Miracle-dz/UniFAR-FTUs huggingface dataset:
Genomic analysis of Pyrenophora teres : avirulence gene mapping, karyotyping and genetic map construction

Pyrenophora teres Drechs. (anamorph: Drechslera teres (Sacc.) Shoem. ) is the causal agent of barley net blotch. Net blotch is an economically important disease commonly found throughout the barley producing regions of the world. Significant financial losses result from yield reductions, ranging from 15-35%, and decreased grain quality. Despite its prevalence, it is unclear if the P. teres-barley pathosystem follows a gene-for-gene model, and more generally, little is known about its genetic organization. Three studies were initiated to address these questions. The first study investigated the genetic control of avirulence in P. teres. To establish an appropriate study system, a collection of ten net form (P. teres f. teres) and spot form (P. teres f. maculata) isolates were evaluated on a set of eight differential barley lines to identify two isolates with differential virulence on a specific host line. WRS 1906, exhibiting low virulence on the cultivar ‘Heartland,’ and WRS 1607, exhibiting high virulence, were mated and 67 progeny were isolated and phenotyped for virulence on Heartland. The population segregated in a 1:1 ratio, 34 avirulent to 33 virulent (χ = 0.0, P = 1.0), indicating single gene control of WRS 1906 avirulence on Heartland. Bulked segregant analysis was used to identify six amplified fragment length polymorphism (AFLP) markers closely linked to the avirulence gene (AvrHeartland). This work provides evidence that the P. teres-barley pathosystem conforms to the gene-for-gene model. In the second study, five isolates of P. teres, representing both net and spot forms, were analyzed by the germ tube burst method (GTBM) and pulsed field gel electrophoresis (PFGE) to determine the species’ karyotype. Nine chromosomes were observed in all isolates using the GTBM and estimation of chromosome lengths varied from 0.5 to 3.0 μm. PFGE separated 7 to 8 bands depending on isolate, but analysis of bands by densitometry indicated nine chromosomes. Chromosome size ranged from 1.8 to ~6.0 Mb providing a genome size estimate of 32 to 39 Mb. Significant chromosome-length polymorphisms (CLP) were observed between isolates. These CLP did not hinder
Effects of nest temperature and moisture on phenotypic traits of hatchling snakes (Tropidonophis mairii, Colubridae) from tropical Australia

Previous research on developmentally plastic responses by reptile embryos has paid relatively little attention to tropical species, or to possible interactions between the effects of thermal and hydric regimes. In the present study, eggs of keelback snakes ( Tropidonophis mairii ), from a tropical area with strong temporal and spatial variation in soil temperatures and moisture levels, were incubated. The phenotypic traits of hatchling snakes (body size, shape, muscular strength) were affected by moisture content of the incubation medium (vermiculite plus 100% vs. 50% water by mass), by mean incubation temperatures (25.7 vs. 27.9 ° C) and by diel thermal variation (diel range 6.0 vs. 8.4 ° C). Interactions between these factors were negligible. Cooler, more thermostable, moister conditions resulted in larger offspring, a trait under strong selection in this population. Thermal and hydric conditions covary in potential nestsites (e.g. deeper nests are more thermostable as well as moister). This covariation may influence the evolution of reaction norms for embryogenesis. For example, if moister nests enhance offspring fitness and are cooler, then selection will favour the ability to develop in cool as well as moist conditions. Thus, the evolution of optimal incubation conditions with respect to one variable (e.g. temperature) may be driven by patterns of association with another variable (e.g. soil moisture) among natural nest-sites. Perhaps for this reason, the thermal optimum for incubation is surprisingly low in this tropical species. © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 89 , 159‐168.
Chemical-genetic interrogation of small molecule mechanism of action in S. cerevisiae

