Miracle-dz/UniFAR-FTUs huggingface dataset:
Balancing transcriptional activity in Drosophila through protein-protein interactions on chromatin

Chromatin plays a vital role in the implementation of gene expression programs. Several disparate groups of regulatory proteins alter chromatin state through post-translational modification of histone proteins, nucleosome remodeling, and higher order chromatin structure in order to affect gene expression. Several of these key groups, such as the Male-Specific Lethal complex and Polycomb Group have been well characterized in Drosophila. Yet aspects of their biology at the molecular level, such as the means by which they are faithfully targeted to regulated loci throughout the genome and the molecular mechanisms they employ to alter transcriptional state, still remain unexplained. In this dissertation I explore how identifying protein-protein interactions on chromatin reveals insights into these unanswered questions critical to chromatin biology. My results highlight the importance of balancing active and repressive chromatin states for the proper maintenance of gene expression. The Male-Specific Lethal complex is the dosage compensation complex in Drosophila, which upregulates gene expression on the male X chromosome approximately two-fold. The MSL complex catalyzes an acetyl mark which may create a uniquely permissive chromatin state to promote transcriptional elongation. A proteomic screen for MSL-interacting proteins identified UpSET, the Drosophila homolog of yeast SET3 and mammalian MLL5. Interestingly, SET3 and UpSET have been characterized to assemble into histone deacetylase complexes. I employed genetic, genomic, and proteomic techniques to assess whether UpSET plays a role in dosage compensation. UpSET appears to play a role in limiting the level of activation of the MSL complex. Surprisingly, UpSET appears to play a more important role in the maintenance of heterochromatin.
Studies relating to the breast, its tumours and fluids

This thesis comprises 61 papers which describe work undertaken between 1972 and 1 985. The research was performed in order to obtain basic information on the environment and the biochemical processes existing within the female breast. It was thereby hoped to achieve a better understanding of events which occur during the development of breast disease, particularly breast cancer. Hormones are involved not only in the natural development of normal breast but also in the aetiology of many breast abnormalities and, most importantly, in the continued growth of a proportion of breast cancers. A major aspect of the research described in this thesis is concerned with the measurement of steroid hormones, their metabolism and receptors in the breast, its tumours and secretions. Additionally studies have been performed to assess the significance of other markers of tumour behaviour and to determine whether agents such as LHRH analogues have direct effects within the breast. The potential of the breast to modify its own hormonal environment has been investigated by performing in vitro incubations with steroid precursors. Pathways leading to both active androgens and oestrogens have been identified. Biosynthesis of 5 «C reduced androgens occurs in all types of breast tissue but is particularly associated with apocrine differentiation. The production of oestrogen or "aromatization" was detected in a proportion of breast cancers but not in non-malignant tissue. The significance of tumour aromatase is controversial but it may be important in oestrogen-dependent cancers growing in post-menopausal women who have low circulating levels of oestrogen.
Organization of Postsynaptic Assembly by Filamin at the Drosophila Neuromuscular Junction

Proper postsynaptic assembly is a fundamental requirement for circuit function, yet our understanding of its molecular mechanism is incomplete. The Drosophila neuromuscular junction is a powerful system for genetically dissecting synapse organization at the molecular level. Taking advantage of its features, I sought to identify novel molecular mechanisms governing synapse assembly. The Ral pathway for activity-dependent membrane addition is highly localized at the postsynapse and is essential to proper postsynaptic development, thus offering a tractable ideal starting point. Through a candidate-based genetic approach using Ral localization as the initial readout, I initially discovered that filamin is required for localizing the Ral pathway at the postsynapse. Filamin is a scaffolding and actin-binding protein not previously known to be required for synaptic development. My findings now show that the Drosophila ortholog filamin/cheerio localizes key signaling proteins that govern morphological plasticity and the composition of glutamate receptor clusters at the neuromuscular junction (NMJ). Genetic and biochemical analy-
Autophagy- and RNS2-mediated mechanism of ribosomal RNA degradation in Arabidopsis thaliana

