Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of host genes involved in the biotrophic interaction between grapevine and powdery mildew

VI Declaration . IX Acknowledgements. X Abbreviations.XII Chapter 1 – General introduction . 1 1.1 Infection process of powdery mildew fungi. 3 1.2 Haustorium structure and function . 5 1.3 Host responses: compatibility and defence. 10 1.4 Host responses: amino acids and carbohydrates . 13 1.5 Carbohydrate distribution in plants . 16 1.6 Pathogen associated changes to host invertase activity . 18 1.7 Induction of sink metabolism in response to pathogens and wounding. 18 1.8 Role of plant growth regulators in biotrophic interactions . 20 1.9 Other signals in biotrophic interactions . 23 1.10 Identification of host susceptibility genes . 24 1.11 Aims of this study . 26 Chapter 2 – General Materials and Methods.28 2.1 Materials . 28 2.1.1 Solutions, chemicals and growth media. 28 2.1.2 Oligodeoxyribonucleotide primers. 29 2.1.3 Bacterial and yeast strains. 31 2.1.4 Grapevine tissue. 32 2.1.5 Erysiphe necator culture and maintenance . 32 2.1.6 Plasmopara viticola culture and maintenance . 33 2.2 Methods . 33 2.2.1 Polymerase chain reaction (PCR) . 34 2.2.2 Agarose gel electrophoresis . 34 2.2. 3 Purification of DNA from agarose gel slices . 35 2.2. 4 Dephosphorylation of DNA 5’ termini . 35 2.2. 5 Purification of DNA samples following enzymatic reactions. 35 2.2. 6 DNA ligation. 35 2.2. 7 Preparation of electro-competent E. coli cells . 36 2.2. 8 Transformation of bacteria with recombinant plasmids. 36 2.2. 9 Preparation of plasmid DNA. 37 2.2.10 Preparation of bacterial glycerol stocks . 37 2.2.11 Preparation of DNA samples for sequencing. 38 2.2.12 Preparation of total grape RNA. 38 2.2.13 First-strand cDNA synthesis . 39 2.2.14 Sequence analysis and manipulation. 39
Anther-derived callus induction based on culture medium, myo-inositol, AgNO3 and Fe-EDTA in Seolhyang strawberries

Haploid breeding is an effective method of shortening the breeding period of plants. In this study, to develop a haploid breeding technique, optimum conditions of the culture medium were investigated for anther-derived callus induction in the strawberry cultivar Seolhyang. The effects of the culture medium type, myo-inositol, auxin and cytokinin combination treatment, silver nitrate (AgNO3), and ferric ethylenediaminetetraacetic acid (Fe-EDTA) on anther-derived callus induction were analyzed. Anthers were incubated in Murashige and Skoog (MS) medium, Gamborg B5 medium (B5), and Lichter medium (NLN) for 8 weeks. Each culture medium had 0.4 mg∙L–1 of 6-benzyladenine (BA), 0.1 mg∙L−1 of indole-3 acetic acid (IAA), and 2.0 mg∙L−1 of 2,4-dichlorophenoxyacetic acid (2,4-D) added to it. Results showed that MS medium was most effective in callus induction. When 100 mg∙L−1 of myo-inositol was added to each medium, the callus induction rate increased. Auxin and cytokinin combination treatment was more effective with the addition of 0.4 mg∙L−1 of BA, 0.1 mg∙L−1 of IAA, and 2.0 mg∙L−1 of 2,4-D to MS medium compared to the addition of 0.1 mg∙L−1 of BA, 2.0 mg∙L−1 of IAA, and 0.4 mg∙L−1 of 2,4-D. With AgNO3 treatment, the highest callus induction rate was found at a concentration of 25 mg∙L−1. The callus induction rate increased as the AgNO3 concentration increased; however, a significant decrease was seen at 30 mg∙L−1. In the case of Fe-EDTA, the most effective concentration for callus induction was 25 mg∙L−1. Therefore, supplementing myo-inositol, AgNO3 and Fe-EDTA can help in anther-derived callus induction in Seolhyang strawberries. Key words: Anther culture, auxin, B5 medium, callus induction, cytokinin, haploid breeding, NLN medium.
A simplified spiking model of grid-cell scale and intrinsic frequencies