The budding yeast S. cerevisiae is widely used as a model organism to study biological processes that are conserved among eukaryotes. Different genomic approaches have been applied successfully to interrogate the mode of action of small molecules and their combinations. In this thesis, these technologies were applied to different sets of chemical compounds in the context of two collaborative projects. In addition to insight into the mode of action of these molecules, novel approaches for analysis of chemical-genetic profiles to integrate GO annotation, genetic interactions and protein complex data have been developed. The first project was motivated by a pressing need to design novel therapeutic strategies to combat infections caused by opportunistic fungal pathogens. Systematic screens of 1180 FDA approved drugs identified 148 small molecules that exhibit synergy in combination with fluconcazole, a widely used anti-fungal drug (Wright lab, McMaster University, Canada). Genome-wide chemical-genetic profiles for 6 of these drugs revealed two different modes of action of synergy. Five of the compounds affected membrane integrity; these chemical-genetic interactions were supported by microscopy analysis and sorbitol rescue assays. The sixth compound targets a distinct membrane-associated pathway, sphingolipid biosynthesis. These results not only give insight into the mechanism of the synergistic interactions, they also provide starting points for the prediction of synergistic anti-fungal combinations with potential clinical applications. v The second project characterised compounds that affected melanocytes in a chemical screen in zebrafish (Patton lab, Edinburgh). Chemical-genetic screens in S.cerevisiae enabled us to show that melanocyte pigmentation reducing compounds do so by interfering with copper metabolism. Further, we found that defects in intracellular AP1 and AP3 trafficking pathways cause sensitivity to low copper conditions. Surprisingly, we observed that the widely-used MAP-kinase inhibitor U0126 affects copper metabolism. A nitrofuran compound was found to specifically promote melanocyte cell death in zebrafish. This enabled us to study off-target effects of these compounds that are used to treat trypanosome infections. Nifurtimox is a nitrofuran prodrug that is activated by pathogen-specific nitroreductases. Using yeast and zebrafish we were able to show that nitrofurans are also bioactivated by host-specific aldehyde dehydrogenases suggesting that a combination therapy with an aldehyde dehydrogenase inhibitor might reduce side effects associated with nifurtimox.
BIOCONTROL POTENTIALS OF PLANT GROWTH PROMOTING RHIZOBACTERIA AGAINST FUSARIUM WILT DISEASE OF CUCURBIT

Fusarium spp. , are the major soil-borne as well as seed borne pathogens causing wilt and rot diseases in more than 80 plant species including cucurbits. Fusarium spp. , causes up to 100 % yield loss in the worldwide. Eleven isolates including three standard isolates were tested both in-vitro and in-vivo . In-vitro assay was done by dual culture method. Maximum inhibition was in case of Fusarium solani by Bacillus cereus MIC5. Sarratia spp. MIC1 antagonized the F. verticillodes and F. solani2 . P. aeruginosa MIC2 inhibits all tested isolates F. oxysporum1. P. aeruginosa MTCC2581 suppressed the radial growth rate of F. oxysporum 2. The two systemic fungicides used were chlorothalonil + mefenoxam (1000 ppm) and carbendazim (75 ppm to 500 ppm) which checked the growth of F. oxysporum . Carbendazim was more effective compared to mefenoxam + chlorothalonil at all tested concentrations. The crude extract of P. aeruginosa MIC2 developed in chloroform: methanol (9:1) showed a metabolite at R f - 0.77 which it may be 2,4- diacetylphloroglucinol (DAPG), a broad-spectrum antimicrobial agent. Increased cucurbit seeds germination and seedling vigour was observed in B. amyloliquefaciens MIC6 (68% & 1576) and P. aeruginosa MTCC2581 (70% & 1929) in primed seeds. Further P. aeruginosa MTCC2581 can be tested in the field against the Fusarium wilt.
Use of molecular approaches to study the occurrence of extremophiles and extremodures in non-extreme environments

A number of samples were collected from various extreme and non-extreme environments. A range of molecular approaches, in addition to classical microbiology techniques, were used to isolate microorganisms, mainly archaea and bacteria from unusual environments. Halo-bacteria and archaea from non-saline environments and alkaliphilic bacteria and archaea capable of withstanding low pH values were isolated and identified using 16S rRNA gene cloning, PCR amplification and phylogenetic analysis. Detailed analysis of their halophilic and alkaliphilic physiology for adaptation in the environment was investigated using nuclear magnetic resonance spectroscopy (NMR) to detect the compatible solutes and atomic emission spectophotometery (AES) to measure the cellular potassium ions. In addition, ultraviolet-type C tolerant bacteria were isolated from terrestrial environments using phylogenetic analysis of the 16S rRNA gene sequences. A selection of other molecular techniques were used in this thesis. Fluorescent in situ hybridisation (FISH) allowed simultaneous identification, enumeration and visualization of microbial cells of the two domains; Archaea and Bacteria within a community in their natural habitat. In addition, using EZ-PCR test, culturable-independent Mycoplasma DNA in environmental samples was detected. Further investigation, using other advanced molecular techniques, into the physiology of extremophilic microorganisms found in non-extreme environment may provide a better understanding of the microbial interactions and the essential roles which different species play in the environment.
Epidemiology of Ustilago bullata Berk. on Bromus tectorum L. and Implication for Biological Control

