Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantitative microscopy workflows for the study of cellular receptor trafficking

The trafficking and signalling of cellular receptors are complex, intertwined processes with many feedback mechanisms. Confocal microscopy is a powerful tool to study the trafficking of receptors. The aim of this thesis was to report and develop workflows to quantify the spatio-temporal dynamics of receptor trafficking and colocalization using confocal microscopy. Importantly, the workflows should be reproducible and unbiased, as well as automated and accurate. A 4D level set approach is developed to enable accurate cellular segmentation. Temporal constraints are introduced to further improve segmentation accuracy. This novel approach is thoroughly validated, and statistically significant performance increase over equivalent 2D and 3D approaches is demonstrated. We present a confocal microscopy based RNAi depletion screen. Specifically, quantitative workflows to identify genes which perturb the trafficking of receptor are described. Finally, a critical review of current approaches to the quantification of colocalization between receptors and endosomes is presented. Improvements to existing techniques and complete workflows are provided for 4D data (3D time-lapse). Together the described protocols provide a complete microscopy based platform to identify and investigate regulators of receptor signalling and trafficking.
EFFECT OF COMPETITIVE INTERACTIONS AND WATER STRESS ON THE MORPHOLOGICAL CHARACTERISTICS OF RED CLOVER (Trifolium pratense L.) CULTIVATED WITH SPRING BARLEY (Hordeum vulgare L.)

On the basis of a pot experiment set up according to the additive design, the effect of competitive actions of spring barley on the morphological characteristics of red clover in the conditions of water stress was evaluated. Biometric analyses were carried out on five dates set by the growth rhythm of barley in pure sowing with a higher water dose. The study included: plant height, number of shoots and leaves per plant, and root length. On the basis of plant biomass, relative yield, relative yield total, and competitive balance index were determined. It was demonstrated that spring barley, from tillering to the end of growth, limited red clover plant height and root length. At the straw-shooting stage, negative effect of the cereal intensified and caused the formation of a smaller number of leaves and shoots than in clover in pure sowing. Water shortage caused plant shortening (from barley tillering to the end of growth) and reduction in the number of leaves (tillering – earing) and shoots (straw-shooting and ripening) of clover.
The mitochondrial-cytosolic pathway of FeS cluster assembly in Arabidopsis thaliana

The aim of this work was to unravel the molecular basis of the connection of mitochondrial and cytosolic FeS assembly. Following on from previous work showing that the mitochondrial ABC-transporter ATM3 is required for cytosolic FeS assembly (Bernard et al., 2009), one part of my project was to provide in-vivo evidence for the substrate of ATM3. I found that the mitochondrial glutathione pool in atm3 seedlings is shifted towards oxidation, indicating accumulation of oxidised glutathione. Furthermore I showed that ATM3 genetically interacts with two enzymes involved in persulfide metabolism (ETHE1, NFS1). This complemented invitro studies by Dr. Schaedler (Schaedler et al., 2014) who showed that oxidised glutathione is a preferred substrate and glutathione carrying additional S0 can be transported by yeast Atm1. To gather further insight into biosynthesis of the ATM3 substrate I investigated the role of a cytosolic and a mitochondrial glutaredoxin (GRXS17, GRXS15). Mutants had minor but specific effects on FeS enzymes and I concluded that the glutaredoxins are not generally involved in de-novo cluster assembly. Another approach was to identify unknown components of mitochondrial-cytosolic persulfide transport. I characterised two mutants with phenotypic resemblance to atm3 mutants. For one, I located a point mutation in the sequence of ATM3 leading to an amino acid exchange in the 6th transmembrane domain and showed that the ATM3 protein was lacking. The second line was a mutant of CNX2, a mitochondrial enzyme necessary for generation of the first MoCo intermediate cPMP. I found ATM3 protein breakdown in cnx2-2 and in a mutant of CNX5 which is involved in MoCo assembly and t-RNA thiomodification. ATM3 was previously suggested to export cPMP (Teschner et al., 2010). My findings give new evidence for a link between ATM3 and MoCo assembly.
Size, season and offspring sex affect milk composition and juvenile survival in wild kangaroos

