Miracle-dz/UniFAR-FTUs huggingface dataset:
Understanding the physiological mechanisms of ripening in capsicum.

iv Thesis Declaration . vi Acknowledgements . vii Abbreviations . ix Chapter 1: Literature Review . 1 1.1 Background . 2 1.2 Fruit ripening physiology and biochemistry . 4 1.2. 1 A comparison of the physiology of climacteric and non-climacteric fruit ripening . 4 1.2. 2 Ethylene biosynthesis and the role of the ripening transcription factor (RIN) . 6 1.2. 3 Ethylene perception for ripening . 9 1.2. 4 Respiration of fruit during ripening . 11 1.2. 5 Colour-related processes that occur during ripening . 14 1.2. 6 Other processes that occur during ripening . 17 1.2. 7 Ripening changes in capsicum . 19 1.3 Comparison-based approaches in ripening research . 20 1.4 Research rationale . 24 Chapter 2: Preliminary studies for the proteomic analysis of capsicum and the characterisation of capsicum ripening behaviour (cv. Aries) . 25 2.
Baseline Susceptibility of the Fall Armyworm (Lepidoptera: Noctuidae) to CrylAb Toxin: 1998–2000

‘Attribute’ sweet corn containing a crylAb gene (Bt11 Event) from Bacillus thuringiensis Berliner was registered for commercial use in 1998. A requirement of registration was to conduct baseline susceptibility studies to CrylAb toxin in fall armyworm populations collected from sweet corn growing areas in south Texas and south Florida. In addition, fall armyworm populations collected in sweet corn growing areas must be annually monitored for changes in susceptibility to the CrylAb protein. Fall armyworm larvae were collected near Belle Glade, FL, Homestead, FL, Weslaco, TX, and Corpus Christi, TX, in 1998 through 2000 and evaluated for susceptibility to CrylAb toxin. The Tifton Laboratory colony of fall armyworm that has been in culture for more than 10 yrs was used as the susceptible control. Comparison of the calculated LC50S for the various colonies did not indicate an appreciable change in susceptibility during the period 1998–2000. These data provide baseline information as to the susceptibility of th.
Induction of 2n pollen by colchicine in Populus × popularis and its triploids breeding

Abstract Induction of 2n pollen is a required technique for cultivating polyploid via sexual polyploidy. Orthogonal design or Taguchi Design was applied to select the best treatment process of 2n pollen induction in Populus × popularis from different levels of the meiosis stage of male flower buds, colchicine concentration, times of injection, and interval between injections. Flow cytometry and chromosome counting were used to identify the triploids from the offspring of P. × euramericana. (Dode) Guinier pollinated with induced pollen of P. × popularis. The results showed that high 2n pollen rate can be achieved by selecting the flower buds during diakinesis stage in meiosis, and then injecting 0.6% colchicine 4 times with 2 hours interval. The 2n pollen rate reached 62.10% by this process, and two triploids were obtained, which indicates that it is possible for cultivating triploids via 2n pollen induction by colchicine treatment in poplar. Results and protocol related to 2n pollen induction, polyploid identification and effect of 2n pollen in this study might be applicable in polyploidy breeding in section Aigeiros and Tacamahaca of poplar.
Association between serum transferrin receptor levels and malaria recurrence in a malaria endemic area in Tanzania

Background: The relationship between body iron levels and malaria presents a complex interaction that provide variable and contradicting results. We designed a study to investigate associations between concentrations of biomarkers of body iron and malaria recurrence among children. Methods: We conducted a longitudinal descriptive community based study in a malaria endemic area in northeastern Tanzania. The study involved 428 children of ≤5 years of age who were positive for malaria. Over a period of 6 months, sick children visited the study clinic for screening of malaria and measurement of iron storage biomarkers by serological assays. Correlations between levels of biomarkers and malaria was determined by Spearman correlations and Mann-Whitney U-Test. Associations between malaria recurrence and serum levels of iron biomarkers were determined by odds ratio (OR) with significance cutoff points of <0.15 in univariate and <0.05 in multivariate logistic regression analyses. Results: Only serum Transferrin Receptor (sTfR) levels had a positive correlation with malaria recurrence. When Mann-Whitney U test was used higher Hepcidin, sTfR and Leptin levels were significantly associated with malaria recurrence when malaria incidence was grouped into ‘once’ versus ‘more than once’. When malaria incidence was recategorised to ‘up to twice’ versus ‘more than twice’, only higher level of sTfR was associated with recurrence of malaria. With univariate regression analysis, only sTfR was found to be significantly associated with malaria recurrence, although this associated was not observed in Multivariate analyses. Conclusion: Despite the absence of association in multivariate analyses, univariate analyses suggest elevated levels of sTFR as a likely predictor of Plasmodium falciparum re-infection.
Representation of Borders and Swimming Kinematics in the Brain of Freely-Navigating Fish

