Miracle-dz/UniFAR-FTUs huggingface dataset:
POPULATION DYNAMICS OF AEROMYCOFLORA AT THREE SITES OF RAWALPINDI BY EVALUATING TWO SAMPLING METHODS

The air borne mycoflora of three sites (PMAS-AAUR, Adyalla and Sohan village) were studied with main emphasis on its occurrence, density, diversity for three consecutive years, by employing bioaerosol sampling method, (All glass impinger ) and Gravimetric plate culture plate method ) on four media. A total of 20,409 fungal spores belonging to fifteen genera viz. Alternaria, Aspergillus, Cladosporium , Curvularia , Drechslera , Epicocum, Fusarium, Mucor, Rhizopus, Penicillium, Geotrichum, Epicocum and Helminthosporium , Stemphylium, Stachybotrys and Trichoderma species were recovered. Out of fifteen genera the highest relative contribution was attributed to Aspergillus with 16.73% of total fungal spore count, followed by Alternaria, Cladosporium, Mucor and Penicillium with 15.83, 13.79 , 10.71 and 9.39 percent share respectively. Fuasrium with 0.33% contribution in the total fungal spore count was established as the lowest in occurrence followed by Stachybotrys (0.62%), Helminthosporium (0.85%) and Geotrichum (0.85%). There was a significant difference between the efficiency of two methods i.e. Gravimetric Plate (GPM) and All Glass Impinger (AGI) in trapping individual spore type as well as mean concentration of all fungal spores during three years of the study. The Gravimetric Plate Method was found outrival and statistically significant than AGI in capturing all sixteen types of airborne fungal spores were calculated t value for each fungal genera was much elevated than critical value of t (2.131) at 5% level of significance ( P ≤ 0.05). In conclusion, a range of fungal spores were present throughout the year and the land use type may vary likely have an impact on the course of spore occurrence. Thus present information would help to identifying the fungal infection by employing Gravimetric plate method.
Thermal Effects on Bioaccumulation and Antioxidant Enzyme Response in the Liver and Gills of Tilapia Oreochromis niloticus Exposed to Arsenic

The effects of waterborne arsenic (As) exposure on bioaccumulation and antioxidant defenses were examined in the liver and gills of tilapia, Oreochromis niloticus, under thermal stress. Tilapia were exposed to different As concentrations (0, 200, and 400 μg L -1 ) at three water temperatures (20, 25, and 30°C) for 20 days. After As exposure, higher levels of As accumulation were observed in the gills compared with the liver in elevated water temperatures. In terms of the antioxidant response, glutathione (GSH) levels and the activities of glutathione reductase (GR), glutathione peroxidase (GPx), and glutathione S-transferase (GST) significantly decreased in the liver and gills of tilapia exposed to As for 20 days, regardless of the As concentration (200 and 400 μg L -1 ) or water temperature. These enzyme activities exhibited greater fluctuations in the liver and gills of tilapia after As exposure in water warmer than 20°C. The present findings suggest that the simultaneous stress of temperature change and As exposure can accelerate As accumulation and alter the antioxidant enzymes activities of tilapia.
The graph-guided group lasso for genome-wide association studies

In this work we propose a penalised regression model in which the covariates are known to be clustered into groups, and the clusters are arranged as nodes in a graph. We are motivated by an application to genome-wide association studies in which the objective is to identify important predictors, single nucleotide polymorphisms (SNPs), that account for the variability of a quantitative trait. In this applications, SNPs naturally cluster into SNP sets representing genes, and genes are treated as nodes of a biological network encoding the functional relatedness of genes. Our proposed graph-guided group lasso (GGGL) takes into account such prior knowledge available on the covariates at two dierent levels, and allows to select important SNPs sets while also favouring the selection of functionally related genes. We describe a computationally ecient algorithm for parameter estimation, provide experimental results and present a GWA study on lipids levels in two Asian populations.
Regulation of UV-Protective Pathways Downstream of the Melanocortin 1 Receptor in Melanocytes