The main component of mammalian maternal care is milk production. The composition of milk has been hypothesized to determine offspring survival, and to vary with offspring sex. Few studies, however, have examined variation in milk composition of wild mammals in seasonal environments, where environmental conditions can impact the ability of mothers to provide care. We investigated individual differences in milk composition and offspring survival in wild eastern grey kangaroos (Macropus giganteus). We analyzed total protein and lipid concentrations in 103 milk samples from 91 females over 2 years. In a year of low forage production, few females that lactated were in poorer condition and produced milk of lower energy content compared to females lactating in a year of high forage production. Females nursing in late winter produced milk with more lipids compared to females at the same stage of lactation in late spring, whose milk had a higher proportion of protein. The milk of larger females contained more protein than lipid, and females in better condition allocated higher proportions of protein to sons than to daughters. Increased protein concentration in milk was correlated with offspring longevity, and this effect was stronger for sons than daughters. A seasonally modulated lactation strategy enables the adjustment of milk composition to available resources. Condition-specific protein allocation in favor of sons for mothers of higher caring ability suggests adaptive sex-biased maternal care in this highly sexually dimorphic mammal.
Dry Matter Accumulation and Partitioning Of Two Taro (Colocasia Esculenta (L.) Schott) Cultivars under Inceptisol Soils in Samoa

Taro (Colocasia esculenta) crop is widely grown throughout the humid tropics for its edible leaves, petioles and corms. In this research total dry matter (DM) accumulation and its partitioning between different plant parts were studied to determine their growth pattern over the plants’ life cycle (i.e. 35, 70, 105, 140 and 175 days after planting (DAP)). An experiment with randomised complete block design (RCBD) having five treatments (DAP) and three replications (blocks) was setup for each of the two improved taro cultivars (Samoa 1 and Samoa 2). After harvest dry matter of each taro plant was estimated for its five parts: leaf blades, petioles, corms, roots and suckers. The data analysis showed that in both the cultivars the DM accumulation and its partitioning to different plant parts (i.e. the leaf blades (LDM), petioles (PDM), roots (RDM), corms (CDM) and suckers (SDM)) varied significantly (p < 0.001) over the five growth stages of plant growth (DAP)
Population dynamics of penaeid prawn Penaeus merguiensis off Mumbai coast

Stock dynamics of Penaeus merguiensis was studied using length composition data collected separately for males and females during the period 1995-1998, at New Ferry Warf landing, centre in Greater Mumbai. Food and feeding, sex ratio, fecundity and length-weight relationships were worked out on a representative sub-sample. Asymptotic length (Loo) and growth coefficient (K) were estimated to be 220 mm and 1.80 per annum respectively for males. These parameters were respectively 281 mm and 1. 72 per annum in the case of females. The instantaneous rate of total mortality coefficient (Z) was found to be 9.79 and 7.44 per annum for males and females respectively. The annual natural mortality coefficient (M) was estimated to be 2.80 for males and 2.60 for females. As the exploitation ratio exceeded 0.5 in the case of both the males and females, the study suggests the necessity for reduction in fishing pressure in order to achieve Maximum Sustainable Yield (MSY).
Finding Safe and Cheap Exchanges to Hydrogen Cyanamide on “Flame Seedless” grapevines

