Miracle-dz/UniFAR-FTUs huggingface dataset:
The Production and Use of Transgenic Mouse Models to Study the Role of Complement Pathway Activation in Progressive Kidney Disease

The complement system mediates inflammatory diseases, including kidney disease, through one or more of three pathways named the classical, the alternative and the lectin pathway. The existing experimental data do not allow comprehensive understanding of the individual complement pathway or pathways that mediate the renal injury. This study therefore aimed to determine the complement pathway(s) that are involved in mediating the injury in three models of kidney disease: protein overload proteinuria, unilateral ureteric obstruction nephropathy and adriamycin nephropathy. In protein overload proteinuria, a highly significant increase in the expression levels of TGF-β, TNF-α and IL-6 was observed in WT mice compared to the lectin pathway deficient mice. Macrophage infiltration, apoptosis and the expression of the gene for Col4α1 were also significantly increased. These data suggested a significant role for the lectin pathway in mediating the injury. Most interestingly, the results indicated that antibody mediated inhibition of the lectin pathway led to less injury in some of the examined parameters. These data might suggest a novel therapeutic approach to relief the renal injury in proteinuric nephropathies by targeting the activation of the lectin pathway. In unilateral ureteric obstruction nephropathy, results indicated that deficiency in either the lectin or the classical pathways led to reduced macrophage infiltration and renal fibrosis. The expression levels of Il6, Ifn-γ, TGFβ-1 and Col4α1were reduced in the lectin pathway deficient mice but not in C1q KO mice when compared to WT. However, lower expression levels of these genes were not up to statistical significance. These data suggested that both the lectin and the classical pathways mediate the injury. Similarly, adriamycin nephropathy mice deficient in the lectin pathway showed significant reduction in renal inflammation and fibrosis when compared to WT mice. Additionally, two gene targeting approaches were utilized in order to establish a novel mouse line with specific deficiencies of both the lectin and the classical pathways of the complement. This mouse model should provide a powerful tool to investigate the possible synergetic cooperation between these two pathways in mediating inflammatory renal pathology. VI Table of
Identification of quantitative trait loci underlying lutein content in soybean seeds across multiple environments

SUMMARY Lutein benefits human health significantly, including that of the eyes, skin and heart. Therefore, increasing lutein content in soybean seeds is an important objective for breeding programmes. However, no information about soybean lutein-related quantitative trait loci (QTL) has been reported, as of 2016. The aim of the present study was to identify QTLs underlying the lutein content in soybean seeds. A population including 129 recombinant inbred lines was developed from the cross between ‘Dongnong46’ (lutein 13·10 µg/g) and ‘L-100’ (lutein 23·96 µg/g), which significantly differed in seed lutein contents. This population was grown in ten environments including Harbin in 2012, 2013, 2014 and 2015; Hulan in 2013, 2014 and 2015; and Acheng in 2013, 2014 and 2015. A total of 213 simple sequence repeat markers were used to construct the genetic linkage map, which covered approximately 3623·39 cM, with an average distance of 17·01 cM between markers. In the present study, eight QTLs associated with lutein content were found initially, which could explain 1·01–19·66% of the observed phenotypic variation in ten different tested environments. The phenotypic contribution of qLU-1 (located near BARC-Satt588 on chromosome 9 (Chr 9; linkage group (LG) K)) was >10% across seven tested environments, while qLU-2 (located near Satt192 of Chr 12 (LG H)) and qLU-3 (located near Satt353 of Chr12 (LGH)) could explain 5–10% of the observed phenotypic variation in more than seven environments, respectively. qLU-5, qLU-6, qLU-7 and qLU-8 could be detected in more than four environments. These eight QTLs were novel, and have considerable potential value for marker-assistant selection of higher lutein content in soybean lines.
Safety of selected botanical and synthetic insecticides against braconid parasitoids of vegetable ecosystems

