Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification and analysis of Gene Regulatory Networks involved in the drought stress response in Arabidopsis thaliana

There is a growing need to engineer an increased yield in food crops coupled with greater resistance to environmental stresses, such as drought, to meet the requirement of a growing population. As plant responses to drought (and other abiotic stress) are complex, many studies have attempted to understand the drought response in a holistic manner, for example, by analysing transcriptomics data obtained from plants subjected to drought. Preliminary work of obtaining time-series microarray data from a slow-drying experiment of Arabidopsis was used to construct Gene Regulatory Networks using Variational Bayesian State Space Modelling. This led to the identification of a number of transcription factors RAP2.12, FD, BHLH038, ANL2, and two unknown genes, UKTF and POZ, as possibly being important regulatory genes in the drought response. Loss- and gain-of-function mutants of these genes, as well as those of AGL22 identified by Bechtold et al. (2016), were phenotyped under drought conditions. Only the flowering time AGL22 showed a drought phenotype. Network connections in the gene network of AGL22 were tested by qPCR. Drought responsive transcription factors, such as DREB1A and WRKY20 were found to be induced by AGL22.
Development of antibodies against the canine CSF-1R

Tumour-associated macrophages (TAMs) can constitute a large proportion of the cellular mass of solid tumours. Within tumours, macrophages can be in an alternative state of activation that acts in favour of carcinogenesis, instead of counteracting it. Consequently, TAMs can lead to poorer clinical prognosis, as they assist in cancer progression such as local tissue invasion and immunosuppression. In this chapter, it is demonstrated that canine mammary carcinoma cells reduced macrophage responses to LPS stimulation. CSF-1 is an important factor for macrophage survival and is highly expressed in several cancers. Blocking CSF-1 reduced the effect of cancer cells on macrophages, indicating that this is an important factor in the interaction between these cells. Independently, this cytokine induced macrophage activation, but it reduced LPS-induced activation. Macrophages also exerted an effect on cancer cells, inducing canine mammary carcinoma cells to up-regulate CSF-1R and glucose uptake. Canine mammary cancer cells showed increased proliferation in the presence of CSF-1 and were sensitive to a CSF-1R tyrosine kinase inhibitor. Overall, these
Meiotic behavior and pollinic viability in bean cultivars

The aims of this study were to determine the meiotic behavior and to estimate pollen grains via- bility in bean ( Phaseolus vulgaris L.) cultivars. Flower buds were collected during different developmental stages of the Mesoamerican bean cultivars IAPAR 44, Guapo Brilhante, BRS Expedito, BRS Valente, Guateian 6662 and Perola, and the Andean bean cultivar Irai, grown in a greenhouse. The meiotic index was determined by anther squashing of material fixed in absolute ethanol-glacial acetic acid (3:1) and stained with acetic orcein. No meiotic abnormalities were observed and the meiotic indices were high for all cultivars, indicating that the mismatch generated during crosses is not related to any meiotic changes. Estimation of pollen viability was made by comparing acetic orcein staining vs. Alexander's reactive: pollen viability was high in all cultivars with either stain, but was significantly higher when using the acetic orcein stain (>99%). Though some cultivar showed a significantly smaller pollen size, the range of variation among cultivars was low (means' range 51-66 μm).
Structural studies of two cancer targets involved in protein-protein interactions

3 DECLARATION . 4 PREFACE . 5 LIST OF TABLES . 9 LIST OF FIGURES . 10 UNITS OF MEASUREMENTS . 12 ABBREVIATIONS . 13 CHAPTER 1 | LITERATURE REVIEW . 16 1.1 Protein-protein interactions . 16 1.2 Types of protein-protein interactions . 18 1.3 Challenges in identifying and targeting protein-protein interactions . 19 1.4 Approaches to developing protein-protein modulators . 20 1.4. 1 Scaffold reduction and epitope transfer . 20 1.4. 2 High-throughput screening . 21 1.4. 3 Structure-based design . 22 1.4. 4 Peptidomimetics . 23 1.4. 5 Virtual screening . 23 1.4. 6 Fragment-based lead discovery . 24 1.5 Validation of the mechanism of protein-protein inhibitors . 25 1.6 Inhibitors of protein-protein interactions in cancer . 27 1.6. 1 The BCL2 family . 27 1.6. 2 p53 interactions with MDM2 . 30 1.6. 3 XIAP and Smac interactions . 31 1.6. 4 Integrin LFA-1 and CAMs interactions . 32 1.6. 5 Inhibition to the hypoxia-inducible factor pathway . 34 1.7 Inhibiting protein-protein interactions of cancer target CD151 . 35 1.7.
When road‐kill hotspots do not indicate the best sites for road‐kill mitigation