The hexagonal tessellation pattern of grid cells scales up progressively along the dorsal-to-ventral axis of the medial entorhinal cortex (MEC) layer II. This scaling gradient has been hypothesized to originate either from inter population synaptic dynamics as postulated by attractor networks, from projected theta frequencies to different axis levels, as in oscillatory models, or from cellular dynamics dependent on hyperpolarization-activated cation currents. To test the hypothesis that intrinsic cellular properties account for the scale gradient as well as the different oscillatory frequencies observed along the dorsal-to-ventral axis, we have modeled and analyzed data from a population of grid cells simulated with spiking neurons interacting through low-dimensional attractor dynamics. To investigate the causal relationship between oscillatory frequencies and grid scale increase, we analyzed the dominant frequencies of the membrane potential for cells with distinct after-spike dynamics. We observed that intrinsic neuronal membrane properties of simulated cells could induce an increase of grid scale when modulated by after-spike reset values. Differences in the membrane potential oscillatory frequency were observed along the simulated dorsal-to-ventral axis, suggesting that, rather than driving to the increase of grid scale as proposed by interference models of grid cells, they are the result of intrinsic cellular properties of neurons at each axis level. Overall, our results suggest that the after-spike dynamics of cation currents may play a major role in determining the grid cells’ scale and that oscillatory frequencies are a consequence of intrinsic cellular properties that are specific to different levels of the dorsal-to-ventral axis in the MEC layer II.
Generation of Epstein‐Barr Virus (EBV)–Immortalized B Cell Lines

Immortalization of B lymphocytes by EBV is an effective procedure for inducing long‐term growth of certain human B lymphocytes. The protocol described in this unit to accomplish this can be divided into three stages: preparation of virus, preparation of target cells to be immortalized, and EBV infection and growth of infected cells.
Physiological synchrony predicts observational threat learning in humans

Understanding how information about threats in the environment is shared and transmitted between individuals is crucial for explaining adaptive, survival-related behavior in humans and other animals, and for developing treatments for phobias and other anxiety disorders. Research across species has shown that observing a conspecific’s, a “demonstrator’s”, threat responses causes strong and persistent threat memories in the “observer”. Such observational threat learning is hypothesized to be supported by empathic processes. Here, we examined if physiological synchrony between demonstrator and observer can serve as a biomarker of the hypothesized empathic transfer. We find that synchronization of phasic skin conductance, which directly reflects autonomic nervous system activity and captures an organism’s arousal when facing and responding to threats, between the demonstrator and observer during observational learning predicts the strength of the observer’s later threat memories. Dynamic coupling between an observer’s and a demonstrator’s autonomic nervous system activity may reflect empathic experience sharing and determine the formation and later retrieval of observational threat associations.
Evaluation of the Redox State of Wistar Rats Submitted to High-Fat Diet Supplemented With Infusion of Ilex paraguariensis

This study aimed to evaluate the effect of Ilex paraguariensis infusion on redox state of Wistar rats submitted to high-fat and standard diet. Glutathione determination and lipid peroxidation in the hippocampus tissues and liver was performed, as well as the analysis of gene expression of superoxide dismutase, catalase and glutathione peroxidase by real-time polymerase chain reaction. The results from hippocampus showed that the groups fed with standard diet exhibited significant reduction of lipid peroxidation when supplemented with Ilex paraguariensis. The analysis from glutathione determination in the hippocampus showed a significant increase in glutathione activity in the group treated with high-fat diet and Ilex paraguariensis. In the liver, results showed no significant difference in both glutatione and lipid peroxidation analisys. Gene expression of superoxide dismutase, catalase and glutathione peroxidase showed that there was significant difference in the groups treated with high-fat diet and Ilex paraguariensis. In summary, the Ilex paraguariensis showed substantial potential for antioxidant activities.
A preliminary molecular survey of Babesia divergens and first evidence of Theileria annulata in cattle from Saudi Arabia