Ribosomal RNA degradation is necessary to remove nonfunctional rRNA and maintain homeostasis through degradation of aging or normal rRNA. While pathways for surveillance of nonfunctional rRNA have been characterized, mechanisms of degradation of normal rRNA are not yet well understood. Ribosomal RNA, the majority of cellular RNA, forms a massive resource sink. These studies examine the mechanism of degradation of rRNA in Arabidopsis and the effects of disruption of this process through mutation of key genes. Ribosomal RNA in many organisms, including yeast, zebrafish, Tetrahymena and Arabidopsis, is degraded by the RNase T2 family of enzymes, a family highly conserved throughout eukaryotes. Mutation of the Arabidopsis RNase T2, RNS2, results in increased rRNA half-life and constitutive autophagy. An autophagy-dependent mechanism of ribosomal degradation, known as ribophagy, has been shown in yeast but not plants. Here, I report the effects of mutation of autophagy genes on rRNA accumulation in Arabidopsis. I show that RNA accumulates in rns2-2 and autophagy mutants atg9-4 and atg5-1, indicating that RNS2 and the autophagy machinery are necessary to maintain normal rRNA levels in Arabidopsis. This accumulation is vacuolar in rns2-2 but not atg5-1. These evidence support an autophagy-dependent rRNA degradation by RNase T2 in plants. To further examine the effects of mutation in this rRNA degradation pathway, I performed two transcriptomic studies. My initial analysis of WT and rns2-2 in seedlings revealed differentially expressed genes (DEG) related to carbon flux pathways and cell wall modifying processes. Alteration of carbon flux in the mutant was verified using metabolite
Distribution and abundance of pteropods in the western Barents Sea

Abstract The abundance and horizontal distribution of three pteropod species, Limacina helicina, Limacina retroversa and Clione limacina were examined in the western entrance of the Barents Sea (Polar Front region) in August 2011. Sixteen samples were collected from 8 sampling sites located along a latitudinal transect. The southern part of the study area (south of 73°N) was dominated by L. retroversa, while L. helicina was mostly observed north of 73°N. Surface water temperature differences between the coldest and the warmest station were around 8°C. The highest density of L. retroversa was found in the south, near the Norwegian coast (nearly 52 000 ind. 1000 m−3), while the highest density of L. helicina was observed in the region of the Arctic water masses (nearly 13 000 ind. 1000 m−3). The sampled population of pteropods comprised mainly juvenile stages. Redundancy analysis (RDA) of the relationships between environmental factors (mean and surface salinity, mean temperature, sampling depth, chlorophyll concentration) and the population structure showed that mean temperature was the most important factor in the study area, explaining 70.5% of the pteropod community variation.
Profiling Rhizosphere Microbes on the Root of Maize (Zea mays) Planted in an Alfisol for Selection as Plant Growth Promoting Rhizobacteria (PGPR)

Maize ( Zea mays L. Merill) root rhizosphere, being a metabolite-enriched niche was profiled with the objective of isolating Plant Growth Promoting Rhizobacteria (PGPR) for bio-fertilizer production. Isolation was carried out from the root surface and rhizosphere soil samples of the plant using standard procedures. Cultural, physiological and biochemical procedures were used to identify the isolates. Eighty (80) isolates obtained were screened for growth promoting attributes and sixteen (16) representative isolates selected, and further identified using molecular methods by sequencing of their 16S rDNA gene. Sixty three percent of the characterized organisms exhibited sequence homology level equal or greater than 90% with those of the gene bank. Microorganisms with pathogenic characteristics were eliminated. As a result of this, Bacillus thuringiensis, Pseudomonas putida and Klebsiella varricola selected, were further screened in vitro for Indole acetic acid (IAA), Gibberellic acid (GA) and Cytokinin production using standard assay methods. Klebsiella varricola produced 19.697 mg/L of GA, 0.348 mg/L of IAA and 1.804 mg/L of Cytokinin. Pseudomonas putida had 2.693 mg/L of GA, 0.152 mg/L and of IAA and 5.066 mg/L of Cytokinin in solution while Bacillus thuringiensis excreted 15.091 mg/L, 0.132 mg/L and 2.410 mg/L of GA, IAA and Cytokinin respectively. The 3 PGPR are considered suitable for biofertilization programme.
The roles of residue position and charge in the cryoprotective behaviour of the Vitis riparia K2 and YSK2 dehydrins