OF DISSERTATION REGULATION OF UV-PROTECTIVE PATHWAYS DOWNSTREAM OF THE MELANOCORTIN 1 RECEPTOR IN MELANOCYTES Malignant cutaneous melanoma is the deadliest form of skin cancer, and a majority of melanoma diagnoses are a result of exposure to ultraviolet (UV) radiation. UV radiation causes DNA damage, which if not repaired correctly via nucleotide excision repair (NER) can result in mutations and melanomagenesis. The melanocortin 1 receptor (MC1R) is a Gs protein coupled receptor located on melanocyte plasma membranes and is involved in protecting the skin from UV induced damage. MC1R signaling results in the activation of two protective pathways: 1) induction of eumelanin synthesis downstream of micropthalmiaassociated transcription factor (MITF) and 2) acceleration of NER downstream of ataxia telangiectaseia mutated and Rad3 related (ATR). MC1R signaling, however, also promotes melanocyte proliferation, therefore, the activation of the MC1R pathway must be regulated. The overall hypothesis of this dissertation is that the pathways downstream of MC1R can be manipulated to protect against UV induced damage. Chapter 2 investigates the regulation of the MC1R neutral antagonist human βdefensin 3 (βD3). UV damage did not induce βD3 mRNA expression in ex vivo human skin explants. The induction of βD3 expression instead correlated with inflammatory cytokines including TNFα. Chapter 3 investigates the interdependence and cross talk between the two protective pathways downstream of MC1R. We directly tested the effect of MITF on the acceleration of NER and the effect of ATR on the induction of eumelanin synthesis following MC1R activation. MITF was not required for the acceleration of NER as mediated by ATR, however, the induction of transcription of enzymes involved in eumelanin synthesis was dependent upon ATR kinase activity. Finally, Chapter 4 investigates the mechanism by which MC1R promoted proliferation and whether the two UV protective pathways downstream of MC1R could be selectively activated without the risk of melanocyte proliferation. MC1R signaling resulted in activation of the mechanistic target of rapamycin complex 1 (mTORC1), a major regulator of cell growth and proliferation. Inhibition of mTORC1 signaling via rapamycin prevented MC1R induced proliferation in vitro. Rapamycin, however, did not prevent MC1R induced eumelanin synthesis or the acceleration of NER in vitro or in vivo suggesting it is possible to selectively activate the beneficial signaling pathways without the risk of melanocyte proliferation. The results of this dissertation suggest that MC1R signaling could be augmented in individuals to prevent UV induced damage.
Mitochondrial Diversity and Phylogenetic Structure of Marghoz Goat Population

The genetic diversity and phylogenetic structure was analyzed in Marghoz goat population by mitochondrial DNA sequences. Phylogenetic analysis was carried out using hyper variable region 1 (968 bp) obtained form 40 animals. Marghoz goat proved to be extremely diverse (average haplotype diversity of 0.999) and the nucleotide diversity values 0.022. A total of 40 Marghoz goats were grouped into six haplotypes and the large majority of haplotypes were present in 15 animals. All Marghoz haplotypes were classiﬁed into C haplogroup and revealed remarkably high genetic distances within the population when compared with other Asian goat populations, indicating high genetic variation in the Marghoz goat. These results indicate high-divergence status of the Marghoz goat and will influence breeding and conservation strategies adopted for this breed.
Production and characterization of monoclonal antibodies directed against glucosyltransferase synthesizing water-insoluble glucan from Streptococcus mutans (sobrinus) B13.

Four hybrid cell lines secreting monoclonal antibodies (McAbs) against glucosyltransferase synthesizing water-insoluble glucan (GTase-I) were generated after fusing myeloma cells P3U1 with splenocytes from mice immunized with GTase-I from Streptococcus mutans (sobrinus) B13-N. A total of 495 colonies were detected in 340 wells. Four cell lines were established from single cells, each producing antibody to GTase. Cell lines 29E7, 21GC7 and 42HB8 were found to secrete an IgG2a type immunoglobulin and 29EG, an IgM type immunoglobulin. McAb 29EG was found to inhibit water-insoluble glucan synthesis by GTase-I by 50% and 29E7 to inhibit weakly. However, other McAbs did not show any inhibitory effect in spite of binding to GTase-I. In the experiment testing McAb 29EG for binding to GTase preparations from different serotypes of S. mutans, McAb 29EG was found to bind serotypes a. d and g but not other serotypes, suggesting that this McAb was specific in binding the crossreactive site on the GTase molecule from the three serotypes.
The ecology of root disease fungi in Missouri forests

