly high proportions of dead offspring, suggesting that (1) this species has a relatively high background rate of natural stillbirth; and/or (2) it is not always as suitable a species for behavioral/reproductive work in the laboratory as it seems to be. Whether or not the first proposition is true, I conclude that T. sirtalis in this study behaved differently from snakes in the field, exacerbating the rate of stillbirth. Thus, laboratory studies of behavior will be most fruitful if informed by field studies.
Random Amplified Polymorphic Dna-PCR Typing of Vibrio parahaemolyticus Isolated from Local Cockles (Anadara granosa)

Randomly amplified polymorphic DNA (RAPD) was used in this study to examine the genetic relatedness among the Vibrio parahaemolyticus strains. In the analysis by RAPD-PCR, the size for RAPD fragments ranged from 0.25 to 10.0 kb with average number of ten bands. The RAPD profiles revealed a high level of DNA sequence diversity within the Vibrio parahaemolyticus strains tested. Hence, this study, demonstrated that the local cockles (Anadara granosa) in the study area are populated by genetically polymorphic strains of V. parahaemolyticus. In addition, RAPD-PCR is simple, robust and sensitive typing methods to differentiate the V. parahaemolyticus strains.
Predicting climate warming effects on green turtle hatchling viability and dispersal performance

Ectotherms are taxa considered highly sensitive to rapid climate warming. This is because body temperature profoundly governs their performance, fitness and life history. Yet, while several modelling approaches currently predict thermal effects on some aspects of life history and demography, they do not consider how temperature simultaneously affects developmental success and offspring phenotypic performance, two additional key attributes that are needed to comprehensively understand species responses to climate warming. Here, we developed a stepwise, individual-level modelling approach linking biophysical and developmental models with empirically derived performance functions to predict the effects of temperature-induced changes to offspring viability, phenotype and performance, using green sea turtle hatchlings as an ectotherm model. Climate warming is expected to particularly threaten sea turtles, as their life-history traits may preclude them from rapid adaptation. Under conservative and extreme warming, our model predicted large effects on performance attributes key to dispersal, as well as a reduction in offspring viability. Forecast sand temperatures produced smaller, weaker hatchlings, which were up to 40% slower than at present, albeit with increased energy stores. Conversely, increases in sea surface temperatures aided swimming performance. Our exploratory study points to the need for further development of integrative individual-based modelling frameworks to better understand the complex outcomes of climate change for ectotherm species. Such advances could better serve ecologists to highlight the most vulnerable species and populations, encouraging prioritization of conservation effort to the most threatened systems.