This study was carried out to study the effect of safe alternatives as compared to hydrogen cyanamide on breaking dormancy of" Flame seedless" grapevines. The vines were subjected the following spray treatments; control, garlic oil, hydrogen peroxide, copper sulphate, zinc sulphate, boric acid and hydrogen cyanamide in the second week of January. All treatments except zinc sulphate in the second season had higher bud burst% than control. The results also showed that copper sulphate and hydrogen cyanamide applications significantly increased bud burst % than other treatments in both seasons. In both seasons, hydrogen cyanamide gave higher yield and juice volume than the rest treatments, except hydrogen peroxide for yield in the second season. Hydrogen cyanamide and zinc sulphate applications increased cluster weight in the second season only. Weight and size of 100 berries were significantly increased by copper and zinc sulphate and hydrogen cyanamide. In the first season, copper sulphate and hydrogen peroxide treatments increased berry length and diameter. On the other hand, the results showed that there were non significant differences among tested treatments concerning berry length and diameter in the second season and L/D ratio in both seasons. In the first season, the highest percentage of T.S. S was obtained by vines sprayed with garlic oil. In the second season, T.S. S% was not affected by different applications. Data showed that zinc, copper sulphate and garlic oil significantly decreased acidity in the second season. The results in both seasons indicated that garlic oil, copper and zinc sulphate applications lead to increase T.S. S/acid ratio. The data in both seasons indicated that anthocyanin content was increased by garlic oil treatment. In both seasons, garlic oil and hydrogen cyanamide considerable increased shoot length. Hydrogen peroxide caused increase in fruitfulness%, number of clusters and leaves in both seasons. Generally, there were non significant differences among used treatments concerning peroxidase activity. Catalase activity was highly increased with bud burst which appeared as achromatic zone with high intensity in all treatments, except boric acid in the first season and copper, zinc sulphate and hydrogen cyanamide treatments in the second season.
Effects of Codon Usage on mRNA Translation and Decay

by VLADIMIR PRESNYAK Gene expression is a complex process regulated at many steps. One important step is the degradation of mRNA. The major pathways and enzymes in mRNA decay have been identified and described, but this has not yet led to a good understanding of the mechanisms for the observed differences in mRNA half-lives. Previous research has elucidated several examples of regulation through 3’ UTR elements, but general mechanisms are not clear. The translation of mRNA is intricately linked to decay, thus the two processes must be evaluated together to uncover regulation that frequently affects both. We show that the choice of codons in the body of an mRNA can dictate the stability of the mRNA. Messages with a high percentage of optimal codons are relatively stable, whereas messages with a high percentage of non-optimal codons are relatively unstable. Reducing the optimal codon content of a stable message with naturally high occurrence of optimal codon leads to a reduction in stability, and
Characterization of Local Chickens in Akwa Ibom State Using Hatch Weights

This study was conducted to determine hatch weights of male and female local chickens in Akwa Ibom State; to evaluate the effects of hatch batch on hatch weights and also characterize local chickens in Akwa Ibom state using hatch weights. A total of 84 local chickens (60 pullets and 24 cocks) used for the experiment were purchased from Uyo, Nsit Atai, Eket and Ikot Ekpene Local Government Areas. Chickens from all localities were assembled on deep litter to generate a broad-based population for random mating. Mating ratio of males and females was maintained at 1:5 to ensure fertilization of eggs. From inception, chickens were fed growers mash (15% CP). Feed was changed to layer’s mash (16.5% CP) when 5% egg production was attained. At 4 months egg production, collection of egg for incubation commenced. Data were collected on hatch weights of male and females chicks. Means and ranges were computed for hatch batches and sexes. Significant means were separated using Duncan’s Multiple Range Test. Mean hatch weights ranged between 22.33±0.75 and 27.03±0.82. Mean hatch weight of 25.99±0.61 for males was significantly higher (P<0.05) than 24.53±0.66 for females. Hatch weights of local chickens in Akwa Ibom State are low. Hatch batches had no effects on hatch weights. Variations observed in hatch weights constitute a valuable genetic resource for breeding programmes and in designing proper conservation strategies. Key Words: Local chickens, hatch weights, characterization, conservation.
Exploring the ethnobotany of Haloxylon recurvum (Khar) and Haloxylon salicornicum (Lana) in Cholistan desert, Pakistan.