Like most animals, the survival of fish depends crucially on navigation in space. This capacity has been documented in numerous behavioral studies that have revealed navigation strategies and the sensory modalities used for navigation. However, virtually nothing is known about how freely swimming fish represent space and locomotion in the brain to enable successful navigation. Using a novel wireless neural recording system, we measured the activity of single neurons in the goldfish lateral pallium, a brain region known to be involved in spatial memory and navigation, while the fish swam freely in a two-dimensional water tank. Four cell types were identified: border cells, head direction cells, speed cells and conjunction head direction with speed. Border cells were active when the fish was near the boundary of the environment. Head direction cells were shown to encode head direction. Speed cells only encoded the absolute speed independent of direction suggestive of an odometry signal. Finally, the conjunction of head direction with speed cells represented the velocity of the fish. This study thus sheds light on how information related to navigation is represented in the brain of swimming fish, and addresses the fundamental question of the neural basis of navigation in this diverse group of vertebrates. The similarities between our observations in fish and earlier findings in mammals may indicate that the networks controlling navigation in vertebrate originate from an ancient circuit common across vertebrates. Summary Navigation is a fundamental behavioral capacity facilitating survival in many animal species. Fish is one lineage where navigation has been explored behaviorally, but it remains unclear how freely swimming fish represent space and locomotion in the brain. This is a key open question in our understanding of navigation in fish and more generally in understanding the evolutionary origin of the brain’s navigation system. To address this issue, we recorded neuronal signals from the brain of freely swimming goldfish and successfully identified representations of border and swimming kinematics in a brain region known to be associated with navigation. Our findings thus provide a glimpse into the building blocks of the neural representation underlying fish navigation. The similarity of the representation in fish with that of mammals may be key evidence supporting a preserved ancient mechanism across brain evolution.
Developing Models to Predict the Number of Fire Hotspots from an Accumulated Fuel Dryness Index by Vegetation Type and Region in Mexico

Understanding the linkage between accumulated fuel dryness and temporal fire occurrence risk is key for improving decision-making in forest fire management, especially under growing conditions of vegetation stress associated with climate change. This study addresses the development of models to predict the number of 10-day observed Moderate-Resolution Imaging Spectroradiometer (MODIS) active fire hotspots—expressed as a Fire Hotspot Density index (FHD)—from an Accumulated Fuel Dryness Index (AcFDI), for 17 main vegetation types and regions in Mexico, for the period 2011–2015. The AcFDI was calculated by applying vegetation-specific thresholds for fire occurrence to a satellite-based fuel dryness index (FDI), which was developed after the structure of the Fire Potential Index (FPI). Linear and non-linear models were tested for the prediction of FHD from FDI and AcFDI. Non-linear quantile regression models gave the best results for predicting FHD using AcFDI, together with auto-regression from previously observed hotspot density values. The predictions of 10-day observed FHD values were reasonably good with R2 values of 0.5 to 0.7 suggesting the potential to be used as an operational tool for predicting the expected number of fire hotspots by vegetation type and region in Mexico. The presented modeling strategy could be replicated for any fire danger index in any region, based on information from MODIS or other remote sensors.
ALTERNATIVES TO ANTIBIOTICS: PHAGE LYTIC ENZYMES AND PHAGE THERAPY

