Implementation of X-ray diffraction in the measurement of residual thermal strains

Microelectronic systems are multi-material, multi-layer structures, fabricated and exposed to environmental stresses over a wide range of temperatures. Thermal and residual stresses created by thermal mismatches in films and interconnections are a major cause of failure in microelectronic devices. Due to new device materials, increasing die size and the introduction of new materials for enhanced thermal management, differences in thermal expansions of various packaging materials have become exceedingly important and can no longer be neglected. X-ray diffraction is an analytical method using a monochromatic characteristic X-ray beam to characterize the crystal structure of various materials, by measuring the distances between planes in atomic crystalline lattice structures. As a material is strained, this interplanar spacing is correspondingly altered, and this microscopic strain is used to determine the macroscopic strain. This thesis investigates and describes the theory and implementation of X-ray diffraction in the measurement of residual thermal strains. The design of a computer controlled stress attachment stage fully compatible with an Anton Paar heat stage will be detailed. The stress determined by the diffraction method will be compared with bimetallic strip theory and finite element models.

Reduction of salt in yeasted wheat bread: impact on bread quality and solutions using sourdough fermented by functional lactic acid bacteria strains

The dietary intake of sodium chloride has increased considerably over the last few decades due to changes in the human diet. This higher intake has been linked to a number of diseases including hypertension and other cardiovascular diseases. Numerous international health agencies, as well as the food industry, have now recommended a salt intake level of 5-6 g daily, approximately half of the average current daily intake level. Cereal products, and in particular bread, are a major source of salt in the Western diet. Therefore, any reduction in the level of salt in bread could have a major impact on global health. However, salt is a critical ingredient in bread production, and its reduction can have a deleterious effect on the production process as well as on the final bread quality characteristics such as shelf-life, bread volume and sensory characteristics, all deviating from the bakers’ and consumers’ expectations. This work addresses the feasibility of NaCl reduction in wheat bread focusing on options to compensate NaCl with the use of functional sourdoughs. Three strains were used for the application of low-salt bread; L. amylovorus DSM19280, W. cibaria MG1 and L. reuteri FF2hh2. The multifunctional strain L. reuteri FF2hh2 was tested the first time and its application could be demonstrated successfully. The functionalities were based on the production of exopolysaccharides as well as the production of antifungal compounds. While the exopolysaccharides, mainly high molecular dextrans, positively influenced mainly bread loaf volume, crumb structure and staling rate, the strains producing antifungal compounds prolonged the microbial shelf life significantly and compensated the lack of salt. The impact on the sensory characteristics of bread were evaluated by descriptive sensory evaluation. The increase in surface area as well as the presence of organic acids impacted significantly on the flavour profile of the sourdough bread samples. The flavour attribute “salt” could be enhanced by sourdough addition and increased the salty perception. Furthermore, a trained sensory panel evaluated for the first time the impact of yeast activity, based on different salt and yeast concentrations, on the volatile aroma profile of bread crumb samples. The analytical measurements using high resolution gas chromatography and proton-transfer-reaction mass spectrometry (PTR-MS) resulted in significantly different results based on different yeast activities. Nevertheless, the extent of the result could not be recognised by the sensory panel analysing the odour profile of the bread crumb samples. Hence, the consumer cannot recognised low-salt bread by its odour. The use of sourdough is a natural option to overcome the broad range of technological issues caused by salt reduction and also a more popular alternative compared to existing chemical salt replacers.

Seawater carbonate chemistry and effects of CO2 and their modulation by light in the life-cycle stages of the coccolithophore Emiliania huxleyi strains RCC 1216 and 1217 during experiments, 2012

The effects of ocean acidification on the life-cycle stages of the coccolithophore Emiliania huxleyi and their by light were examined. Calcifying diploid and noncalcifying haploid cells (Roscoff culture collection 1216 and 1217) were acclimated to present-day and elevated CO2 partial pressures (PCO2; 38.5 vs. 101.3 Pa, ., 380 vs. 1000 matm) under low and high light (50 vs. 300 mmol photons m-2 s-1). Growth rates as well as quotas and production rates of C and N were measured. Sources of inorganic C for biomass buildup were using a 14C disequilibrium assay. Photosynthetic O2 evolution was measured as a function of dissolved inorganic C and light by means of membrane-inlet mass spectrometry. The diploid stage responded to elevated PCO2 by shunting resources from the production of particulate inorganic C toward organic C yet keeping the production of total particulate C constant. As the effect of ocean acidification was stronger under low light, the diploid stage might be less affected by increased acidity when energy availability is high. The haploid stage maintained elemental composition and production rates under elevated PCO2. Although both life-cycle stages involve different ways of dealing with elevated PCO2, the responses were generally modulated by energy availability, being typically most pronounced under low light. Additionally, PCO2 responses resembled those induced by high irradiances, indicating that ocean acidification affects the interplay between energy-generating processes (photosynthetic light reactions) and processes competing for energy (biomass buildup and calcification). A conceptual model is put forward explaining why the magnitude of single responses is determined by energy availability.