Insecticides are unavoidable in pest management programmes especially when the pest crosses economic threshold level (ETL). In this context, some of the insecticides and botanicals that are used in vegetable ecosystem were test verified for their relative safety against the commonly encountered parasitoids viz., Bracon brevicornis Wesmael, Chelonus blackburni Cameron and Cotesia plutellae Kurdjumov. Toxicity effects of five insecticides viz . , Acephate 75SP, Chlorpyriphos 20EC, Cypermethrin 10EC, Profenofos 50EC, Quinalphos 25EC and NSKE 5 per cent against B. brevicornis, C. blackburni and Hexane extracts of Lantana camara var. aculeate tested against C. plutellae were evaluated under laboratory conditions. Amongst insecticides tested, Profenofos 50EC was found to be most toxic with LC 50 value of 22.27 and 16.280 ppm; Chlorpyriphos 20EC was the least toxic with the highest LC 50 value of 198.53 and 314.255 ppm and NSKE 5 per cent had no effect against B. brevicornis and C. blackburni , respectively. C. plutellae pupae were treated with hexane extracts of L. camara resulted of 66.67 and 76.67 per cent with reduction of adult emergence at 8 and 10 per cent, respectively. While, C. plutellae adults were found to be safe at all concentrations except 8 and 10 per cent and its contact toxicity of 63.33 and 96.67 per cent adult mortality recorded within 24h by dry film method. The results suggest that the Chlorpyriphos 20EC and botanical extracts can very well integrate in the management of vegetable insect pests.
Relationships of shredders, leaf processing and organic matter along a canopy cover gradient in tropical streams

Terrestrial allochthonous organic matter represents a structuring element and an important source of energy and carbon to fauna in small forested streams. However, the role of this matter as a food resource for benthic macroinvertebrates, and consequently, for shredders and their performance in riverine processes, is not clear in low-order tropical streams. Aiming to investigate the relationship between shredders and leaves, we analyzed along a gradient of 8-93% canopy cover biomass and abundance of shredders, accumulated leaves and breakdown rates of local leaves to verify if these parameters were related to shade conditions and to each other. Three hypotheses were tested: i) shredder biomass, accumulated leaves and breakdown rates are related to canopy cover and exhibit higher values in shaded sites; ii) shredder biomass is positively related to accumulated leaves and breakdown rates; and iii) due to the relatively large body size of the important shredders, the association of shredders with leaves and importance to leaf processing should be better expressed in terms of guild biomass than abundance. Shredder biomass varied between 846 and 1506 mg DM m ‑2 and accumulated leaves varied between 479 and 1120 g AFDM m -2 across sites. Leaf breakdown rate ( k ), the only measured variable that varied significantly among sites, varied between -0.0015 and -0.0238 day -1 . Neither shredder biomass nor leaf biomass were associated with the shading gradient. On the other hand, shredder abundance and biomass, mainly represented by Triplectides (Trichoptera, Leptoceridae), was positively related to accumulated leaves within sites and to breakdown rates assessed by leaf packs. Leaf breakdown, as assessed by the experimental leaf packs, was associated with shredder biomass, but not with shredder abundance. This result suggests that macroinvertebrates are important for leaf detritus processing and that their biomass reflects their activity, presumably because it is related to their secondary production and perhaps non-consumptive action. Their activity was observed at the scale of leaf packs and not at the scale of variation in canopy cover because apparently canopy did not modulate availability of leaves, which were apparently not limiting to the shredders.
Performance of 'Tupy' and 'Xavante' blackberries under subtropical conditions.

Introduction – An increasing interest in blackberry consumption worldwide demands higher production, both for fresh and processed industries. Blackberry cultivation in subtropical conditions may be used to extended areas of worldwide production by using high yielding cultivars. The objective of this study was to evaluate the performances of ‘Tupy’ and ‘Xavante’ blackberries under subtropical conditions, with the aim of increasing the availability of cultivars with high yields and adaptation to low input conditions. Materials and methods – Evaluations were conducted at the Experimental Station at Londrina State University, PR, Brazil, during two consecutive seasons, 2013 and 2014. The variables evaluated were length, diameter, weight, total soluble solids (TSS), titratable acidity (TA), TSS/TA ratio, pH, color, total berry anthocyanin and polyphenol concentrations, yield and the percentage distribution of the cumulative yield. Results and discussion – Considering all the evaluated variables, ‘Xavante’ presented berries with poorer physical characteristics and had lower yields than ‘Tupy’. However, ‘Xavante’ had good chemical characteristics and a higher percentage of early cumulative yield compared to ‘Tupy’ blackberry. ‘Tupy’ produced large fruits with optimum TSS and pH values, presented an attractive color, and obtained high yields and a higher percentage distribution of the cumulative yield towards the end of the harvest season. The production of these cultivars under subtropical conditions could be a good choice for growers to commercially produce fruit for fresh consumption and the processing industry due to their good yield and optimum quality attributes. Conclusion – The good adaptation of ‘Tupy’ and ‘Xavante’ blackberries to subtropical areas allows growers to produce fresh fruit using agroecological management. This management allows for an early harvest within approximately two months and an expanded harvest season to fulfill the market demand for fresh consumption.
The sex chromosomes of bryophytes: Recent insights, open questions, and reinvestigations of Frullania dilatata and Plagiochila asplenioides