EPIDEMIOLOGY OF USTILAGO BULLATA BERK. ON BROMUS TECTORUM L. AND IMPLICATIONS FOR BIOLOGICAL CONTROL Toupta Boguena Department of Integrative Biology Doctor of Philosophy The seedling-infecting pathogen Ustilago bullata Berk. is a naturally occurring biological control agent for cheatgrass (Bromus tectorum L.). The effects of temperature and nutrients on pathogen teliospore germination behavior and the effects of temperature on host seed germination were examined. The effects of temperature on sporidial proliferation, host infection in a temperature-controlled environment and in a field setting for eight populations were investigated. The infection success of Ustilago bullata on Bromus tectorum in cultivated fields as a function of seeding date, inoculation method, inoculum density, supplemental watering, and litter was also investigated. Teliospores germinated faster on potato dextrose agar than on water agar. Teliospores germinated slowly at temperatures far from the optimum of 15 and 20C. There were amongpopulation variations in teliospore germination and sporidial proliferation, but differences among populations were much more pronounced at temperatures below 15C. Infection
Spiderwebs and silk : tracing evolution from molecules to genes to phenotypes

Preface 1 Breaking down silk proteins and their evolutionary pathways 2 The comparative architecture of silks, fibrous proteins and their encoding genes in insects and spiders 3. The mechanical functions of silk and their correlated structural properties 4. Insect spatial vision is potential selective factor on the evolution of silk achromatic properties and web architecture 5. Insect color vision is a potential selective factor on the evolution of silk chromatic properties and web design 6. Insect learning capacity is a potential selective factor in the evolution of silk color and the decorative silk patterns spun by spiders 7. Inter-gland competition for amino acids and the ATP costs of silk synthesis 8. One-dimensional developmental system and life-long silk synthesis may preclude the evolution of high eusociality in spiders 9. Conclusions and looking forward Bibliography Index
Kinetic and Crystallographic Studies of Drug-Resistant Mutants of HIV-1 Protease: Insights into the Drug Resistance Mechanisms

HIV-1 protease (PR) inhibitors (PIs) are important anti-HIV drugs for the treatment of AIDS and have shown great success in reducing mortality and prolonging the life of HIV-infected individuals. However, the rapid development of drug resistance is one of the major factors causing the reduced effectiveness of PIs. Consequently, various drug resistant mutants of HIV-1 PR have been extensively studied to gain insight into the mechanisms of drug resistance. In this study, the crystal structures, dimer stabilities, and kinetics data have been analyzed for wild type PR and over 10 resistant mutants including PRL24I, PRI32V, PRM46L, PRG48V, PRI50V, PRF53L, PRI54V, PRI54M, PRG73S and PRL90M. These mutations lie in varied structural regions of PR: adjacent to the active site, in the inhibitor binding site, the flap or at protein surface. The enzymatic activity and inhibition were altered in mutant PR to
Growth, body composition and intestinal enzyme activities of juvenile Jian carp (Cyprinus carpio var. Jian) fed graded levels of dietary zinc

A 6-week trial was carried out with 900 juvenile Jian carp (Cyprinus carpio var. Jian) to investigate the effects of dietary zinc on growth, body composition and intestinal enzyme activities. Diets supplemented with increasing levels (15.3, 26.9, 40.8, 58.2, 68.9 and 92.5 mg Zn kg−1) of zinc lactate were fed to Jian carp (mean initial weight 15.7 ± 0.01 g). Results indicated that per cent weight gain (PWG), feed efficiency (FE), protein efficiency ratio (PER) and lipid productive value (LPV) enhanced with dietary zinc levels up to 40.8 mg kg−1 diet (P 0.05). Feed intake (FI) was similar to that observed for PWG. Intestosomatic index (ISI), relative gut length (RGL), hepatopancreas protein content (HPC), intestine protein content (IPC), trypsin, chymotrypsin, lipase, amylase, alkaline phosphatase (AKP), Na+, K+-ATPase and γ-glutamyl transpeptidase (γ-GT) activities were all higher by dietary zinc supplementation than zinc un-supplementation (P < 0.05). These results suggested that zinc could promote growth and increase nutrient deposition and intestinal enzyme activities. The dietary zinc requirements (use zinc lactate as zinc source) of juvenile Jian carp (15.7–42.2 g) based on PWG and serum zinc were 48.7 and 43.2 mg Zn kg−1 diet, respectively.
Novel compact antenna designs for future wireless communication systems