Seawater carbonate chemistry and biological processes of Emiliania huxleyi (strains RCC1256 and NZEH) during experiments, 2011

With respect to their sensitivity to ocean acidification, calcifiers such as the coccolithophore Emiliania huxleyi have received special attention, as the process of calcification seems to be particularly sensitive to changes in the marine carbonate system. For E. huxleyi, apparently conflicting results regarding its sensitivity to ocean acidification have been published (Iglesias-Rodriguez et al., 2008a; Riebesell et al., 2000). As possible causes for discrepancies, intra-specific variability and different effects of CO2 manipulation methods, i.e. the manipulation of total alkalinity (TA) or total dissolved inorganic carbon (DIC), have been discussed. While Langer et al. (2009) demonstrate a high degree of intra-specific variability between strains of E. huxleyi, the question whether different CO2 manipulation methods influence the cellular responses has not been resolved yet. In this study, closed TA as well as open and closed DIC manipulation methods were compared with respect to E. huxleyi's CO2-dependence in growth rate, POC- and PIC-production. The differences in the carbonate chemistry between TA and DIC manipulations were shown not to cause any differences in response patterns, while the latter differed between open and closed DIC manipulation. The two strains investigated showed different sensitivities to acidification of seawater, RCC1256 being more negatively affected in growth rates and PIC production than NZEH.

Environmental carbonate chemistry selects for phenotype of recently isolated strains of Emiliania huxleyi

Coccolithophorid algae, particularly Emiliania huxleyi, are prolific biomineralisers that, under many conditions, dominate communities of marine eukaryotic plankton. Their ability to photosynthesise and form calcified scales (coccoliths) has placed them in a unique position in the global carbon cycle. Contrasting reports have been made with regards to the response of E. huxleyi to ocean acidification. Therefore, there is a pressing need to further determine the fate of this key organism in a rising CO2 world. In this paper, we investigate the phenotype of newly isolated, genetically diverse, strains of E. huxleyi from UK Ocean Acidification Research Programme (UKOA) cruises around the British Isles, the Arctic, and the Southern Ocean. We find a continuum of diversity amongst the physiological and photosynthetic parameters of different strains of E. huxleyi morphotype A under uniform, ambient conditions imposed in the laboratory. This physiology is best explained by adaptation to carbonate chemistry in the former habitat rather than being prescribed by genetic fingerprints such as the coccolithophore morphology motif (CMM). To a first order, the photosynthetic capacity of each strain is a function of both aqueous CO2 availability, and calcification rate, suggestive of a link between carbon concentrating ability and calcification. The calcification rate of each strain is related linearly to the natural environmental [CO32−] at the site of isolation, but a few exceptional strains display low calcification rates at the highest [CO32−] when calcification is limited by low CO2 availability and/or a lack of a carbon concentrating mechanism. We present O2-electrode measurements alongside coccolith oxygen isotopic composition and the uronic acid content (UAC) of the coccolith associated polysaccharide (CAP), that act as indirect tools to show the differing carbon concentrating ability of the strains. The environmental selection revealed amongst our recently isolated strain collection points to the future outcompetition of the slow growing morphotypes B/C and R (which also lack a carbon concentrating mechanism) by more rapidly photosynthesising, and lightly calcified strains of morphotype A but with their rate of calcification highly dependent on the surface ocean saturation state. The mechanism of E. huxleyi response to carbonate chemistry in the modern ocean appears to be selection from a continuum of phenotype.

Environmental carbonate chemistry selects for phenotype of recently isolated strains of Emiliania huxleyi

Coccolithophorid algae, particularly Emiliania huxleyi, are prolific biomineralisers that, under many conditions, dominate communities of marine eukaryotic plankton. Their ability to photosynthesise and form calcified scales (coccoliths) has placed them in a unique position in the global carbon cycle. Contrasting reports have been made with regards to the response of E. huxleyi to ocean acidification. Therefore, there is a pressing need to further determine the fate of this key organism in a rising CO2 world. In this paper, we investigate the phenotype of newly isolated, genetically diverse, strains of E. huxleyi from UK Ocean Acidification Research Programme (UKOA) cruises around the British Isles, the Arctic, and the Southern Ocean. We find a continuum of diversity amongst the physiological and photosynthetic parameters of different strains of E. huxleyi morphotype A under uniform, ambient conditions imposed in the laboratory. This physiology is best explained by adaptation to carbonate chemistry in the former habitat rather than being prescribed by genetic fingerprints such as the coccolithophore morphology motif (CMM). To a first order, the photosynthetic capacity of each strain is a function of both aqueous CO2 availability, and calcification rate, suggestive of a link between carbon concentrating ability and calcification. The calcification rate of each strain is related linearly to the natural environmental [CO32−] at the site of isolation, but a few exceptional strains display low calcification rates at the highest [CO32−] when calcification is limited by low CO2 availability and/or a lack of a carbon concentrating mechanism. We present O2-electrode measurements alongside coccolith oxygen isotopic composition and the uronic acid content (UAC) of the coccolith associated polysaccharide (CAP), that act as indirect tools to show the differing carbon concentrating ability of the strains. The environmental selection revealed amongst our recently isolated strain collection points to the future outcompetition of the slow growing morphotypes B/C and R (which also lack a carbon concentrating mechanism) by more rapidly photosynthesising, and lightly calcified strains of morphotype A but with their rate of calcification highly dependent on the surface ocean saturation state. The mechanism of E. huxleyi response to carbonate chemistry in the modern ocean appears to be selection from a continuum of phenotype.