I surveyed the Missouri Ozarks region for the pathogenic fungus Heterobasidion irregulare, a parasite that has gone largely disregarded within the region since the 1960s despite its potential to cause major problems for the restoration and management of shortleaf pine (Pinus echinata Mill.). Using spring surveys, I recovered the pathogen (as both spores and basidiomata) at 21 of 31 surveyed sites throughout the extent of the Ozarks region. Using a more intensive spore-trapping procedure, I also surveyed pure hardwood stands within the oak-pine matrix and pure hardwood forests outside the distribution of shortleaf pine. I detected some spores from pure hardwood stands that were relatively near overstory pines, but I detected no spores from pure hardwood forests at long distances (>100 m) from pines. I conducted a GIS-based analysis of pathogen presence and relative spore abundance relative to pine patch distance, pine patch size, and pine patch edge length within the surrounding landscape and determined that distance to the nearest overstory pine as well as the number of pine patches within 500 m were important predictive variables. These data indicate that Heterobasidion irregulare inoculum is likely to be detected within 100 m of overstory pines in the Missouri Ozarks region and demonstrate the ability of this pathogen to persist and spread inoculum even in a landscape with significantly reduced host plant density.
Communities of epigeic beetles in tree line from montane spruce forest to secondary meadow in the different stage of the forest decline in the area of Modrava (Bohemian forest, Czech Republic)

Abstract Communities of epigeic beetles were studied using pitfall trapping on 10 plots with the different stage of decline and clear-cut plots without coarse woody debris. Species richness (number of all species, S), total species diversity as the Shannon-Wiener’s index (H) and equitability (e) were calculated in the DBreleve. The Ward’s method of hierarchical agglomerative classification with Euclidean distance was used for the differentiation of the communities on the plots. Species data for this analyse were represented by logarithm-transformed activities [log(x+1)]. The single-factor analysis of variance (ANOVA) was used for statistical testing of differences in structural parameters (e.g. species richness and diversity) amongst distinguished groups of the plots. The species diversity and activity differs on glades without trees and coarse woody debris. The highest number of species was found in clear-cut areas. The lowest number of species was found on the plots with the living forest particularly invaded by bark beetle. This fact is caused by the fact that the clear-cut plots are invaded by ubiquitous and anthropotolerant species with good migration possibilities. These species are adapted to habitats without trees and are able to leave even in the habitats with very sparse or without vegetation. Species living in the forest even under the bark beetle attack are often stenotopic and adapted to the forest microclimate (higher humidity and low average temperature). These species are very sensitive to great difference in the daily changes of microclimate. The study of beetle communities support the hypothesis that the keeping of dead tree stands on plots after bark beetle outbreak is better for biodiversity conservation than the cutting down of trees and the abolishment of stems.
Isolation by distance, not rivers, control the distribution of termite species in the Amazonian rain forest

The spatial distribution of species is affected by dispersal barriers, local environmental conditions and climate. However, the effect of species dispersal and their adaptation to the environment across geographic scales is poorly understood. To investigate the distribution of species from local to broad geographic scales, we sampled termites in 198 transects distributed in 13 sampling grids in the Brazilian Amazonian forest. The sampling grids encompassed an area of 271,500 km2 and included the five major biogeographic regions delimited by Amazonian rivers. Environmental data for each transect were obtained from local measurements and remote sensing. Similar to previous studies, termite species composition at the local scale was mostly associated with measures of soil texture and chemistry. In contrast, termite species composition at broad geographic scales was associated with soil nutrients, and the geographic position of the transects. Between 17% and 30% of the variance in termite species composition could be attributed exclusively to the geographic position of the transects, but could not be attributed to measured environmental variables or the presence of major rivers. Isolation by distance may have strong effects on termite species composition due to historic processes and the spatially structured environments along distinct geological formations of Amazonia. However, in contrast to many taxa in Amazonia, there is no evidence that major rivers are important barriers to termite dispersal. This article is protected by copyright. All rights reserved.
Pathogenic and molecular characterisation of Pythium spp. inducing root rot symptoms in other crops intercropped with beans in Southwestern Uganda