The three bryophyte lineages have long‐lived gametophytes that are either bisexual, producing both male‐ and female gametes, or sexually specialized and then producing only one type of gamete. Phylogenies suggest repeated evolutionary switches between these systems, implying that bryophyte sex chromosomes may have been gained and lost repeatedly. How this occurred is poorly understood, even though plant sex chromosomes were first discovered in liverworts. We explain how the sex chromosomes of haploid‐dominant organisms are distinct from the better‐studied X‐Y and Z‐W systems in the tree of life, summarise what is known about their distribution and genetic composition, and present new cytogenetic data for Frullania dilatata and Plagiochila asplenioides, the former with two U chromosomes and one V chromosome, the latter with one U chromosome and two V chromosomes; male and female C‐values in F. dilatata are correspondingly asymmetric (the C‐value of P. asplenioides is only known for female nuclei). So far, there is a lack of high‐throughput sequencing, quantification, and in situ study of the repetitive DNA, organellar DNA, and transposable elements, and it is therefore not known what causes the size difference of U and V chromosomes from the autosomes or each other. Heterochromatin was also first discovered in bryophytes, but its function in their sex regulation has not been addressed. Studies of bryophyte sex chromosomes with combined cytogenetic and genomic approaches are fundamental for a fuller understanding of sex chromosome evolution across the tree of life.
PATTERNS OF HERBACEOUS PLANT SPECIES RICHNESS, COMPOSITION AND SOIL PROPERTIES IN AN ORGANIC CULTIVATION

Aromatic plants constitute a major segment of the flora, which provides raw materials for use in the pharmaceuticals, cosmetics, and drug industries. Lemon verbena is one of more than 30 species of aromatic shrubs in the genus Aloysia (family Verbenaceae) with high environmental and economic value. More attention is paid in Greece to the Lemon verbena essential oil while their effects on the parameters influencing multiple aspects of ecosystem structure (e.g. biodiversity, soil properties etc) are generally overlooked. Hence, this exploratory study aims to evaluate the effects of Lemon verbena and neighboring abandoned (10 years) ecosystems on the herbaceous plant species richness and composition, and soil properties. Also, the multiple regression method was used to investigate the relationship between herbaceous plant species richness and soil properties. The study was conducted in April-May 2016 and 2017 of central Greece. In total, 24 species of herbaceous plants (16 plant species in Lemon verbena ecosystem and 12 plant species in abandoned ecosystem) were recorded in the study area. The most frequently occurring plant was Avena sterilis (Family: Poaceae) in both types of ecosystems. Moreover, there were significant differences (p<0.05) between Lemon verbena and neighboring abandoned (10 years) ecosystems for any of the soil properties [soil organic matter, pH, CaCO3, P, K and Mg] measured. Furthermore, multiple regression method showed that soil properties had significant effects on herbaceous plant species richness in which soil organic matter, pH, P and K were the most prominent factors influencing species richness in Lemon verbena ecosystem.
Circadian rhythms and dynamic dietary calcium feeding affect laying performance, calcium and phosphorus levels in laying hens