Temperature affects the morphology and calcification of Emiliania huxleyi strains

The global warming debate has sparked an unprecedented interest in temperature effects on coccolithophores. The calcification response to temperature changes reported in the literature, however, is ambiguous. The two main sources of this ambiguity are putatively differences in experimental setup and strain specificity. In this study we therefore compare three strains isolated in the North Pacific under identical experimental conditions. Three strains of Emiliania huxleyi type A were grown under non-limiting nutrient and light conditions, at 10, 15, 20 and 25 °C. All three strains displayed similar growth rate versus temperature relationships, with an optimum at 20–25 °C. Elemental production (particulate inorganic carbon (PIC), particulate organic carbon (POC), total particulate nitrogen (TPN)), coccolith mass, coccolith size, and width of the tube element cycle were positively correlated with temperature over the sub-optimum to optimum temperature range. The correlation between PIC production and coccolith mass/size supports the notion that coccolith mass can be used as a proxy for PIC production in sediment samples. Increasing PIC production was significantly positively correlated with the percentage of incomplete coccoliths in one strain only. Generally, coccoliths were heavier when PIC production was higher. This shows that incompleteness of coccoliths is not due to time shortage at high PIC production. Sub-optimal growth temperatures lead to an increase in the percentage of malformed coccoliths in a strain-specific fashion. Since in total only six strains have been tested thus far, it is presently difficult to say whether sub-optimal temperature is an important factor causing malformations in the field. The most important parameter in biogeochemical terms, the PIC : POC ratio, shows a minimum at optimum growth temperature in all investigated strains. This clarifies the ambiguous picture featuring in the literature, i.e. discrepancies between PIC : POC–temperature relationships reported in different studies using different strains and different experimental setups. In summary, global warming might cause a decline in coccolithophore's PIC contribution to the rain ratio, as well as improved fitness in some genotypes due to fewer coccolith malformations.

Temperature affects the morphology and calcification of Emiliania huxleyi strains

The global warming debate has sparked an unprecedented interest in temperature effects on coccolithophores. The calcification response to temperature changes reported in the literature, however, is ambiguous. The two main sources of this ambiguity are putatively differences in experimental setup and strain specificity. In this study we therefore compare three strains isolated in the North Pacific under identical experimental conditions. Three strains of Emiliania huxleyi type A were grown under non-limiting nutrient and light conditions, at 10, 15, 20 and 25 °C. All three strains displayed similar growth rate versus temperature relationships, with an optimum at 20–25 °C. Elemental production (particulate inorganic carbon (PIC), particulate organic carbon (POC), total particulate nitrogen (TPN)), coccolith mass, coccolith size, and width of the tube element cycle were positively correlated with temperature over the sub-optimum to optimum temperature range. The correlation between PIC production and coccolith mass/size supports the notion that coccolith mass can be used as a proxy for PIC production in sediment samples. Increasing PIC production was significantly positively correlated with the percentage of incomplete coccoliths in one strain only. Generally, coccoliths were heavier when PIC production was higher. This shows that incompleteness of coccoliths is not due to time shortage at high PIC production. Sub-optimal growth temperatures lead to an increase in the percentage of malformed coccoliths in a strain-specific fashion. Since in total only six strains have been tested thus far, it is presently difficult to say whether sub-optimal temperature is an important factor causing malformations in the field. The most important parameter in biogeochemical terms, the PIC : POC ratio, shows a minimum at optimum growth temperature in all investigated strains. This clarifies the ambiguous picture featuring in the literature, i.e. discrepancies between PIC : POC–temperature relationships reported in different studies using different strains and different experimental setups. In summary, global warming might cause a decline in coccolithophore's PIC contribution to the rain ratio, as well as improved fitness in some genotypes due to fewer coccolith malformations.

