Miracle-dz/UniFAR-FTUs huggingface dataset:
Paramyxoviruses in Australian snakes

This thesis describes the isolation and molecular identification of a novel paramyxovirus found in Australian snakes. The virus is named Sunshine virus after the geographical origin of the first isolate: the Sunshine Coast of Queensland, Australia. For decades, Australian veterinarians have been presented with snakes displaying neurorespiratory signs. The clinical signs, pathological findings and the results of overseas diagnostic testing, have suggested that at least some of these snakes were infected with paramyxoviruses, most likely ferlaviruses. Australian veterinarians provided 463 samples to be screened for the presence of viruses and nine were found from five snakes from two collections. For all isolates, cytopathic effects consisted of extensive syncytial cell formation with minimal cell lysis. Further characterisation was performed on one of these isolates, BHP1-Lung (from a lung homogenate of a black-headed python [BHP], Aspidites melanocephalus with mild respiratory signs and stomatitis). Testing this isolate for haemagglutinating and neuraminidase activity provided equivocal results. The virus could not be found by electron microscopy. Polymerase chain reaction to detect a broad range of paramyxoviruses, reoviruses, adenoviruses and herpesviruses was also non-contributory. Through the use of high-throughput sequencing, BHP1-Lung was identified as a novel paramyxovirus. Phylogenetic analysis of the nucleoprotein (N), matrix (M), fusion (F) and polymerase (L) proteins clustered this virus within the family Paramyxoviridae but outside of both subfamilies. Primers were designed that could detect Sunshine virus which enabled clinical data that is associated with Sunshine virus infection to be described. Clinical signs are typically non-specific (e.g. regurgitation, lethargy, inappetence) and/or can be localised to the neurological and/or respiratory systems. Gross pathology is usually unremarkable. Histopathological findings consist primarily of white matter spongiosis and gliosis of the hindbrain with a mild bronchointerstitial pneumonia.
SYNTHESIS, ANTI-INFLAMMATORY AND ANTI-MICROBIAL ACTIVITY OF PYRIMIDINE-5-CARBOXYLATE DERIVATIVES

Ethyl-2-amino-4-chloro-6-(2, 4, 6 trichloro phenyl amino) pyrimidine-5-carboxylate and ethyl-2-amino 4-chloro-1, 3-dimethyl-6-(phenyl amino)-1,2,3,4 tetrahydro pyrimidine-5-carboxylate derivatives were synthesized through Cyclocondensation and Michel type of addition reaction with the aromatic anilines, guanidine and benzamidines. Synthesized novelderivatives were confirmed by elemental analysis viz., IR, 1HNMR and Mass spectroscopy. These novel derivatives have been screened for Antibacterial, Antifungal and Antiinflammatoryactivity.
Glucose metabolism of the swimbladder tissue of the european eel Anguilla anguilla

Glucose uptake from, and lactate release into, the blood have been analysed in the active gas- depositing swimbladder of the immobilized European eel Anguilla anguilla. Under normoxic conditions, 0.72 micromole min-1 glucose was removed from the blood supply, while lactate was released into it at a rate of 1.16 micromole min-1. The rate of gas deposition into the swimbladder was significantly correlated with the rate of lactate production. Under hypoxic conditions, glucose consumption by, and lactate production of, the swimbladder tissue were reduced, as was the rate of gas deposition. Compared with normoxic conditions, lactate concentration in the swimbladder tissue was elevated after 1 h of hypoxia, indicating a decrease in lactate release. No difference in the osmolality of arterial and venous blood could be detected in these experiments. Combining the data for glucose uptake and lactate release measured under normoxic conditions with the values for O2 uptake and CO2 production of the swimbladder tissue measured under similar conditions in a previous study, a quantitative evaluation of glucose catabolism was performed. According to the O2 uptake of the tissue, only about 1 % of the glucose was oxidized, while about 80 % was fermented to lactic acid. The remaining 0.14 micromole min-1 glucose was presumably catabolized through the pentose phosphate shunt, as indicated by the CO2 production of 0.16 micromole min-1 that cannot be explained by aerobic metabolism.
The Finance-Growth Nexus: Evidence from Emerging Markets