Objective: In Southwestern Uganda, bean root rot epidemics associated with Pythium species are frequent despite the use of various management methods. This study set out to determine whether other crops in bean cropping systems of Southwestern Uganda are affected by Pythium root rots and to characterise the Pythium species using Internal transcribed sequence (ITS) DNA primers. Methodology and Results: Root rots were found to occur on maize, sorghum, peas and potato sampled from farmer’s fields where they were found to be intercropped with beans affected by root rot. Pythium species were isolated using Corn meal agar (CMA). DNA was subsequently extracted and polymerase chain reaction ( PCR) analysis carried out using ITS DNA region primers and then the PCR products were sequenced. Twenty-one Pythium species were isolated. Cross pathogenicity tests were done in a screen house using bean pathogenic Pythium species and Pythium , species derived from other crops intercropped with beans. The Pythium species were moderately to non-pathogenic in maize and millet while those in sorghum and peas were highly pathogenic. Conclusion and application of results: This study found that other crops intercropped with beans in Southwestern Uganda were affected by Pythium root rots. Peas and sorghum were highly susceptible to the pathogenic Pythium species and could therefore be contributing to the continuous bean root rot epiphytotics in the region. On the other hand, maize and millet were non pathogenic to the Pythium species. This knowledge could be used to advice farmers not to include sorghum and peas when intercropping with beans, as they seem to be contributing to the Pythium inoculum load. They could alternatively use maize and millet, as they are not susceptible to the pathogenic Pythium species. Keywords: Pythium , root rots, Southwestern Uganda, ITS DNA, pathogenic
Fungicide sensitivity of Dothistroma septosporum isolates in the UK

Summary Dothistroma septosporum, a causal agent of Dothistroma needle blight (DNB), is a damaging fungal pathogen of pines that has recently started to affect native Scots pine woodlands in the UK. In addition to silvicultural methods, fungicide spraying of forest nursery stock can help prevent the spread of DNB. However, the effectiveness of modern single-site fungicides against D. septosporum and the risk of fungicide resistance evolution remain largely unknown. In this project, we aimed to establish sensitivity profiles of D. septosporum to some widely used single-site fungicide classes in vitro, and to determine whether fungicide resistance is already present, as this could increase the spread of D. septosporum genotypes on planting stock in native woodlands. For this purpose, we compared isolates of D. septosporum, originating from pine stands unexposed to fungicides, with isolates from nursery outbreaks, for sensitivity to a range of commonly applied fungicides. Most of the fungicides we tested were effective in vitro and we observed no significant shifts in sensitivity in forest nurseries. Although further tests in planta are required to confirm effectiveness of single-site fungicides against D. septosporum, our results suggest that they can be successfully used in DNB control, although appropriate measures to prevent the evolution of fungicide resistance are strongly recommended.
Cranial and chromosomal geographic variation in manatees (Mammalia: Sirenia: Trichechidae) with the description of the Antillean manatee karyotype in Brazil

We employed landmark-based 3D geometric morphometrics to assess cranial size and shape diversification in Trichechus manatus and T. inunguis to compare it with patterns among all manatee taxa (T. manatus latirostris, T. m. manatus, T. inunguis and T. senegalensis), and to analyse geographic variation within American manatee populations, using a sample of 189 skulls. Chromosome G- and C-banding techniques were performed in T. m. manatus from Brazil. All taxa were statistically discriminated by skull shape. Trichechus m. manatus and T. m. latirostris have larger skulls than T. inunguis. A morphological discontinuity was noted within T. m. manatus, with the Brazilian population south of the Amazon discriminated from the T. m. manatus Caribbean and T. m. latirostris USA populations. Specimens from Suriname and Guyana had a skull shape more similar to the one from the Caribbean population. The Brazil Antillean manatee population exhibited morphological differences similar in magnitude to those found between the Amazonian and African species. Additionally, structural chromosome differences were detected between that population (chromosome pair 4 is metacentric and 10 is submetacentric) and manatees from Puerto Rico and Florida. Based on such morphological discontinuity and chromosomal divergence, we hypothesize that the Amazon River mouth may be acting as a reproductive barrier for the T. m. manatus population in Brazil, thus indicating that its taxonomic status and conservation strategies need an urgent reassessment.
The genetic architecture of life history in Drosophila