Summary The effectiveness of measures installed to mitigate wildlife road-kill depends on their placement along the road. Road-kill hotspots are frequently used to identify priority locations for mitigation measures. However, in situations where previous road mortality has reduced population size, road-kill hotspots may not indicate the best sites for mitigation. The purpose of this study was to identify circumstances in which road-kill hotspots are not appropriate indicators for the selection of the best road-kill mitigation sites. We predicted that: (i) road-kill hotspots can move in time from high-traffic road segments to low-traffic segments, due to population depression near the high-traffic segment caused by road mortality; (ii) this shift will occur earlier for more mobile species because they should interact more often with the road; (iii) this shift can occur even if the low-traffic segment runs through lower quality habitat than the high-traffic segment. To test these predictions, we simulated population size and road-kill over time for two populations, one exposed to a road segment with high traffic and the other to a road segment with low traffic. Our simulation results supported Predictions 1 and 3, while Prediction 2 was not supported. Synthesis and applications. Our results indicate that, for new roads, road-kill hotspots can be useful to indicate appropriate sites for mitigation. On older roads, road-kill hotspots may not indicate the best sites for road mitigation due to population depression caused by road mortality. Direct measures of the road impact on the population, such as per capita mortality, are better indicators of appropriate mitigation sites than road-kill hotspots.
The Stomata of the Fern Adiantum capillus-veneris Do Not Respond to CO 2 in the Dark and Open by Photosynthesis

matched that of photosynthesis. The simultaneous application of red (2 mmol m 22 s 21 ) and far-red (50 mmol m 22 s 21 ) light synergistically induced stomatal opening, but application of only one of these wavelengths was ineffective.Adiantum stomata did not respond to CO 2 in the dark; the stomata neither opened under a low intercellular CO 2 concentration nor closed under high intercellular CO 2 concentration. Stomata in Arabidopsis (Arabidopsis thaliana), which were used as a control, showed clear sensitivity to CO 2 . I nAdiantum, stomatal conductance showed much higher light sensitivity when the light was applied to the lower leaf surface, where stomata exist, than when it was applied to the upper surface. This suggests that guard cells likely sensed the light required for stomatal opening. In the epidermal fragments, red light induced both stomatal opening and K 1 accumulation in guard cells, and both of these responses were inhibited by a photosynthetic inhibitor, 3-(3,4-dichlorophenyl)-1, 1-dimethylurea. The stomatal opening was completely inhibited by CsCl, a K 1 channel blocker. In intact fern leaves, red lightinduced stomatal opening was also suppressed by 3-(3,4-dichlorophenyl)-1,1-dimethylurea. These results indicate thatAdiantum stomata lack sensitivity to CO2 in the dark and that stomatal opening is driven by photosynthetic electron transport in guard cell chloroplasts, probably via K 1 uptake.
Virosomes as a vaccine delivery system

Virosomes retain the cell entry, and membrane fusion characteristics of the native virus. Thus, influenza-derived virosomes are taken up by cells via receptor-mediated endocytosis, which directs the particles to the endosomes. Subsequently, the virosomal membrane fuses with the endosomal membrane from within the lumen of the endosomes. The fusion process establishes continuity between the lumen of the virosome, and the cell cytosol. Therefore, protein encapsulated in virosomes will be delivered into the cytosol of the cell as shown here for the A subunit of diphtheria toxin. Antigen-containing virosomes interacting with APCs are expected to introduce part of the antigen into the cell cytosol and, thus, into the MHC class I presentation pathway. Delivery of antigens in vivo indeed results in efficient priming of a class I MHC-restricted CTL response making virosomes a promising vehicle for in vivo targeting.
Genetic and physiological studies of heat tolerance in hexaploid wheat (Triticum aestivum L.)