Back in the early 19th century an opinion prevailed that disease is caused by imbalances in the body. It was only in the midcentury that Louis Pasteur linked infections to their causative agents, germs. The day in 1928 when penicillin was discovered by the British bacteriologist Alexander Fleming became a milestone in the history of medicine, marking the advent of the antibiotic era. Antibiotics were initially seen as a universal remedy, a super weapon capable of turning the tide in the war against infectious diseases. But the euphoria did not last long. As our knowledge accumulated, more new antibiotics were discovered with various mechanisms of action, different properties and spectra of activity; but bacteria struck back by developing resistance to those drugs, frustrating the efforts of researchers and doctors [1]. So hopes were pinned on lastresort antibiotics, such as colistin and daptomycin. In May 2015 the World Health Organization (WHO) admitted that bacterial resistance to antibiotics was the underlying cause of the ongoing healthcare crisis and proposed the Global Action Plan on Antimicrobial Resistance [2]. However, it was only a few months after that a mobile colistin-resistance gene was discovered in November 2015 [3]. A similar report followed in October 2016 describing a daptomycin-resistant Staphilococcus aureus strain capable of inactivating the antibiotic by releasing membrane phospholipids into the surrounding environment once they have bound daptomycin [4]. In September 2016, a month before that report, an П. А. Назаров АЛЬТЕРНАТИВЫ АНТИБИОТИКАМ: ЛИТИЧЕСКИЕ ФЕРМЕНТЫ БАКТЕРИОФАГОВ И ФАГОВАЯ ТЕРАПИЯ
Recreational fishing alters dingo foraging behavior on Fraser Island

Supplemental feeding, whether intentional or accidental, alters wildlife foraging behaviors and may have consequences at the population and ecosystem levels. Wildlife feeding may also cause animals to develop aggressive behaviors toward conspecifics and people. The risks to humans is potentially accrued when the species is a native predator. Food-based attraction has been implicated in the development of human-directed aggression in the dingo (Canis lupus dingo) population on Fraser Island, Queensland, Australia. Management strategies such as education programs, prohibition of inappropriate human behaviors, and fencing of garbage dumps have been implemented to stop the (intentional or inadvertent) feeding of dingoes by people. Despite these efforts, dingoes continue to obtain human-sourced food, suggesting that other means of supplemental feeding are still available. One possible source of subsidized food is recreational fishing, which is a popular activity on the island. We conducted a quasi-experimental study during May–June 2014 of dingo foraging behaviors on the eastern beach of Fraser Island. We video-recorded the behaviors of lone and groups of dingoes when they were in the vicinity of anglers or by themselves. We hypothesized that if recreational fishing was a source of subsidies to dingoes, then there would be differences in dingo foraging behavior among the 2 groups. We found that in the absence of anglers, dingoes spent 81% of their time engaged in mobile food-related behaviors. When anglers were present, however, they spent 52% of their time sitting and resting. These results suggest that dingoes shifted from active searching to a sit and wait foraging mode upon detecting recreational anglers. We observed an event in which a dingo spent 2 hours resting near an angler, then dug up the fish remains buried by the man as soon as he had left the area. This and other anecdotal evidence support the view that the changes in dingo foraging activity detected in this study were related to increased opportunities to secure food from anglers. Recreational fishing may play an important role in the inadvertent subsidizing of dingoes on Fraser Island, although further investigations are needed before proposing and implementing additional conservation and management actions. © 2017 The Wildlife Society.
The use of orange peel essential oil microemulsion and nanoemulsion in pectin‐based coating to extend the shelf life of fresh‐cut orange

This study was conducted to evaluate the effect of pectin-based edible coatings containing orange peel essential oil (OPEO) at 0.5 and 1.0% concentrations on quality parameters of orange slices stored at 4 °C for 17 days. The variations of pH and titratable acidity in coated samples containing microemulsion and nanoemulsion were significantly higher than the controls and pectin-coated slices. The highest and lowest increases of the total soluble solids were observed in controls and 1% OPEO nanoemulsion samples, respectively. The weight and ascorbic acid losses of all coated samples were significantly lower than the controls. Higher antibacterial and antifungal effects were observed in the nanoemulsion-coated samples. In sensory evaluation, no significant differences were observed in the samples coated with microemulsion and nanoemulsion. The results showed that the nanoemulsion-based edible coatings containing OPEO can extend the shelf life of orange slices without any undesirable impacts on sensory attributes. Practical applications It is recommended to use edible coatings incorporated with essential oils to overcome the concerns of minimally processed fruit. Microemulsion and nanoemulsion of orange peel essential oil in pectin-based coatings reduced the quality loss. Also, higher antimicrobial effects were observed in nanoemulsion-coated orange slices.
Investigating the effective population size of animals