ii! Co-Authorship. iv! Acknowledgements . v! List of Figures . ix! List of Tables . x! List of Abbreviations . xi! Chapter 1 General Introduction: The Genetic Architecture of Life History in Drosophila 1! 1.1 Overview . 1! 1.2 Laboratory Selection and Experimental Evolution in Drosophila . 4! 1.3 Genetic Variation for Life History . 6! 1.4 A Web of Pleiotropy . 8! 1.5 Interactions Between New Mutations . 11! 1.6 Sexual Dimorphism, Sexual Conflict, and Sex-limited Variation . 14! 1.7 Sex-Limited Selection, Mitochondria, and Mito-Nuclear Coevolution . 16! 1.8 Experimental Goals . 18! Chapter 2 Mutation, Condition, and the Maintenance of Extended Lifespan in Drosophila . 23! 2.1! Summary . 23! 2.2! Results and Discussion . 24! 2.2.1 Does longevity decline with long-term domestication? 26! 2.2.2 Positive pleiotropy can maintain extended post-selection lifespan . 28! 2.3! Experimental Procedures . 36! 2.3.1 IV population . 37! 2.3.2 Cytogenetic Cloning and Mutation-Accumulation Protocol . 37! 2.3.3 Fitness and Longevity Assays . 38! 2.3.4 Statistical Analysis . 39! 2.4! Acknowledgements . 39! Chapter 3 Sex-Specificity of Mutational Effects on Life Span in Drosophila melanogaster . 40! 3.1 Abstract . 40! 3.2 Introduction . 41! 3.3 Materials and Methods . 49! 3.3.1 Fly Population . 49! 3.3.2 Hemiclonal Analysis . 50! 3.3.3 Creation of Hemiclones and Mutation-Accumulation Protocol . 51! 3.3.4 Longevity Assays . 54! 3.3.5 Statistical Analysis . 56! 3.4 Results . 59! 3.4. 1 Sex Differences in Longevity and Mortality Rates . 59! 3.4. 2 MA Effects on Life Span: Means and Genetic Variation . 59! 3.4. 3 MA Effects on Life Span: Intrasexual and Intersexual Genetic Correlations . 66! 3.4. 4 MA Effects on Mortality Rate Parameters . 70! 3.4. 5 Repeatability of Life Span Measurements . 72! 3.5 Discussion . 74!
Spatial differences in the diet of the Magellanic horned owl Bubo magellanicus (Gmelin, 1788) in central Chile

ABSTRACT Bubo magellanicus is a nocturnal raptor with a wide distribution in the southern cone of South America. The diet of B. magellanicus in central Chile was analysed, using the pellet analysis method. Bubo magellanicus was found to consume mainly rodents (44.8%), lagomorphs (22.0%) and birds (23.6%). The most frequent rodents were Abrocoma bennetti (18.2%) and Abrothrix longipilis (7.3%). On the other hand, a comparison of the diet of B. magellanicus with previous studies showed that the main prey species were small mammals and that the proportion of birds and insects was higher in sites located in central Chile. In addition, the geometric mean weight of prey captured decreased in sites located in southern Chile; however, the trophic niche breadth showed no clear change in the five locations analysed. Finally, the prey diversity in the diet of the B. magellanicus between sites located in three eco-regions of Chile showed significant differences.
CONTROL ON Mycogone perniciosa (Magnus) Delacr. CAUSING WET BUBBLE DISEASE OF Agaricus bisporus (Lang) Sing.

Present investigation entitled “control on Mycogone perniciosa (Magnus) Delacr. causing wet bubble disease of Agaricus bisporus (Lang) Sing. ” was conducted for in vitro toxicity analysis of four chemicals namely, carbendazim, formaldehyde, thiram and zineb against Agaricus bisporus strain (U3). A. bisporus was found sensitive to formaldehyde @ 10ppm. Carbendazim , thiram and zineb were less inhibitory for the growth of Agaricus bisporus. These chemicals further used against Mycogone perniciosa to show complete suppression (100%) of M. perniciosa was at 10 ppm carbendazim and 30 ppm formaldehyde whereas only 26.15 and 21.54% inhibition were observed in case of zineb and thiram upto 40ppm concentration. Carbendazim was selected for the in vivo control of M. perniciosa @5 and 10 times higher concentrations than that of promising in vitro dose (10ppm). Carbendazim (50ppm or 100ppm) was added at the time of casing and spawning + casing time. The maximum disease incidence (45.5%) of M. perniciosa was recorded in negative control with 3.8kg/100kg yield loss and minimum yield loss (1.8kg/100kg) with 100ppm carbendazim when sprayed at the time of spawning + casing. High yield potential of healthy fruit bodies was recorded in positive control (11.6kg/100kgcompost) as well as 100ppm carbendazim sprayed at casing (11.9kg/100kgcompost) in uninoculated M. perniciosa bags. Out of bags inoculated with Mycogone perniciosa , maximum yield of healthy mushroom was observed when100ppm carbendazim sprayed at spawning and casing (10kg/100kg compost) as compare to negative control (4.56kg/100kg). The residue analysis of mushrooms appeared in 100 ppm carbendazim sprayed at time spawning and casing was found below the detectable limit to suggest safe consumption of mushrooms.