xxi Declaration . xxiii Acknowledgements . xxiv Specific contribution to the research . xxv Dedication . xxvi Chapter 1: General introduction. 1 Chapter 2: Literature review . 3 2.1 Wheat as an important crop . 3 2.2 Impact of heat on the wheat industry . 3 2.3 Mechanisms of growth rate responses . 5 2.4 Mechanism of grain size reduction . 6 2.5 Mechanisms of dough quality effects . 7 2.6 Mechanisms of fertility effects . 9 2.7 Traits and parameters for evaluation of heat tolerance . 9 2.8 Stay-green and stress tolerance. 10 2.9 Quantitative trait loci (QTL) mapping . 12 2.10 Non-destructive imaging methods for phenotyping . 13 2.11 Mapping populations . 14 2.12 Molecular markers . 14 2.13 Methods for QTL analysis . 14 2.14 Genetics of heat tolerance/responses in wheat . 15 2.15 Aims of the thesis . 17 Chapter 3: Genetic variation for grain-filling response to a brief post-anthesis heat stress in wheat (Triticum aestivum L.): Relationships to flag leaf senescence, plant architecture, and development . 19 3.
The Influence of Silicon and Multinutrient Fertilizer On the Quality and Chemical Composition of Gazania Rigens ‘Kiss Yellow’, Salvia Farinacea ‘Fairy Queen’ and Verbena ‘Obsession Lilac’ Plants

Abstract Silicon supplementation may lead to positive changes in plant quality, including their appearance. The two-factorial experiment with three ornamental plant taxa Gazania rigens ‘Kiss Yellow’, Salvia farinacea ‘Fairy Queen’ and Verbena ‘Obsession Lilac’ was conducted in the years 2012-2013. The first factor was foliar application of Si in form of ortho-silicic acid stabilized with choline (YaraVita Actisil) at the concentrations of 60, 120 and 180 mg·dm-3, while the second was soil application of multinutrient fertilizer (Insol U) at the concentrations of 0.25% and 0.50%. Biometric measurements of plants were carried out at the beginning of flowering. The laboratory analyses included the determination of the content of P, K, Ca, Mg and Si as well as chlorophyll content in the leaves. Silicon had a beneficial influence on a majority of the analysed morphological features. Plants reacted best to high silicon doses (120 and 180 mg·dm-3). Particularly beneficial effects were noted with respect to improved flowering of all analysed plant taxa and to the vegetative development of Salvia and Gazania. Insol U supplementation noticeably improved the flowering of Verbena.
Multicast routing algorithm based on tabu search

The delay and delay variation-bounded Steiner tree problem is an important multicast routing issue in real-time multimedia networks.Such a constrained Steiner tree problem is known to be NP-complete.A multicast routing algorithm is presented,which is based on tabu search to produce routing trees having a minimal network cost under delay and delay variation constraints.The simulation shows that the algorithm is efficient for actual networks.This approach makes IP multicast utilize resources efficiently in delivering data to a group of members simultaneously.
IMPACT OF DOXORUBICIN AND VITAMIN E, A SEPERATELY AND IN COMBINATION ON RAT TISSUES ORGANIC CONSTITUENTS

The in vivo effect of 20 mg / kg weight of Dox, 100 mg / kg weight of vitamin E and 50 IU / kg weight of vitamin A separately and in combination over 10 weeks period (weekly doses), the state of rat tissues based organic constituents like total proteins, total carbohydrates total lipid, free amino acids, free fatty acids, glycogen and pyruvate, lactate and serum glucose levels were reported. The data indicated decreased total proteins, total carbohydrates total lipid, glycogen and pyruvate content followed by increased levels of free amino acids, free fatty acids, and serum glucose and lactate in all the rat tissues under Dox stress were observed. All these Dox altered rat tissues organic constituents appear to be neutralized by in the presence of Dox plus vitamin E and Dox plus vitamin A. From the result it is reported that Dox impair the overall general metabolism of rat tissues and the antioxidants like vitamin E and A by their antioxidant mechanism might be neutralizing the Dox altered rat tissues organic constituents in vivo.
Abundance and activity patterns of the Cape parrot (Poicephalus robustus) in two afromontane forests in South Africa