Background and Aim: Babesia divergens causes human babesiosis in Europe where the parasite utilizes cattle as animal reservoir and Ixodes ricinus as tick vector. Importation of infected animals and passive carriage of infected ticks through migratory birds can lead to tick/pathogen geographic expansion and emergence of diseases in naïve land. Given the information that Saudi Arabia imports cattle from the European countries and that two global bird flyways pass through the country geographic coordinates, we speculate that B. divergens might be introduced into the Kingdom. Therefore, the aim of this preliminary study was to molecularly detect and characterize B. divergens and other piroplasms (including Theileria spp.) in cattle from Taif district, Kingdom of Saudi Arabia. Materials and Methods: Blood samples from 20 cattle residing Taif district were collected, and polymerase chain reaction tested using wide and species-specific primers. Amplicons from a positive genus-wide reaction were purified, sequenced, and analyzed. Phylogenetic trees were constructed, and similarity to existing GenBank zoonotic piroplasms was also assessed. Results: All samples were negative for B. divergens, and only one sample proved positive for Theileria annulata in a wide reaction. Phylogeny clustered our strain with T. annulata from Spanish dog and another one detected in a cow from France. BLAST analysis showed genetic distance from zoonotic piroplasms with identity ranged from 88% to 91%. Conclusion: Although B. divergens was not detected, we are not able to rule out or affirm the existence of the pathogen in the country. On the other hand, identifying T. annulata strain with a southern European origin strongly supports our speculation that bovine zoonotic Babesia might be introduced into KSA. This study is not only the first molecular survey of B. divergens but also the first report of the molecular identity of T. annulata in Saudi Arabia. A national-wide bovine and tick surveillance are needed to further prove our speculation.
The role of strigolactones in regulation of stomatal conductance and plant-pathogen interactions in Arabidopsis thaliana

Strigolactones are a group of phytohormones that control shoot branching in Arabidopsis thaliana. However, in recent years they have been shown to affect many other plant processes. We previously showed that the strigolactone perception mutant more axillary branches 2 (max2) has increased susceptibility to plant pathogenic bacteria as a result of more open stomata as well as alterations in hormonal signalling. Here we show that both, strigolactone biosynthesis- (max3 and max4), and perception mutants (max2 and dwarf14) are significantly more sensitive to Pseudomonas syringae DC3000. Moreover, in response to P. syringae infection, high levels of SA accumulated in max2 and this mutant was ozone sensitive. To search for the mechanisms that could explain pathogen- and ozone sensitivity we performed gene expression analysis and several different assays that explore the function of guard cells and regulation of guard cell signalling. Treatments with GR24 (a strigolactone analogue) resulted in very modest changes in defence-related gene expression. In contrast, guard cell function was clearly impaired in max2 and depending on the assay used, also in max3, max4 and d14 mutants. Moreover, stomatal responses to stimuli that cause stomatal closure in wild-type plants (darkness, high CO2 and ABA) were analysed in the strigolactone mutants. In darkness both strigolactone biosynthesis and perception mutants showed reduced stomatal closure, whereas the response to high CO2 was impaired only in max2 and d14. The response to ABA was not impaired in any of the mutants. To position the role of MAX2 in the guard cell signalling network, max2 was crossed with mutants defective in ABA biosynthesis (aba2), in guard cell ABA signalling (ost1) and a scaffold protein required for proper ion channel activity (ghr1). The stomatal conductance of double mutants was consistently higher than the corresponding single mutants, suggesting that MAX2 acts in a signalling pathway that functions in parallel to the well characterized guard cell ABA signalling pathway. We propose that the impaired defence responses of max2 is related to more open stomata that allows increased entry of bacteria or air pollutants like ozone. Furthermore, as MAX2 appears to act in a specific branch of guard cell signalling (related to CO2 signalling), this protein could be one of the elusive components that allow guard cells to distinguish between different environmental conditions.
Analysis of rural people’s attitude towards the management of tribal forests in South Africa