Wireless and mobile devices are becoming packed with more applications that require an increasing number of communication technologies as well as a constant desire for size reduction. Ideally, every single communication technology should have a dedicated antenna system. This puts pressure on antenna engineers as the available space for the radiation elements is becoming very limited, particularly for small mobile phones and small cell base stations. Traditionally, reducing the size of the antenna was enough to accommodate these requirements. However, making antennas smaller strongly affects their performance. In order to further shrink a multi-radio transmitting system, antenna reconfiguration provides an option to converge multiple radiating elements into a single one, and hence, save space in wireless and mobile devices. The creation of novel materials such as carbon nanotubes, graphene and metamaterials, which present extraordinary electrical and mechanical properties, has opened new possibilities within the antenna field. The most interesting properties of these materials are the presence of plasmons in carbon nanotubes and graphene at much lower frequencies than in metals, the ability to tune the surface impedance of graphene by applying a DC voltage bias and the possibility of generating size-independent resonances in metamaterials. These materials are studied here as alternative methods to achieve antenna size reduction and reconfigurability at microwave frequencies. This thesis presents an initial study of the advantages and disadvantages of designing small and reconfigurable antennas fully made of carbon nanotubes and
Identification of metabolic genes essential for proliferation of clear cell Renal Cell Carcinoma (ccRCC) cells

Kidney cancer accounts for 2-3% of adult malignancies with clear cell renal cell carcinoma (ccRCC) being the most common histological subtype (70-80% of cases). Interestingly, ccRCCs show a highly distinct metabolic phenotype making this disease stand out amongst other cancer types. The underlying causes of the aberrant metabolism in ccRCC are not fully understood, but metabolic transformation could provide novel strategies for targeted therapies in this disease. The pVHL tumour suppressor is located on chromosome 3p21, which is frequently lost in ccRCC. pVHL is a negative regulator of the Hypoxia-inducible factor (HIF), which orchestrates the cellular response to oxygen deprivation and might contribute to the aberrant metabolic phenotype of ccRCC cells. In order to reveal metabolic weaknesses in ccRCC, a customised RNAi screen targeting 230 different metabolic enzymes, regulators and nutrient transporters was performed. The screen was performed in a panel of 5 ccRCC pVHL-null cell lines and included their counterparts with reconstituted pVHL, in order to also identify potential vulnerabilities that depend on VHL function. With this approach, several genes that are essential for ccRCC cell viability but dispensable for the survival of non-malignant renal epithelial cells were identified. It was found that ccRCC cell lines are highly sensitive to ablation of components of the glutathione-dependent reactive oxygen species (ROS) detoxification system. Silencing of enzymes of the glutathione biosynthesis pathway or different glutathione peroxidases (GPXs) severely impaired cell viability. One of the precursors of glutathione biosynthesis is glutamate, which is generated from glutamine by glutaminase (GLS). Interestingly, there is evidence that ccRCCs are highly dependent on the MYC oncogene, which induces many enzymes within the glutaminolysis pathway. Indeed, we found that glutamine starvation or chemical inhibition of GLS reduced proliferation and viability of ccRCC cells, confirming the importance of this pathway in ccRCC. In conclusion, the study reported in this thesis provides insight into the metabolic dependencies of ccRCC cells and emphasises the need for a solid anti-oxidant system for ccRCC cell survival and proliferation. Concomitantly, the reliance of ccRCC cells on glutamine and glutathione is a vulnerability that could potentially be exploited for diagnostic and/or therapeutical applications.
Molecular Cloning of PhoR Sensor Domain from Mycobacterium tuberculosis for Structure-Based Discovery of Novel Anti-Tubercular