Abstract This study was conducted to determine the effects of dynamic feeding low and high Ca in layer diets on laying performance, calcium, and phosphate concentration in both serum and tibia. 180 Brown Hy-line, 41 weeks old of laying hens were randomly distributed into 3 groups with 6 replicates and each replicate was 10 birds. During the 10-week experiment period, control group (CON group) received control diet (contained 3.4% Ca) at both 0730 and 1530 h, low–high group (LH group) received low Ca diet (contained 3.2% Ca) at 0730 h and high Ca diet (contained 3.6% Ca) at 1530 h, while high–low group (HL group) received the contrary to the LH group. Blood and tibia samples were collected at 4 h intervals. The dynamic Ca feeding schedule exerted significant effects on Ca intake in the morning and afternoon, also on feed conversion ratio (FCR) of the HL group comparing to the LH group (p<0.05). Serum Ca in the LH group were lower at 0000, 0400 and 1600 h comparing with the CON group (p < 0.05), and serum Ca: P ratio values in the LH group were lower at 0000, 0800, and 2000 h comparing with the CON group (p<0.05). These results indicated that dynamic feeding Ca improved FCR and affected the circadian variation of serum Ca concentration in laying hens.
Investigation on the Effects of Planting Time and Plant Geometry on the Activity of Sucking Pests of Chilli Capsicum Annuum L

Field experiments were conducted at the Main Agricultural Research Station, UAS, Dharwad, Karnataka, India to investigate the effect of planting time and plant geometry on the activity of chilli sucking pests. Pooled data from two years revealed that, the interaction effect between the date of planting and different spacings was significant. Significantly lower level of sucking pest and leaf curl index was observed in the interaction of July 15th planting and 90x60cm spacing followed by July 15th and 60x60cm and July 15th and 75x45cm treatments. Whereas, it was higher in interaction of June 30th and 60x30cm. Similar pattern of treatment significance was observed in case of natural enemy population also. Significantly highest chilli yield was registered in interaction of July 15th planting and 90x60cm spacing (4.21 q/ha) whereas, lowest chilli yield of 1.99 q/ha was registered in the combination of June30th + 60x30cm treatment. The interaction effect between July 15th and 90x60cm was found to be the most cost effective which recorded highest net returns (Rs 15,921/- per ha).
Recontextualising biodiversity in school practice

Abstract The finding that biodiversity is a concept with different context-specific meanings has implications for its conceptual development when students are required to apply it in a diversity of contexts. An approach that may overcome these implications is that students learn to recontextualise one meaning to another. Since no empirical studies were available when this study started, it was decided to conduct a design study to develop a learning and teaching strategy for recontextualising biodiversity. In this paper, the design of such a strategy is presented. Testing of the design in two classes in upper secondary biology education showed that it is largely practisable.
Computational Modeling of Drug Resistance: Structural and Evolutionary Models

Computational Modeling of Drug Resistance: Structural and Evolutionary Models Maryah Safi Doctor of Philosophy Graduate Department of Computer Science University of Toronto 2013 Active site mutations that disrupt drug binding are an important mechanism of drug resistance. Such resistance causing mutations impair drug binding, thus reducing drug efficacy. Knowledge of potential resistance mutations, before they are clinically observed, would be useful in a number of ways. During the lead prioritization phase of drug development, this knowledge may direct the research team away from candidate drugs that are most likely to experience resistance. In the clinical setting, knowledge of potential resistance mutations could allow the development of treatment regimens, with drug cocktails likely to maximize efficacy. In this thesis I present a structure-based approach to predict resistance and its evolution. This method utilizes a two-pass search, which is based on a novel protein design algorithm, to identify mutations that impair drug binding while maintaining affinity for the native substrate. The approach is general and can be applied to any drug-target system where a structure of the target protein, its native substrate and the drug is available. Furthermore, it requires no training data for predictions and instead predicts resistance using structural principles. Finally, I use approximate force-field calculations from MMPBSA and simple assumptions about the relationship between binding energy and fitness to build fitness landscapes for a target protein under selective pressure from either a single drug or a drug cocktail. I use a Markov-chain based model to simulate evolution on this fitness landscape and to predict the likely evolutionary trajectories for resistance starting from a wild-type. The structure-based method was used to probe resistance in four
Lactococcus lactis as a live delivery vector