Plants are the major shareholder of the earth life and provide various services to other life forms including man by so many ways. Plants are also being used in healthcare from ancient times as remedy for different ailments (Newton et al., 2000). In recent times, dependency on plants as medicine is increased manifold due to ease in access, nature of action, minimum side effects and other various reasons. Natural products of plant origin have provided an alternative source for the development of new drugs (Koehn et al., 2005; Newman et al., 2007). Dependency on plants (as medicine, fuel and fodder) is more in developing countries like Pakistan where the maximum population depends on agriculture as major livelihood source. Cholistan is a desert rangeland in Pakistan with great botanic diversity. It also hosts two members of Chenopodiaceae family i.e. Haloxylon salicornicum (Moq.) Bunge and Haloxylon recurvum (Moq.) Bunge ex Boiss. H. salicornicum is a diffuse shrub with pale multi branches having yellowish green scale like leaves. It is locally called as Lani, Lana in Urdu and Rimth in Arabic language (Zaman, 1997). It may attain a height of 5-60 cm. Terminal and lateral spikes bear flowers. Fruiting perianth have 5 membranous wings of 5-8mm diameter and pink yellow in colour (Kostecki, 1999). H. salicornicum is reported by many scientists to be used by various ways in different countries like fuel, fodder, food and medicines (Bhandari, 1995; Arshad et al., 2002; Dogla and Shekhawat, 2006). Different minerals and chemical components from the stem and leaf of this plant are used in making of animal feed (Ashraf et al., 2012). In Oman, its stem is used for dyeing of wool in traditional weaving (Ghazanfar, 1994). H. recurvum is also a densely branched pale diffuse shrub. Locally it is called as Khar or Sajji.Its stem is almost leafless and glabrous which secretes thick fluid on cut. Inflorescence is pale greenish like a small cup with scattered spikes. Wings like fruits are brownish in colour (Ahmad et al., 2004). Khan and Qaiser (2006) mentioned this shrub as an important fodder species. Other reported uses in various countries are, burned plant use in washing of cloths, in glass, soap industry, dye of cloth and medicines (Bhandari, 1990; Singh et al., 2005; Qasim et al., 2010; Iqbal et al., 2011). The local inhabitants of the Cholistan used various local plants for treating various human diseases and of their livestock as well in different traditional recipes. The main objectives of the study were to explore and document the uses of these shrubs by local dwellers of Cholistan desert, to consult the medicinal plant experts for their opinion and to find out the chemical composition of above cited shrubs. Pak. J. Agri. Sci., Vol. 52(4), 1085-1090; 2015 ISSN (Print) 0552-9034, ISSN (Online) 2076-0906 http://www.pakjas. com.pk
Parasites structuring ecological communities: the mistletoe footprint in Mediterranean pine forests

Summary 1. The capacity of parasitic plants in structuring natural communities is increasingly recognized. These plants can affect the structure, composition and productivity of plant communities by modifying the competitive balance between hosts and non-host species and by altering the quantity and quality of resources entering the soil. Despite the progress made in this field, there is still a lack of integrative studies showing the structuring capacity of parasitic plants in forest ecosystems, where their effect may be less detectable due to the long lifespan of the system. 2. In this study we evaluate the long-term impact of Viscum album subsp. austriacum on the woody-plant community of a Mediterranean pineland. This mistletoe remains several years on the same host, exerting long-lasting, spatially concentrated effects on community and ecosystem characteristics. Mistletoe concentrates zoochorous seeds and induces changes in the soil fertility and light availability beneath the canopy of parasitized trees, which have the potential to facilitate zoochorous-plant colonization, recruitment, and growth at the same time as it weakens the host. Here, we analyse whether mistletoe-driven changes could result in a nucleus of zoochorous woody plants nourished by the abundant organic detritus accumulated under the host. We also analyse whether mistletoe effects can expand after host death. 3. We selected unparasitized, parasitized, and dead parasitized Pinus nigra trees, in which we studied the joint effect of mistletoe-mediated changes in soil nutrient and light availability, with the seed rain, seed predation, seedling establishment, plant recruitment, and plant growth. Light- and soil-nutrient resources were greater under parasitized trees, and intensified after host death. The seed rain was maximum under parasitized trees, where seedling recruitment proved more likely. Sapling density, richness, and growth increased with the development of parasitism. 4. Our findings show that Viscum album exerts a strong and lasting impact on the structure and dynamics of Mediterranean pinelands, with parasitized trees acting as centres for the establishment and growth of colonizing fleshy-fruited woody species, which, over the long term, promote vegetation shifts by limiting dominant pine trees and facilitating less represented fleshy-fruited shrubs. This article is protected by copyright. All rights reserved.
Bacterial Exposure and Immune Homeostasis: A Mechanistic View of the Hygiene Hypothesis