The finance growth literature ignores the role of bond markets in financing private investments. Moreover, the impact of bank crisis on the finance growth link has been largely overlooked. This paper aims at casting light at the finance growth link in emerging economies by accounting for bond markets and controlling for banking sector crises. Data on economic growth and financial development indicators for 15 emerging economies (drawn from Africa, Asia, Latin America, and Europe) were analysed using a system generalized-method-of-moments (GMM) technique. It is observed that while banking sector development is related to economic growth (albeit negatively), no statistically significant relation is observed between stock markets and or bonds markets and economic growth. Moreover, a banking crisis is found to affect the finance growth link in such a manner that the link weakens when a banking crisis is introduced to the model. Our results are robust to omitted variable bias, simultaneity problem, heteroscedasticity and autocorrelation.
Production of an interspecific hybrid between Brassica fruticulosa and B. rapa

An interspecific hybrid between a wild species, Brassica fruticulosa (2n = 16, FF) and a crop Brassica species, B. rapa (2n = 20, AA) was synthesized using sequential ovary-ovule culture on MS medium supplemented with casein hydrolysate. Morphological, molecular and cytogenetic analysis confirmed the true hybrid nature of the offspring. The F 1 plants (2n = 18) were intermediate in morphology, highly pollen-sterile as well as self-sterile. A maximum of three bivalents per PMC was recorded, but 14 I + 2 II was the most common meiotic configuration. Normal pollen fertility and regular bivalent (18 II) formation was observed in the amphiploid sectors of the hybrid plants. The F 1 hybrid harboured significantly lower aphid populations than the crop Brassica parent.
EFFICIENCY OF BOVINE IGF-I GENE IN THE IMPROVEMENT OF MILK PRODUCTIVITY USING MARKER-ASSISTED SELECTION (MAS)

Because of insulin-like growth factor-I (IGF-I) gene plays an important regulatory function in milk secretion in cattle, IGF1 gene is potential quantitative trait locus and genetic marker (i.e, SNP) associated with milk production trait in cattle. Consequently, marker-assisted selection (MAS) will be useful to increase and accelerate the rate of genetic improvement on milk productivity. In this study, 48 female Holstein cattle reared under Egyptian conditions were selected based on their milk productivity and DNA from blood was extracted to amplify 249-bp of the gene encoding IGF-I. According to the breeding value, PCR products of IGF-I gene (249-bp) were sequenced only in the 15 highest and lowest milk productivity animals (GenBank accession numbers from gb|HQ183710| to gb|HQ183724|, sequentially). The result indicated that two single nucleotide polymorphisms (SNP's) at two different positions were observed in one of the highest milk productivity animals. Where, all 15 animals have adenine (A) and cytosine (C) bases at the positions 33 and 63, respectively, except, one animal (GenBank Acc. No. gb|HQ183711|) has thymine (T) and guanine (G) bases at the same positions (33 and 63, respectively). Thus, this finding can be used as marker-assisted selection (MAS) for high milk productivity in Holstein cattle.
Nanobacteria as extremophiles

Nanobacteria are the smallest cell-walled bacteria, only recently discovered in human and cow blood and in commercial cell culture serum. Nanobacteria do show several extreme properties, such as growth in over 5% sodium chloride, small size, very slow growth rate and ability to survive under unfavorable conditions, including lack of nutrients, boiling temperature, high pressure and 1.5 Mrad dose of gamma irradiation. Environmental changes can cause drastic changes in their unit size: under unfavorable conditions they form very large multicellular units. Yet, they can release elementary particles, some of which are less than 100 nm in size, smaller than many viruses. Although metabolic rates of nanobacteria are very slow, they can produce carbonate apatite on their cell envelop mineralizing rapidly most of the available calcium and phosphate. Nanobacteria belong to, or may be ancestors of, alpha-2 subgroup of Proteobacteria. They may still partially rely on primordial life-strategies, where minerals and metal atoms associated to membranes, played catalytic and structural roles reducing the number of enzymes and structural proteins needed for life. Simple metabolic pathways apparently only compatible with life in very small cells, may support the 10,000-fold slower growth rate of nanobacteria, as compared to the common bacteria. Simplistic life-strategy may also explain the endurability of this life-form in extreme environmental conditions.
Bumblebee pollination of understorey shrub species in a tropical montane forest in Costa Rica