The emergence of multidrug-resistant strains (MDR-TB) and extensively drug-resistant strains (XDR-TB) has fuelled the quest for novel drugs and drug targets for its successful treatment. One of the potential candidates as novel TB drug target is the PhoR Sensor Domain, an extracellular domain of PhoR histidine kinase. PhoR sensor domain is part of the two component system PhoR-PhoP that senses environmental stimuli and relay the signal to control the expression of 78 virulent associated genes in Mycobacterium tuberculosis. 3D structure of the PhoR sensor domain will facilitate the structure based drug discovery of novel anti tubercular. In this study, we successfully predicted and isolated the gene encoding PhoR Sensor Domain from Mycobacterium tuberculosis H37Rv, cloned it in pGEM-T vector and subcloned it in pRSET emGFP expression vector. PhoR sensor domain was successfully cloned and would be used for further expression, purification and crystallization studies.
PHYTOCHEMICAL SCREENING AND ANTI-INFLAMMATORY POTENTIAL OF DREGEA VOLUBILIS IN DIFFERENT SOLVENTS

Article history In this present research work roots of Dregea volubilis of family Asclepiadaceae was selected to isolate the phytoconstituents and to evaluate the anti-inflammatory effect of hexane (HE), ethyl acetate (EA) and ethanolic (EE) extracts in either sex of wister albino rats. The method of extraction was carried out with soxhlet apparatus and the process of column chromatography was used to isolate the chemical constituents. The anti-inflammatory effects of hexane, ethyl acetate and ethanolic root extracts of the Dregea volubilis (100, 200 & 400 mg/kg p.o.) were examined on rat paw oedema induced by subplantar injections of carrageenan (0.5 ml/kg). Indomethacin (50 mg/kg p.o.) was used as the reference anti- inflammatory agent for comparison. Both the ethyl acetate and ethanolic extracts of D. volubilis roots (200 and 400 mg/kg p.o.) significantly reduced rat paw oedema induced by subplantar injections of carrageenan. However, the ethyl acetate and ethanol extracts of the plant produced relatively greater and more pronounced anti-inflammatory effect than hexane extract counterpart in the experimental animal model used. The ethyl acetate and ethanol extracts were potent as indomethacin but hexane extract of root of D. volubilis was found to be markedly less potent than indomethacin as anti-inflammatory agent. The results of this experimental animal study indicate that all the extracts of roots of D. volubilis possess anti- inflammatory activity, and thus lend credence to the suggested folkloric use of the plant in the management and control of inflammatory conditions in India.
Analysis of plasminogen activator inhibitor type 2 (PAI-2) expression on the cell surface of monocytic cell lines and human peripheral blood leukocytes

Plasminogen activator inhibitor type 2 (PAI-2) is one of the inhibitors of the plasminogen cascade, a powerful proteolytic cascade involved in many physiological processes. The main aim of this thesis was to evaluate if PAI-2 could be detected on the cell surface of monocytic cell lines and human peripheral blood leukocytes, which could regulate the activity of cell surface urokinase type plasminogen activator (uPA). By flow cytometry PAI-2 could only be detected very weakly on the surface of U937 cells. By ELISA and Western blotting, monomeric non-glycosylated PAI-2 was very abundant in cytosol enriched preparations from U937, MM6 and HaCaT cells, and present in lower amounts in plasma membrane enriched preparations. In addition, Jurkat cells were observed not to express PAI-2 antigen or mRNA. Since PAI-2 could not be detected on the surface of cells, the second aim of this thesis was to determine if PAI-2 could localise to the extracellular matrix (ECM) surface by transglutaminase activity in an in vitro fibrin clot model. By autoradiography it was observed that three species of PAI-2 associated with a fibrin clot: monomeric PAI-2, PAI-2 cross-linked to the fibrin and a high molecular weight PAI-2. Addition of IuPA revealed that the only species of PAI-2 that was active in the fibrin clot, was the monomer. Therefore, rather than inhibiting plasminogen activation as a cell surface moiety, it seems more likely that PAI-2 inhibits plasminogen activation by localising to the surface of the ECM.
Sport Nutrition for Health and Performance

Chapter 1. Introduction to Nutrition for Exercise and Health Chapter 2. Carbohydrate as a Fuel for Exercise Chapter 3. Fat As a Fuel for Exercise Chapter 4. Protein and Exercise Chapter 5. Energy and Nutrient Balance Chapter 6. Achieving Healthy Body Weight Chapter 7. Body Composition Chapter 8. Fluid and Electrolyte Balance Chapter 9. B-Vitamins Important in Energy Metabolism Chapter 10. Antioxidant Nutrients Chapter 11. Minerals and Exercise Chapter 12. Micronutrients Important in Blood Formation Chapter 13. Nutrients for Bone Health Chapter 14. Nutrition and Fitness Assessment Chapter 15. Nutrition and the Active Female Chapter 16. Ergogenic Substances.