THE ROLE OF RESIDUE POSITION AND CHARGE IN THE CRYOPROTECTIVE BEHAVIOUR OF THE VITIS RIPARIA K2 AND YSK2 DEHYDRINS Sharall R. Palmer Advisor: University of Guelph, 2017 Prof. Steffen P. Graether Dehydrins are group II Late Embryogenesis Abundant proteins that accumulate in plants during seed development and in response to abiotic stresses. The biological function of dehydrins remain elusive, as they are multi-functional in vitro. The contribution of sequence and charge to the cryoprotective behaviour of dehydrins was analyzed using synthetic variants of the Vitis riparia YSK2 and K2 proteins: ScYSK2, a scrambled version of YSK2; and AntiK2, a charge-reversed version of K2. Circular dichroism (CD) spectroscopy analysis revealed that dehydrin-induced changes in the structure of YFH1 was dependent on sequence and independent of residue charge. An LDH cryoprotection assay showed that the efficiency of YSK2 was unrelated to its sequence, whereas the efficiency of K2 depended on its residue charge type. CD spectroscopy analysis also suggested that the mechanism of protein stabilization by dehydrins may be more like glycerol than polyethylene glycol. Identifying functionally important residues in dehydrins would provide insight into the potential mechanism(s) of their protective behaviour.
Phytoseiid mites (Acari: Mesostigmata: Phytoseiidae) associated with Cerrado biome plants in Brazil, with description of a new species

Abstract A survey of plants in 24 areas of the Cerrado biome in the states of Goiás and Minas Gerais (Brazil) revealed a total of 34 species of phytoseiid mites belonging to 16 genera and three subfamilies of the Phytoseiidae. A new species, Neoseiulus goiano n. sp. , is described and illustrated. Morphological information is provided for the species collected in this study.
The resilience of pollination interactions: importance of temporal phases

The loss of species that engage in close ecological interactions, such as pollination, has been shown to lead to secondary extinctions, ultimately threatening the overall ecosystem stability and functioning. Pollination studies are currently flourishing at all possible levels of interaction organization (i.e., species, guild, group and network), and different methodological protocols aimed to define the resilience of pollination interactions have been proposed. However, the temporal dimension of the resilience of pollination interactions has been often overlooked. In the light of these considerations, we addressed the following questions: does a temporal approach help to reveal critical moments during the flowering season, when pollination interactions are less resilient to perturbations? Do pollination interactions evaluated at species, guild, group and network level show different patterns when assessed through time? We monitored contacts between plant and pollinator species in dry grassland communities every 15 days during the overall community flowering season (12 surveys). For each survey, we built a quantitative plant–pollinator interaction matrix and we calculated two sets of metrics characterizing, respectively, the diversity and the distribution of interactions across hierarchical levels. To describe the diversity of interactions, we calculated partner diversity (PD) at the species level, vulnerability/generality (V/G) at the guild level, and interaction diversity and evenness at the network level. The distribution of interactions was characterized by calculating selectiveness at the species and the network level, and modularity at the group level. We assessed the temporal variation of PD, V/G at the level of plants and pollinators, and species selectiveness, by means of Linear Mixed Models (LMMs). To investigate the temporal variation of indexes calculated at group and network level, we applied simple linear and quadratic regressions after checking for temporal autocorrelation in residuals. When taking into account the temporal dimension of interactions, the diversity of interactions showed different patterns at different levels of organization. At the species level, no relationship was disclosed between PD and time, when assessing the temporal trend of V/G separately for the guild of plants and pollinators we observed an asymmetric structure of interactions. Pollination interactions showed to be asymmetric throughout the flowering season; however, evenness of interactions and network selectiveness showed significant positive relationships with time, revealing a poorer network of interactions during the end of the flowering season. The temporal analysis of pollination interactions revealed a stronger risk of secondary extinctions at the end of the flowering season, due to a lower degree of redundancy and thus of resilience of the overall network of interactions.
The Drosophila SK potassium channel negatively regulates nociception