This study addresses the pollination ecology of shrub species in an upper montane forest in Costa Rica, where the diversity of insect visitors is much below that of the well-studied tropical forests of lower elevations. Data are presented on visitation rates by the tropical bumblebee Bombus ephippiatus to flowers of three species, pollen loads on bumblebee bodies, and pollen loads on stigmas of two of the species. High visitation rates to flowers of Palicourea brenesii were found, a species which produces copious amounts of nectar. Visitation rates to nectarless Leandra subseriata and Deppea grandiflora were much lower. Conspecific pollen comprised on average 90% of the pollen load on stigmas of Leandra, while Palicourea stigmas carried only 26 to 55% conspecific pollen. With only two ovules per flower, fruit and seed set in Palicourea were not limited by a shortage of conspecific pollen. In Leandra, 20–25% of the flowers received too few conspecific pollen grains for maximum seed set among 440 ovules per flower. Individual bumblebees showed no constancy in plant choice, judging from the high number of different pollen types (6–12) on their bodies. Workers returned frequently to the same Palicourea patch without visiting nearby Palicourea plants, which suggests the use of foraging paths.
Mass Spectrometry Data Analysis in the Proteomics Era

With the advent of whole genome sequencing, large-scale proteomics has rapidly come to dominate the post- genomic age. As such, tandem mass spectrometry has emerged as the most promising and powerful technique in this area but analysis of raw spectra remains one of the principle bottlenecks to making effective use of the technology. Analytical approaches for identifying proteins from MS/MS data fall into two categories: comparing measured fragment spectra to theoretical spectra from sequence databases and de novo peptide sequencing. Available methods still have weaknesses, highlighting the need for new powerful algorithms that are able to exploit the enormous volume of data generated by pro- teomic experiments. Recent efforts have also been directed towards the identification of post-translational modifications, biomarker discovery and quantitative proteomics. Overall, the intended goal of this review is to give as thorough as possi- ble an overview of state-of-the-art approaches and tools developed to analyze tandem mass spectra in different fields and discuss future directions aimed at overcoming the limits of present methods.
Demographic Trends and Community Stability in a Montane Amphibian Assemblage

Abstract: We conducted a long‐term study of a montane amphibian community in Peñalara Natural Park ( central Spain ) to analyze population trends. We recorded larval density and number of ponds used for reproduction for nine species in two time periods: 1982–1986 and 1999. We used chi‐square analysis to compare the observed ratio of extinctions to colonizations to an expected ratio of 1:1 at the ponds used for reproduction for each species. We also compared larval densities of six species in both time periods. Overall, we found no differences in species composition. However, separate analyses for each of the nine species inhabiting the study area showed that underlying this apparent stability were significant opposite population trends in six species. Three species expanded their ranges, whereas three suffered severe range reductions and population decreases. A chytrid infection was responsible for the decline of Alytes obstetricans, almost extirpated from the surveyed area, whereas less dramatic decreases were observed for Salamandra salamandra and Bufo calamita. Our study emphasizes the need to analyze each species separately to assess the conservation status of amphibian assemblages. In this context, the conservation of endemic species with restricted distribution areas should be considered a priority.
Analysis of the niche of two sympatric species of Bombus (Hymenoptera, Apidae) in southeastern Brazil

ABSTRACT The sources of food and the width and overlap of the food niches of Bombus atratus and Bombus morio were determined by field observations and analysis of the pollen loads carried to the colonies by worker bees. The two species together utilized 50 flower species of which 26 were used by both. Solatium paniculatum (Solanaceae) and Psidium guajava (Myrtaceae) were the most frequently visited plants. The food niche width and niche evenness for both species were similar. The correlation between niche width and niche evenness was non-significant showing that evenness does not depend on niche width. In addition, there was no correlation between niche width and overlap, i.e. overlap varied independently of niche width. A high overlap of food sources utilized by the two species was observed in September, October and November. This may be explained in one of two ways: (a) if B. atratus and B. morio compete for resources, competition would be more intense during those three months; (b) the convergency of both species to the same plant species (Solatium paniculatum and Psidium guajava) would only result in more intensive competition if resources were limiting. However, at that period of the year resources are abundant, therefore although the values of overlap were high, competition need not have occurred.
Resurrecting deadly carrots: towards a revision of Thapsia (Apiaceae) based on phylogenetic analysis of nrITS sequences and chemical profiles