ABSTRACT The management of forests for multiple purposes coupled with a varying socioeconomic profile of forest users can result in attitudinal differences towards forest management. This study examines the attitudes of rural people in South Africa towards the management of tribal forests. Attitude towards forest management was analysed with respect to five forest management objectives: 1, forest management for rural livelihood resilience to climate change; 2, forest management for reduction and management of forest fire risk; 3, forest management for sustainable forest-based livelihood; 4, forest management for household socioeconomic wellbeing; and 5, forest management for community-based climate change adaptation initiative. A household questionnaire survey was used to elicit information from 155 rural households using the proportionate random sampling procedure. Chi-square test was used to analyse data from the household survey. Factorial analysis was used to analyse variance in attitude towards forest management. The results showed that rural people generally have positive attitudes toward the management of tribal forests. Factor analysis isolated 2 major factors that explained 61% variance in attitude. Based on the findings we conclude that centralising forest management around the four management objectives (1, 3, 4 & 5) are likely to promote inclusive forest-based development in the study communities.
Comparing Three Methods for Design Analyses of Rankine Cycle for Waste Heat Recovery from Natural Gas Compression

This study applies three methods for design of Rankine cycles utilizing waste heat in the oil and gas industry. The methods differ in the level of detail of heat exchanger model applied and in the flexibility with respect to heat exchanger design. All the methods involve formulating a constrained optimization problem with the objective of maximizing net power output, but vary in the constraints related to limit the size of the heat exchangers. The cycles with using two working fluids, n-butane and a n-butane/n-pentane mixture (30%/70%), are compared for each method. The methods yield different results; both the maximized net power output and the best-performing working fluid differ with respect to the method used, emphasizing the importance of method selection.
A New Approach to SINR-Based Reliability Analysis of IEEE 802.11 Broadcast Ad Hoc Networks

This letter proposes a new approach to the reliability analysis of IEEE 802.11 one-dimensional (1-D) broadcast mobile ad hoc networks. The approach finds a simple and effective way to derive the distribution of signal-to-interference-to-noise ratio (SINR) on each receiver, which is required for evaluation of the reliability metrics and the channel capacity. Having observed that the effective interference area depends on a given SINR threshold, the SINR distribution derivation is converted to estimating the SINR threshold related interference areas that are dynamically changed in a communication channel. The analysis is applied to two network configurations for example, and it is cross validated by the extensive simulations. Compared with the previous models, the new approach is more general, more precise, and faster.
Hybridization between Native and Introduced Individuals of Sika Deer in the Central Part of Toyama Prefecture

Abstract. In recent decades, invasive animals have disturbed the native ecosystem, via intraspecific and interspecific genetic hybridization. Previously, maternally-inherited mitochondrial DNA analysis detected two genetically distinct lineages of the sika deer (Cervus nippon) in the Japanese Archipelago and revealed the coexistence of both lineages mainly in the central part of Toyama Prefecture in Japan. One of the lineages was thought to be derived from introduced individuals. In the present study, using 13 microsatellite DNA markers, the level of hybridization between the two lineages was investigated in Toyama Prefecture. The results revealed deviation from the Hardy-Weinberg equilibrium in both the entire population and individuals from maternally-inherited samples. The Bayesian estimation elucidated the contribution of genetically divergent ancestral sources to the studied population due to the introgression of introduced gene pool and subsequent continuous mating across generations.
Molecular characterization of MHC class II DRA cDNA in Deoni cattle

The present study was undertaken to clone and characterize DRA gene in Deoni cattle. The cDNA for the DRA gene was amplified by using specific primers designed based on available cattle sequences and purified products were cloned in competent E.coli (DH5á) strain. The full length 1013bp product of cDNA of DRA contained a single ORF of 762 nucleotides that coded for 253 amino acids translated product. Twenty four amino acids formed signal peptide while 229 constituted mature peptide. The deduced amino acid sequences resembled those of class II molecules of other species for all the conserved residues having critical functional role. But a single N-linked glycosylation site in á1 was observed in cattle and buffalo when compared to human and swine which contain a second site in á2 domain. The signal peptide was found more variable among the species compared. Comparison of nucleotide and amino acid sequences among related species and dendrogram constructed revealed that the cattle sequences are more similar to buffalo sequences.
Complex Network Modeling of Evidence Theory