Inhibition of nociceptor activity is important for the prevention of spontaneous pain and hyperalgesia. To identify the critical K+ channels that regulate nociceptor excitability we performed a forward genetic screen using a Drosophila larval nociception paradigm. Knockdown of three K+ channel loci, the small conductance calcium-activated potassium channel (SK), seizure and tiwaz, resulted in marked hypersensitive nociception behaviors. In more detailed studies of SK, we found that hypersensitive phenotypes could be recapitulated with a genetically null allele. Importantly, the null mutant phenotype could be rescued with tissue specific expression of an SK cDNA in nociceptors. Optical recordings from nociceptive neurons showed a significant increase in mechanically activated Ca2+ signals in SK mutant nociceptors. SK showed expression in peripheral neurons. Interestingly SK proteins localized to axons of these neurons but were not detected in dendrites. Our findings suggest a major role for SK channels in the regulation of nociceptor excitation and they are inconsistent with the hypothesis that the important site of action is within dendrites. Highlights - Specific potassium channels regulate nociceptor excitability. - SK channels have a critical function in nociception. - SK channels specifically localize to sensory axons - SK channels are not detectable in sensory dendrites.
Antimicrobial Activity of Extracts of "Hairy" Root Culture and Regenerated Plants of Ruta Graveolens L. Against Some Soil and Pathogenic Bacteria

26 ANTIMICROBIAL ACTIVITY OF EXTRACTS OF “HAIRY” ROOT CULTURE AND REGENERATED PLANTS OF RUTA GRAVEOLENS L. AGAINST SOME SOIL AND PATHOGENIC BACTERIA Bielikova Оlena*, Matvieieva Nadiia, Tashyrev Oleksandr, Yastremskaya Larisa Zabolotny Institute of Microbiology and Virology, National Academy of Sciences of Ukraine, Kyiv, Ukraine Institute of Cell Biology and Genetic Engineering NAS of Ukraine, Kyiv, Ukraine National Aviation University, Kyiv, Ukraine
Effekt: Lightweight Effect Polymorphism for Handlers

Effect handlers have recently gained popularity amongst programming language researchers. Existing type-and effect systems for effect handlers are often complicated and potentially hinder a wide-spread adoption. We present the language Effekt with the goal to close the gap between research languages with effect handlers and languages for working programmers. The design of Effekt revolves around a different view of effects and effect types. Traditionally, effect types express which side effects a computation might have. In Effekt , effect types express which capabilities a computation requires from its context. While this new point in the design space of effect systems impedes reasoning about purity, we demonstrate that it simplifies the treatment of effect polymorphism and the related issues of effect parametricity and effect encapsulation. To guarantee effect safety, we separate functions from values and treat all functions as second-class. We define the semantics of Effekt as a translation to System Ξ , a calculus in explicit capability-passing style.
Seed-potato production through sprouts and field multiplication and cultivar performance in organic system