Behaviour, movements and numbers of the rare Cape parrot (Poicephalus robustus) were investigated at two study sites to assess its conservation status and as the basis for an action plan for their conservation. Birds flew regularly to and from nearby forests and were observed arriving at a feeding site (Hlabeni) from roosting sites in the morning. Numbers varied monthly and seasonally between the sites. Mean monthly (±SE) number of birds observed daily was 21.8 ± 2.5 (n = 45) but ranged from 0–80. Activity was bimodal: it commenced at sunrise, lasted several hours, and was followed by inactivity through mid-day; activity recommenced a few hours before sunset and continued until sunset. Activity reflected changing day length. Causes of localized movements included food and water availability, and in summer some birds fed in fruit orchards. The relevance of counts of Cape parrots for the conservation of this species is reviewed.
New tools for biotechnology: Signal peptides for selected protein secretion

Cyanobacteria are Gram-negative photosynthetic prokaryotes that use sunlight and CO2 as energy and carbon sources, respectively. These features makes them attractive candidates to use in industrial/biotechnological applications, e.g. for biofuel production. Previously, the research group started to characterize the poorly known exoproteome of the cyanobacterium Anabaena sp. PCC 7120 and identified HesF (Heterocyst-specific attachment Factor), an exoprotein found in relatively high amounts in the medium of cells grown diazotrophically. Despite the abundance of this protein, no ordinary signal-peptide (SP) was found via bioinformatics analyses. Furthermore, HesF (Alr0267) was also found to be a type I secretion system (T1SS) substrate, and is generally recognized that T1SSsecreted proteins have a C-terminal signal peptide (SP) required for secretion, despite some studies described T1SS-secreted proteins with a N-terminal SP. In this work, we proposed to identity the amino acid sequence which determines HesF secretion, and to demonstrate its applicability for protein secretion. We focused on the N-terminus and Cterminus of the HesF sequence. Thus, the DNA sequences encoding the first HesF 80 amino acids (designated N80 hesF) and the last ones (designated C80 hesF) were used as a starting point. Subsequently, constructs containing N80 hesF portion or C80 hesF portion, or both simultaneously, were fused with gfp (green fluorescent protein reporter gene) and assembled with self-replicating plasmids pRL25C and pNir4. Hence, the cyanobacterium Anabaena sp. PCC 7120 was transformed with pRL25C or pNir4 based constructs using the triparental mating technique. Afterwards, a SDS-PAGE/Western blot approach with an antibody anti-GFP was performed to investigate the proteome and exoproteome of each transformant, in different appropriate growth conditions. Our results indicate that a putative signal peptide is probably present at the C-terminus of HesF protein, since a truncated chimeric protein comprising this portion was successfully secreted. Moreover, a specific post-translational cleavage process occur in the HesF analyzed portions. Overall, these results contributed to the promise of exploiting cyanobacteria as cell factories notably to produce and secrete selected proteins, as well as for the fundamental elucidation of the protein secretion process in cyanobacteria.
A Comparative Study of Lipid Composition of an Undervalued Crustacean (Munida spp.) Captured in Winter and Summer

ABSTRACT This research was focused on the lipid fraction of an undervalued crustacean (lobster krill; Munida spp.) and the comparative study of individuals captured at winter and summer seasons. For this purpose, seasonal variations were analyzed in the muscle (i.e., tail meat) for proximate composition, lipid class distribution, and fatty acid (FA) profile. Mean total lipids ranged from 0.75 ± 0.08% (summer) to 0.92 ± 0.06% (winter), moisture from 77.94 ± 0.25% (winter) to 78.62 ± 0.38% (summer), and protein from 17.93 ± 0.46% (summer) to 18.22 ± 0.46% (winter). Regarding lipid class content (% of total lipids), phospholipids ranged from 64.85 ± 1.29 (summer) to 67.85 ± 2.56 (winter), sterols from 12.15 ± 0.35 (winter) to 13.54 ± 0.54 (summer), triacylglycerols from 0.04 ± 0.02 (summer) to 1.25 ± 0.88 (winter), and free FA from 1.14 ± 0.72 (winter) to 2.19 ± 0.34 (summer). In both seasons, the most abundant FA were C22:6ω3, C16:0, C18:1ω9, and C20:5ω3. Polyunsaturated fatty acids (PUFA) were found to be the most abundant group in samples from both seasons (50.4–55.3%). Higher PUFA values were determined in summer samples, while a highly valuable ω3/ω6 ratio (from 9.11 ± 1.12 in summer to 10.40 ± 1.39 in winter) was observed. It is concluded that in spite of being a low-fat product, the lipid fraction of this underutilized crustacean can provide highly valuable constituents.
All dispersal functions are wrong, but many are useful: A response to Cousens et al.