Mucosal surfaces of the body provide a universal entry portal for all known and emerging infectious pathogenic microbes. Therefore, it seems that special vaccination strategies are needed for vaccines that can hinder the entry capability of pathogenic microbes through the mucosal surfaces. Lactic acid bacteria are widely used in the food industry and are presently applied as delivery vehicles in many biological investigations. Among these bacteria, Lactococcus lactis is considered as a promising candidate for mucosal live vaccines to be used as an antigen delivery vector. This is an attractive alternative and a safer vaccination strategy against the pathogens, compared to other conventional methods. In this review, we summarized the applications of L. lactis as a mucosal vector of vaccine delivery for heterologous expression of proteins and its applications in biotechnology.
The influence of nitrogen source on the nutrition of arbuscular mycorrhizal plants

Arbuscular mycorrhizal fungi (AMF) form a symbiosis with 70% of land plants and may contribute significantly to plant phosphorus (P) and nitrogen (N) acquisition in exchange for photosynthetic carbon. AMF mainly acquire N as simple, inorganic molecules such as ammonium and nitrate, but whether AMF display a preference for either source, or can increase plant N content is uncertain. Furthermore, soil nutrient availability, especially that of N, may determine the extent to which a fungus engages in nutrient-for-C trade with plants; further experimental validation of this suggestion is warranted. Experiments ranging from Petri plate microcosms to field trials were carried out to address these questions. Plant N uptake via AMF was traced using stable isotope 15N, having been added to hyphal-only compartments which allow access to AMF, while excluding plant roots. AMF species Glomus aggregatum and Rhizophagus irregularis were used individually to inoculate plants allowing comparisons between AMF isolates, while N uptake preferences were tested by providing 15N as ammonium, nitrate or ammonium nitrate. R. irregularis contribution to plant nutrient uptake was sufficient to increase host biomass in chapter 2, but limited evidence of AMF preference for nitrate or ammonium-N was seen in any experiment. N acquisition by AMF was highest in a Petri microcosm experiment when supplied as ammonium nitrate. Functional diversity among AMF species was observed in terms of plant growth and nutrient uptake, and carbon acquisition from the plant: G. aggregatum was less beneficial to plant partners than R. irregularis. Experimental field-trial data suggests that soil nutrient levels influence both the community structure of AMF and the extent to which they engage in N-for-C trade with plant partners. These findings highlight the complexities and potential significance of the AM route for N uptake both in simplified experimental systems and full-scale commercial crop field trial plants.
Behavioural response of the invasive Halyomorpha halys (Hemiptera: Pentatomidae) to host plant stimuli augmented with semiochemicals in the field

Although much work has focused on understanding how the invasive brown marmorated stink bug, or Halyomorpha halys, responds to pheromonal stimuli, very little research has explored the response of H. halys to plant volatiles and other host stimuli. The present study aimed to determine (i) whether more acceptable, less acceptable or unacceptable host plants augmented with plant volatile mixes and/or pheromone can enhance the retention capacity of plants for H. halys in the field and (ii) whether plant volatiles [apple, peach or green leaf volatile (GLV) mixtures] can increase attraction to pheromone‐baited pyramid traps. The presence of the H. halys pheromone was the primary factor in increasing the retention capacity of tagged, released adults to host plants, although plant volatile mixtures added a small increase in retention. Plant species helped to modulate the effectiveness of both the pheromone and additional plant volatiles in retaining individuals. Plant volatiles did not increase attraction of adults to baited pyramid traps and may have inhibited the attraction of nymphs. Overall, the results of the present study suggest that host plant stimuli, construed broadly, are important for the foraging decisions of H. halys, although further research is needed to identify the most effective stimuli.
Disease dynamics in a metapopulation of Amietia hymenopus

iii Acknowledgements . iv Declaration . vi List of Figures . vii List of Tables . xi Chapter outlay . xiv Statement on the contribution of others . xv Chapter 1: Introduction and literature review . 1 1.1. The Drakensberg Mountain range . 1 1.1.1. Lesotho and the Drakensberg Mountains . 1 1.1.2. Climate . 5 1.1.3. Conservation status . 6 1.1. 4. Fauna and flora . 9 1.1. 5. Frog diversity . 10 1.2. Amphibian chytrid . 14 1.2. 1. Origin and diversity . 16 1.2. 2. Life cycle and transmission . 17 1.2. 3. Pathogenesis . 18 1.2. 4. Epidemiology . 19 1.3. Aims and objectives . 20 Chapter 2: Long term monitoring . 21 2.