Organic farming requires the production or use of certified seeds from the same cultivation system and, the information of potato cultivars adapted to organic production system is important. The objective of this work was to study the feasibility of utilizing sprouts of different potato cultivars, seed multiplication and yield potential in field conditions without using agrochemicals. Three experiments were conducted: the first experiment using sprouts as seed under protected cultivation in Guarapuava, Paraná State, Brazil, from November 2011 to February 2012; the second experiment was field conducted in Candói, Paraná State, from May to September 2012 and the third experiment was field conducted in Guarapuava, Paraná State, from February to May 2013. The experimental design was a randomized block design with 3 replications in all 3 experiments. In the 2 first experiments the following cultivars were evaluated: BRS Ana, BRS Clara, BRS Eliza, Crystal and Catucha, and in the last experiment Agata, Bintje, Baronesa and BRSIPR Bel were included. The traits analyzed were length of main stem, number of stems, number of leaves, fresh weight and number of tubers, percentage of infection by viruses and in the second experiment the incidence of late blight on leaves. In the third experiment, leaf area index (LAI), tuber, leaves and stem dry weights and late blight severity were also analyzed. In the first experiment, the cultivars showed differences in plant height and minituber production, the highest value was observed in cultivars BRS Clara and BRS Ana for plant height and cultivar BRS Clara for minituber production. In the second experiment, there was difference only in plant height, the tallest cultivars were BRS Ana and BRS Clara. There was low spread of viruses and, it did not directly reflect in tuber yield. In the third experiment the cultivars with lower disease severity were those recommended to organic farming, especially BRS Clara and Catucha; this second cultivar had the higher LAI and tuber yield, as well as resistance to late blight, factors that might have contributed to the recorded highest total tuber yield (13.8 t/ha).
Growth and survival of marine sponges, Stylissa massa (Carter, 1887) and Liosina paradoxa (Thiele, 1899) in sea and land based culture systems

Two species of marine sponges Stylissa massa and Liosina paradoxa were cultured in cages (in situ) and in land based aquaria (ex situ) over a period of 120 days. Growth and survival were evaluated using four substrates viz., tile, block, coral rock and rope) under both in situ and ex situ conditions. L. paradoxa in cages recorded significant increase (p<0.05) on day 90 i.e., by 70% compared to initial volume whereas at 120 days there was a significant (p<0.05) decrease (54.22%). S. massa showed significant increase (p<0.05) in growth by 95.6% at 120 days compared to initial volume. Negative growth was recorded in S. massa under aquarium conditions while L. paradoxa recorded good growth as well as survival and performed exceptionally well in aquarium during the entire experimental period of 120 days. In cages, 90.62% survival was recorded for S. massa in 120 days. Among the different substrates used, coral rocks gave 100% survival whereas other substrates such as tiles, blocks and ropes showed 87.5% survival. Under aquarium conditions, S. massa showed overall survival of 81.25% and among the different substrates, 100% survival was obtained with coral rocks, 87.5% with blocks, 75% with ropes and the lowest survival of 62.5% was recorded with tiles.
FABRICATION OF PERMEAMETER FOR TESTING IN LABORATORY AND EVALUATION OF PERMEABILITY IN BITUMINOUS CONCRETE MIX

Permeability is the hydraulic property of the porous material which is the measure of durability. Since water is the enemy of bituminous topped pavement because when rain water infiltrates and percolate through the pores, break down the bonding between bitumen and aggregate. Ultimately pavement fails before service life. It is well aware that bitumen mixture at different air voids content represents different permeability characteristics for the different composition of bitumen. In order to measure permeability of bituminous mixture, an instrument was fabricated which follows the Darcy’s falling head method. Permeameter is designed in such a way that it can consist of Marshall’s sample and tested in the lab. This equipment is capable to measure vertical as well as horizontal permeability. It was found that the horizontal and vertical permeability varied largely over the entire range of air voids content. However, relationship between horizontal and vertical permeability ratio and percent air voids was established. Four types of asphalt mixtures for different composition namely BC 20mm aggregates, BC stone dust as filler, BC cement as filler and SDBC was used in the lab test for estimation of permeability. However, Composition of bitumen varied over 4.5%-7.0% and percent of air voids varied over 2%-8% on the basis of laboratory investigation of various asphalt mixtures. Permeability increases with increase of void ratio and found ratio of vertical and horizontal permeability is 1.12.