To address the lack of information about the shape and extent of real dispersal kernels, Bullock et al. (Journal of Ecology 105:6‐19, 2017) synthesised empirical information on seed dispersal distances. Testing the fit of a variety of probability density functions, they found no function was the best‐fitting for all datasets but some outperformed others. Cousens et al. (Journal of Ecology, 2017) focus on the specific finding of the generally poor fit of the WALD function to wind dispersal data and use this to argue that mechanistically derived functions would not be expected to fit data particularly well. We agree in part with this argument and discuss the issues that may lead to poor fit, including the simplifying assumptions of the WALD and the complexity of the dispersal process. We explain the fundamental linkage between the mechanistic form of the WALD and the derived function used for fitting to data. We demonstrate, however, that the logic that a mechanistically based function could fit to data is valid, under the hypothesis that it encompasses the key processes determining the dispersal kernel. This argument is supported by the facts that: (1) our analyses and others have shown the WALD performs well in a number of cases; and (2) the WALD is the best‐fitting function for an example in which we simulate dispersal data using a realistic representation of variability in the wind dispersal process. Synthesis. While there are reasons that mechanistically derived functions may not fit well to empirical data, they do in some empirical and simulated cases and this suggests they can capture the dispersal behaviour of real systems. Mechanistic functions should be explored along with other more general functions when describing empirical data to investigate their simplifying assumptions and to add to our arsenal of functions for analysing dispersal data. Analyses using these functions are critical if we are to move from simply describing the system in which the data were gathered to gaining more general insights into dispersal and predicting its consequences.
THE EFFECT OF LENGTH OF THE PREOVULATORY PERIOD ON MECHANISMS REGULATING EMBRYONIC SURVIVAL IN BEEF CATTLE

The objective of the present experiment was to determine the influence of manipulation of preovulatory estradiol concentrations through alteration of the duration of the preovulatory period on gene expression and protein synthesis of interferon tau (IFNτ) and chorionic somatomammotropin hormone 1 (CSH-1) by the conceptus on d 17.5 of pregnancy, and expression of interferon stimulated gene 15 (ISG-15) and Myxovirus resistance 2 (Mx2) in peripheral blood mononuclear cells (PBMC) from d 15 to 17.5 of pregnancy in cows. Nonlactating beef cows were presynchronized to a common day of estrus and ultrasonographic-guided follicle aspiration was performed 6.5 ± 0.3 d after estrus (day of aspiration = d 7 of experiment). The experiment was performed in two replications. Cows were assigned to receive 25 mg of prostaglandin F2α (PGF, Lutalyse®) on either d 3 (high estradiol treatment; Hi-E), or on d 2 (low estradiol
Microsporidia in a woodland pool I. Lanatospora costata sp. n. (opisthosporidia, microsporidia), parasite of megacyclops viridis (Crustacea, Copepoda) : Fine structure and molecular phylogeny

Lanatospora costata sp. n. , a new microsporidian parasite of the adipose and connective tissue cells of Megacyclops viridis (Jurine, 1820) (Copepoda: Cyclopidae) is described. It was isolated from a woodland pool with a rich and diverse fauna of microsporidiainfected small crustaceans and insect larvae. The parasite is structurally similar to the genus Lanatospora Voronin, 1989, characterized by a complex decorated exospore. In the described species the exospore is armoured by a conspicuous layer of interwoven ribs forming labyrinth on the spore surface. SSU rRNA phylogeny places the organism in the “aquatic outgroup” of microsporidia (Vossbrinck et al. 2004), which includes a number of microsporidia from aquatic microcrustacea of the classes Copepoda and Cladocera. The increasing number of available SSU rRNA gene sequences of these microsporidia allows a more detailed interpretation of their developmental histories.