Thapsia is a small genus of herbaceous perennials in Apiaceae. Thapsia occurs around the Mediterranean, extending from the Atlantic coasts of Portugal and Morocco to Crete and other Greek Islands. Thapsia is commonly known as deadly carrot because of its poisonous effects. The resin from Thapsia spp. has been used in traditional medicine and included in European pharmacopoeias, and several species contain biologically important sesquiterpene lactones, such as thapsigargin. Accordingly, Thapsia has for decades been subject to chemical investigations searching for new specialized metabolites with potential as drug leads. However, no generally accepted taxonomic concept of > 40 species and synonyms exists. To address the phylogenetics and circumscription of Thapsia, we present the first molecular phylogenetic hypothesis of Thapsia based on sequences of the nuclear ribosomal internal transcribed spacer (nrITS) region from 50 accessions of Thapsia and representatives of all currently recognized genera in subtribe Daucinae. Phylogenetic analysis using maximum parsimony and Bayesian inference resulted in a well-resolved topology with strong support for inclusion of all the species studied here from Ammodaucus, Distichoselinum, Elaeoselinum, Guillonea and Margotia in Thapsia, in correspondence with previous phylogenetic studies of Apiaceae. Elaeoselinum is not monophyletic. Clades in Thapsia correlate well with previous observations of groupings based on the occurrence of biologically important sesquiterpene lactones, such as thapsigargin and thapsane and derivatives thereof. The result of the phylogenetic analysis necessitates nomenclatural adjustments. Thus, we propose a broader generic concept for Thapsia. Here T. asclepium, T. gummifera and T. tenuifolia are reinstated, new name combinations are made for T. leucotricha, T. scabra and T. thapsioides, and one new species, T. smittii, is established from T. maxima type II. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 174, 620–636.
Biology of the Acacia gall rust, Uromycladium tepperianum

Germinating teliospores of Uromycladium tepperianum formed penetration pegs, which directly penetrated host epidermal cells, on the tip cell of three-celled germ tubes. Diploid nuclei within teliospores appeared to divide soon after germination commenced. Only one of the daughter nuclei moved out of the teliospores with the developing germ tubes. Reactions of seedlings inoculated with teliospores from different host species and differences in teliospore dimensions indicated that distinct genotypes of U. tepperianum adapted to particular host species occur in Australia. Limited hyphal growth occurred in two of 20 African Acacia spp. inoculated with teliospores from Acacia saligna. Fungal development was, however, restricted by necrosis of surrounding host cells. U. tepperianum appears to be suitably host-specific for use as a biological control agent against Ac. saligna, a weed in South Africa.
Yield improvement in soybeans using recurrent selection