In this thesis I have investigated variation in the effective population size (Ne) between species, and the impact that this population genetics parameter has on molecular evolution. In Chapter 1 I review literature in order to outline our present understanding of variation in Ne, both between species and within a genome. In Chapter 2 I determine whether island species have lower effective population sizes than their mainland counterparts. I found that island species did not differ substantially from mainland species in terms of molecular evolution, despite their considerably smaller ranges. Chapter 3 examines the role of life history and demographic traits in shaping molecular evolution in mammals. Using mitochondrial DNA, I found significant correlations with species range for both genetic diversity (pS) and the efficiency of selection (pN/pS). Both latitude and body mass are also predictive of pS. However, these relationships are surprisingly weak. Additionally, no trait was predictive of nuclear molecular evolution. In Chapter 4 I determine whether there is adaptive evolution in animal mitochondrial DNA using McDonald-Kreitman style tests. While mitochondrial evolution is dominated by deleterious mutations, mitochondria also experience adaptive evolution, such that 26% of all nonsynonymous mutations are fixed by adaptive evolution. I also found evidence to suggest that the rate of adaptive evolution is correlated to Ne. In Chapter 5 I explore the relationship between pN/pS and pS, two variables that are expected to depend on Ne. I quantified the relationship between pS and pN/pS, after controlling for the statistical nonindependence between the two, to show that as πS doubles, πN/πS is reduced by 34%. I also investigated whether the slope of the regression between these variables is predicted by the shape parameter of the distribution of fitness effects. In Chapter 6 I give a general overview of my research, and bring together the key findings of this thesis.
First Efficient Transfection in Choanoflagellates using Cell-Penetrating Peptides

Only recently, based on phylogenetic studies choanoflagellates have been confirmed to form the sister group to metazoan. The mechanisms and genes behind the step from single to multicellular organisation and as a consequence the evolution of metazoan multicellularity could not be verified yet, as no reliable and efficient method for transfection of choanoflagellates was available. Here we present cell-penetrating peptides (CPPs) as an alternative to conventional transfection methods. In a series of experiments with the choanoflagellate Diaphanoeca grandis we proof for the first time that the use of CPPs is a reliable and highly efficient method for the transfection of choanoflagellates. We were able to silence the silicon transporter gene (SIT) by siRNA, and hence, to suppress the lorica (characteristic siliceous basket) formation. High gene silencing efficiency was determined and measured by light microscope and RT-qPCR. In addition, only low cytotoxic effects of CPP were detected. Our new method allows the reliable and efficient transfection of choanoflagellates, finally enabling us to verify the function of genes, thought to be involved in cell adhesion or cell signaling by silencing them via siRNA. This is a step stone for the research on the origin of multicellularity in metazoans.
Can galanin also be considered as growth-associated protein 3.2?

,especially the prospect of inducingneuronal differentiation. The finding thatNotch instructs gliogenesis might not beimmediate good news for the attempts todifferentiate stem cells to neurons, but itmight be argued that blocking Notchsignaling at some level in the signalingcascade could make cells more prone tochose a neuronal fate. Given the currentpace in the Notch field, answers to thismight not be far away. In the meantime,we can humbly reflect on the multitude offunctions the Notch signaling system isable to execute in the nervous system andother tissues.
Improving Libido and Sperm Quality of Bali Bulls by Supplementation of Moringa oleifera Leaves