15 Chapter 1: An Introduction to Bacteroides fragilis, PSA, and Asthma . 17 1.1 Hygiene Hypothesis . 18 1.2 Intro to Asthma . 21 1.3 Currently available therapeutics . 22 1.4 Intro to Bacteroides fragilis . 24 1.5 Polysaccharide A . 25 1.6: Immunomodulation by Bacteroides fragilis and Polysaccharide A . 26 Chapter 2: Clonal T cell Expansion Induced by PSA Treatment . 28 2.1: Summary . 29 2.2: Introduction . 30 2.3: Methods . 31 2.3. 1: Mice and Bacteria . 31 2.3. 2: Airway Inflammation Model . 31 2.3. 3: T cell Flow Cytometry. 32 2.3. 4: Histology . 32
Validation Of QTL Associated With Tocopherol Levels In Three Half-Sib Populations Derived From Keszthelyi Aproszemu Sarga Soybean

Validation Of QTL Associated With Tocopherol Levels In Three Half-Sib Populations Derived From Keszthelyi Aproszemu Sarga Soybean Mark MacDuff Advisors: University of Guelph, 2011 Dr. Gary Ablett and Dr. Istvan Rajcan Alpha (α-) tocopherol is the most active component of vitamin E and is a highly desirable and heritable trait in soybean seed. The objectives of this study were to identify and validate regions of the soybean genome that correspond to tocopherol accumulation in seed. A mapping population (07-225) of 190 RILs was derived from a cross between Keszthelyi A.S. x 2355RR which identified that α-tocopherol accumulation in soybean seed was strongly associated with the Satt381 – Satt196 region of chromosome 9 (LG K) in lines with Keszthelyi A.S. in their pedigree. Two other F4:5 validation populations derived from the crosses Keszthelyi A.S. x PRO 2995R (population 07-223; 94 RILs) and Keszthelyi A.S. x 2355RR (population 07-226; 45 RILs) were used to validate QTL in literature. The markers Satt079 (Ch 6; LG C2), Satt440 (Ch 20; LG I) and Satt381 (Ch 9; LG K) were significantly associated with α-tocopherol accumulation in these populations.
Antioxidant Enzyme in Blood Test A Marker for Fructose Metabolism

Excessive fructose consumption can cause metabolic damage. Previous evidence supports that oxidative stress plays a big role in metabolic syndrome (MS)-related manifestations. Recently blood markers like high sensitive-C reactive protein (hs-CRP) and serum lipid profiles are widely used clinical parameters. However, it is unknown if whether antioxidant capacity is related to these changes or not. This study was designed to explore if the concentration of blood markers (triglycerides, cholesterol, glucose, Hs-CRP) is associated to antioxidant capacity in hyperlipidaemia rats. High fructose diet (HFD) was orally given to rats for 80 days to establish hypertriglyceridemia and blood tests were carried on at different time intervals up to 80th day. Serum triglycerides, glucose, glucose, Hs- CRP, SOD, Catalase and LPO were recorded at 50th and 80th days. At last we assessed m- RNA expression of SOD and catalase in WBC. The gradual rise in activities of superoxide dismutase (SOD), catalase and ABTS. +(2,2'- azino-bis(3-ethylbenzothiazoline-6-sulphonic acid)-scavenging potential was recorded without any rise in the serum lipid peroxidation- products, triglycerides (TG), glucose and hs-CRP up to 50th day of HFD feeding. However these changes were reversed on 80th day. The RT-PCR for SOD and catalase mRNA in white blood cells (WBC) also showed similar biphasic. This study suggests that the initial rise in blood antioxidant enzymes to their maximum capability, in early days as adaptive mechanism to encounter the oxidative damage from oxygen free radicals. Thus raised activity of catalase and SOD in blood could be considered as one of the significant biomarkers for early diagnosis of adverse metabolic changes when there is no clinical symptom to MS. This study could be helpful in developing pre-diagnostic parameters to persons, who are likely to develop MS.