The objective of this study was to evaluate the potential of recurrent selection for improving seed yield in a soybean population. Seventeen parents, chosen for their high yield potential in the sub-tropical environments of Southern and Central Queensland were intermated using a diallel cross mating system. F1 plants were intercrossed in pairs for two more generations and then allowed to self for two generations to produce the base population. The selection criterion was the seed yield of S1 lines grown at Hermitage Research Station. The selection intensity was approximately 10%. After five cycles of recurrent selection the mean yield of the population and the mean yield of the lines selected for recombination had improved by 17% and 54% respectively, in comparison with one of the original parents, Davis. Progress from recurrent selection was evaluated using fifty randomly selected lines from the base population and from each of the first three cycles of selection. The average gain per cycle in seed yield, averaged over five sites was 128 kg ha-1 or 5.4% of the yield of the base population. Greater progress (9.8% per cycle) was measured at the testing site for selection (Hermitage Research Station) which was heavily infested with phytophthora root and stem rot than at three other sites (2.7% per cycle) which has nil or low levels of disease. Broad sense heritabilities for the base population and for cycles 1, 2 and 3 in the evaluation trial were 0.34, 0.25, 0.13 and 0.14 respectively compared with a mean heritability of 0-64 for the first five cycles of the selection experiment. Expected gain from further cycles of selection was estimated at 102 kg ha-1 per cycle for three replicates at a single site. In the evaluation trial correlated responses to selection for yield were found in a number of other traits. Days to flowering was reduced by 0.8 days/cycle while days to maturity increased by 1 day/cycle. Seed shattering score was significantly reduced from 0.98 to 0-69 while there were only minor changes in plant height, lodging and seed coat quality score. Resistance to root and stem rot and seed coat mottling, due to primarily to soybean mosaic virus, were also significantly increased. The improvement in phytophthora resistance was expected as the field used for S1 yield testing had become infested with the disease. A covariate analysis indicated that about half the improvement in seed yield at the Hermitage site was due to the correlated response of increased resistance to phytophthora root and stem rot.
How do Learners Make Use of a Space for Self-Directed Learning? Translating the Past, Understanding the Present, and Strategizing for the Future

This article aims to reveal how learners make use of a space for self-directed learning to promote collaborative autonomous learning, drawing on data collected at a Japanese language institution for the Economic Partnership Agreement (EPA) care worker candidates in Osaka. The data analysis shows that, through the activities the learners chose and organized, they imagined an ideal L2 self and created their own L2 world. As soon as the self-directed learning session had started, they created their own group on Facebook and promoted learning activities which were related with their real lives in Japan. These activities on Facebook created a learning space beyond the classroom. These online activities they engaged in eventually returned to the classroom space and led to them increasingly taking ownership of the physical space. This research reveals that an important factor for self-directed learning is providing learners spaces and allowing them to explore the boundaries and possibilities of that space. The learners in this case study used the space to translate their past experiences and present emotions into the second language context, and moreover, to strategize for the future. To encourage collaborative autonomous learning, the activities must be organized around learners’ inner worlds where their emotions, experiences and futures exist.
Genetic refuges for a self‐sustained fishery: experience in wild brown trout populations in the eastern Pyrenees

– Management policies balancing harvest and conservation of natural populations of fish are difficult to establish, both scientifically and politically. This issue is particularly difficult when those populations represent native genetic resources. Since 1997, several brown trout populations in the eastern Pyrenees Mountains (Spain) were designated as ‘genetic refuges’ under varying fishing regulations, where releases of hatchery-origin fish are not permitted. We analysed genetic variation in samples of brown trout from six of those refuge populations and four non-refuge populations within the same region. Each population was sampled in four separate years: 1993, 1999, 2004 and 2006. Our analyses were based on a diagnostic allele (LDH-C*90) that distinguishes native and exogenous hatchery populations. Comparisons were based on stocking histories before and after refuge designations and on three management strategies: fished, unfished and catch-and-release. Overall, we detected significant genetic introgression resulting from past stocking practices despite the current restriction of hatchery releases imposed by the recent genetic refuge policy. However, this new policy has prevented detectable introgression from increasing throughout the region and together with additional measures on length and number of captured fish is contributing to self-sustained fisheries that are achieving conservation goals. Quick acceptance of ‘genetic refuges’ by anglers in one particular river, the Ter River basin, has been a key factor in protecting native gene pools compared with the Segre River basins where refuges were not readily accepted.
DIVERSITY OF CHRYSOPHYCEAE (HETEROCONTOPHYTA) IN THE ZASAVICA RIVER (SERBIA)

Detailed studies of the Chrysophyceae class of algae have not been undertaken in Serbia thus far. The golden al- gae usually occur during the winter and spring months. Chrysophyceae of the Zasavica River in Serbia were studied at two localities from December 2012 to Jun 2013. In our research, 26 taxa were recorded and the genus with the highest diversity was Mallomonas (15 species). The most abundant species during the whole study period were Synura uvella, Dinobryon divergens and Dinobryon sociale. At the beginning of summer, Chrysophyceae disappeared from the phytoplankton com- munity.