Moringa oleifera (Moringa) leaves contain high levels of nutrition that can be utilized as a feed supplement to increase libido and semen quality. This study was aimed to evaluate the effect of Moringa leaves supplementation on libido and sperm quality of Bali bulls. This study used two-sample t-test on four Bali bulls were kept under individual pens for two periods of eight weeks. During the first period (control), the experimental Bali bulls were fed concentrates (1% of body weight) and rice straw ad libitum. During the second period, the experimental Bali bulls were fed similar to the first period with an additional of Moringa leaves 15% of the weight of the concentrate (treatments). Libido and sperm quality were measured twice a week. Plasma samples were taken three times a day (06:00, 14:00, and 22:00h) on the last day of each period. Plasma testosterone concentrations were analyzed by using ELISA techniques. Variables measured were compared using paired student's t-test. Supplementation of Moringa leaves increased testosterone levels (P<0.05) (4.57 vs 4.79, 0.45 vs 4.78, and 2.35 vs 5.63 ng/mL, respectively during 06.00; 14.00; and 22.00h), increased libido (P<0.05) (7.20±1.49 vs 3.49±0.40 min), and increased both the total motility (P<0.05) (63.99±3.37% vs 84.96±3.09%) and the progressive motility (P<0.05) (52.77±1.76% vs 67.03±3.74%) of sperm. Supplementation of Moringa leaves also increased (P<0.05) the velocity and the amplitude and decreased (P<0.05) the linearity of sperm. It can be concluded that the supplementation of Moringa leaves could increase plasma testosterone concentrations, libido, and sperm motility of Bali bulls.
Alterations of Signaling Pathways in Essential Thrombocythemia with Calreticulin Mutation

Purpose Though mutations of the calreticulin (CALR) gene have been identified in essential thrombocythemia patients, the detailed mechanisms for CALR mutations have not been completely clarified. Our study is aimed at characterizing alteration of protein expression in ET patients with mutated CALRdel52 and further recognizing possible involvement of signaling pathways associated with CALR mutations. Patients and Methods Protein pathway array was performed to analyze the expression levels of proteins involved in various signaling pathways in peripheral blood neutrophils from 18 ET patients with mutated CALRdel52, 20 ET patients with JAK2V617F mutation and 20 controls. Results We found 20 proteins differentially expressed in ET patients with mutated CALRdel52 compared with healthy controls. These proteins were associated with molecular mechanisms of cancer in ingenuity pathways analysis (IPA) network. We identified top ten canonical pathways which including apoptotic pathways and cellular cytokine pathways might participate in pathogenesis of ET with mutated CALRdel52. Additionally, there were 8 proteins found to be dysregulated differently between ET patients with mutated CALRdel52 and those with JAK2V617F mutation. These proteins might be related to the unique signaling pathways activated by CALRdel52 mutation which were different to JAK/STATs pathway by JAK2V617F mutation. Conclusion Our study demonstrated that numerous alterations of signaling proteins and pathways in ET patients with mutated CALRdel52. These findings could help to gain insights into the pathological mechanisms of ET.
Effects of dietary supplementation of Trichoderma pseudokoningii fermented enzyme powder on growth performance, intestinal morphology, microflora and serum antioxidantive status in broiler chickens

Abstract This study was conducted to evaluate the dietary supplementation of Trichoderma pseudokoningii enzyme powder (EP) and its effect on the growth performance, intestinal morphology and antioxidative status of broilers. In vitro experiments showed that xylanase and cellulase activities of EP were 487.96 ± 14.14 U/g and 18.55 ± 0.54 U/g, respectively. Total phenolic and ferulic acid content was 4.79 ± 0.35 mg GAE/g DW and 4.38 ± 0.32 μM/g DW, respectively. A total of 240 d-old Ross 308 male broiler chicks were randomly subjected to one of four treatments, namely diets supplemented with dry EP at 0% (control), 0.1%, 0.2% or 0.4% for 35d. Results showed that in the starter phase (1–21 d), the EP supplemented groups had improved body weight, weight gain and FCR compared to the control group. The villus:crypt ratio of both jejunum and ileum in all EP-treated groups was significantly higher than that of the control group. When testing serum antioxidant activity, results showed that 0.2% and 0.4% EP supplementation significantly increased superoxide dismutase activity in both the finisher phase and the overall experimental period. In addition, catalase activity was elevated in all EP supplemented groups in both the finisher phase and throughout the experimental period. 0.1% EP seemed to have no effect during the starter period. Serum malondialdehyde concentration was not affected by EP supplementation. These results suggest that EP is potential feed additive in terms of improving broiler performance and enhancing antioxidative status, while also providing an optimal intestinal environment.