Because of the advantages of graphs in visualizing the relationship between individuals, complex networks have been widely used and greatly developed. In real-world applications of Dempster–Shafer evidence theory, there are usually thousands of sensors collecting information. It is easy to be overwhelmed by the mass of information and ignore the connections between them. The rise of the semisupervised learning method graph convolutional network makes it possible to address this issue. In this article, inspired by complex network, the basic probability assignment function, the base function of evidence theory, is modeled in a novel form of the network graph. Some typical issues of evidence theory, such as conflicting evidence, multiclass evidence clustering, and computational complexity for large-scale fusion are systematically addressed in the framework of the proposed network model. What's more, a new combination rule is presented from the point view of the graph. The empirical results of experiments on real data set demonstrate the potential and feasibility of complex networks in traditional evidence theory.
A LOW-PARASITIC CMOS TRANSISTOR STRUCTURE FOR WIDE LOCKING RANGE ILFD DESIGN

A wide locking range injection locked frequency divider (ILFD) with a low power consumption for 60 GHz applications is presented. The locking range of the ILFD is enhanced by reducing the parasitic capacitances of the transistors. The cross-coupled transistor and injected transistors are integrated to become a compact structure, which exhibits simple routing and induces less parasitic capacitances. To verify the proposed structure, the ILFD was fabricated using 65 nm CMOS technology. It has a measured locking range of 55.3 GHz to 67 GHz (19%) with 0 dBm input power. The circuit dissipates 1.98 mW at 0.5 V supply voltage without the output buffers.
One hill I'm willing to die on: Moral conviction as a catalyst for advocacy on behalf of controversial health- and public-policy-related attitudes

The grassroots spread of health and social movements is a highly important but largely understudied social process. Advocating on behalf of your beliefs to others violates the principles of Politeness Theory (Brown & Levinson, 1978) and therefore poses social risk. However, people do advocate for these beliefs, to a degree; as noted by Skitka (2002), people seem to select a limited number of positions to incorporate into their self-concept, choosing some to represent the self as a symbolic act. She argues that some of these attitudes most deeply ingrained and most motivating to act are those that are “moral mandates”. Within this work, I discussed this construct of morality in the context of attitude structure (e.g. Teeny & Petty, 2018), attitude strength (e.g. Skitka, Bauman, & Sargis, 2005), observed behavioral intentions and effects (e.g. Cole Wright, Cullum, & Schwab, 2008), the self (discussing implication of Skitka, 2002), and regulatory orientation (Zaal, Laar, Ståhl, Ellemers, & Derks, 2011), focusing the discussion and subsequent research on the latter two. I then completed three empirical studies. In Study 1, I tested the factor structure of various operationalizations of morality, as well as attitude structure and strength, and their ability to predict outcomes previously associated with moral conviction. Moral conviction and moral acceptability were determined to be the most theoretically and predictively distinct conceptualizations, and evidence was found for basis being a significant interactor with morality in predicting the replicated outcomes. In Study 2, I examined how morality interacts with perceived controversy and majority status, to elucidate the nature of morality as a counteractive force to social risk. I found that
Effects of dietary Shirazi thyme (Zataria multiﬂora Boiss) and vitamin E on growth and biochemical parameters in common carp (Cyprinus carpio)

Using of phytobiotics as fish feed additives have been interestingly increased during the recent decade. The aim of the current study was to evaluate the effect of individual and combined level of thyme and vitamin E in common carp. Juveniles were separately fed by four distinct diets including control (commercial diet without any additive), supplemented with 1% ground Shirazi thyme, supplemented with 100 mg/kg vitamin E and a mixture of Shirazi thyme and vitamin E (TE) with mentioned concentrations for 45 days. Sampling was done at 15, 30 and 45 days after feeding trial duration and some growth and plasma biochemical parameters were evaluated. The individual thyme supplementation significantly increased weight gain (%), feed conversion efficiency and decreased feed conversion ratio (P<0.05). Plasma enzymes (AST, ALT, ALP and LDH) were not affected in all experimental groups. Comparing to the control, triglyceride and glucose were significantly elevated in TE complex at all sampling times. Plasma proteins (total protein, albumin and globulin), cholesterol and creatinine were not altered in all treatments. In conclusion, dietary supplementation with individual 1% Shirazi thyme had not any harmful effects on plasma biochemical parameters and increased growth performance of the fish. Moreover, positive effects of thyme on fish growth were more than vitamin E. Supplementation by a mixture of vitamin E and thyme also displayed no priority than individual using of Shirazi thyme in the diet.