Updating of Finite Element Models using static and dynamic optical strains with application to damage assessment

In the recent years, vibration-based structural damage identification has been subject of significant research in structural engineering. The basic idea of vibration-based methods is that damage induces mechanical properties changes that cause anomalies in the dynamic response of the structure, which measures allow to localize damage and its extension. Vibration measured data, such as frequencies and mode shapes, can be used in the Finite Element Model Updating in order to adjust structural parameters sensible at damage (e.g. Young’s Modulus). The novel aspect of this thesis is the introduction into the objective function of accurate measures of strains mode shapes, evaluated through FBG sensors. After a review of the relevant literature, the case of study, i.e. an irregular prestressed concrete beam destined for roofing of industrial structures, will be presented. The mathematical model was built through FE models, studying static and dynamic behaviour of the element. Another analytical model was developed, based on the ‘Ritz method’, in order to investigate the possible interaction between the RC beam and the steel supporting table used for testing. Experimental data, recorded through the contemporary use of different measurement techniques (optical fibers, accelerometers, LVDTs) were compared whit theoretical data, allowing to detect the best model, for which have been outlined the settings for the updating procedure.

Effect of galactose metabolising and non-metabolising strains of Streptococcus thermophilus as a starter culture adjunct on the properties of Cheddar cheese made with low or high pH at whey drainage

Cheddar cheese was made using control culture (Lactococcus lactis subsp. lactis), or with control culture plus a galactose-metabolising (Gal+) or galactose-non-metabolising (Gal-) Streptococcus thermophilus adjunct; for each culture type, the pH at whey drainage was either low (pH 6.15) or high (pH 6.45). Sc. thermophilus affected the levels of residual lactose and galactose, and the volatile compound profile and sensory properties of the mature cheese (270 d) to an extent dependent on the drain pH and phenotype (Gal+ or Gal-). For all culture systems, reducing drain pH resulted in lower levels of moisture and lactic acid, a higher concentration of free amino acids, and higher firmness. The results indicate that Sc. thermophilus may be used to diversify the sensory properties of Cheddar cheese, for example from a fruity buttery odour and creamy flavour to a more acid taste, rancid odour, and a sweaty cheese flavour at high drain pH.

Optimization of lipase production from yeasts strains isolated from olive mil wastewater

Dissertação submetida à Universidade de Lisboa, Faculdade de Ciências para a obtenção do Grau de Mestre em Microbiologia Aplicada.

Comparative transcriptome profiling of human foreskin fibroblasts infected with the Sylvio and Y strains of Trypanosoma cruzi

Trypanosoma cruzi, the causative agent of Chagas Disease, is phylogenetically distributed into nearly identical genetic strains which show divergent clinical presentations including differences in rates of cardiomyopathy in humans, different vector species and transmission cycles, and differential congenital transmission in a mouse model. The population structure of these strains divides into two groups, which are geographically and clinically distinct. The aim of this study was to compare the transcriptome of two strains of T. cruzi, Sylvio vs. Y to identify differences in expression that could account for clinical and biochemical differences. We collected and sequenced RNA from T. cruzi-infected and control Human Foreskin Fibroblasts at three timepoints. Differential expression analysis identified gene expression profiles at different timepoints in Sylvio infections, and between Sylvio and Y infections in both parasite and host. The Sylvio strain parasite and the host response to Sylvio infection largely mirrored the host-pathogen interaction seen in our previous Y strain work. IL-8 was more highly expressed in Sylvio-infected HFFs than in Y-infected HFFs.

Comparing the expression of human DNA topoisomerase I in KM71H and X33 strains of Pichia pastoris

Background: Human is an essential cellular enzyme that is found in all human cells. As this enzyme is upregulated in cancer cells exceedingly, it is used as a target for cancer chemotherapeutic drug development. As such, producing the in-house enzyme for the purpose to speed up the search for more cost-effective and target specific hTopoI inhibitors is warranted. This study aims to compare the optimised conditions for the expression of hTopoI in KM71H (MutS) and X33 (Mut+) strains of Pichia pastoris P. pastoris transfected with an hTopoI recombinant vector was used for the optimization of a higher level of hTopoI expression. Results: In the process, fed-batch cultivation parameters that influence the expression of hTopoI, such as culture temperature, methanol induction and feeding strategy, were optimised in the transfected KM71H and X33 P. pastoris strains in a shake flask system. The cell density and total protein concentration (protein level) of transfected P. pastoris were compared to determine the optimum culture conditions for each transfected P. pastoris strain. A higher hTopoI level was observed in the transfected KM71H culture supernatant (2.26 ng/mL) when the culture was incubated in the optimum conditions. Conclusions: This study demonstrated that MutS strain (KM71H) expressed and secreted a higher level of hTopoI heterologous protein in the presence of methanol compared to the Mut+ strain; X33 (0.75 ng/mL). However, other aspects of optimization, such as pH, should also be considered in the future, to obtain the optimum expression level of hTopoI in P. pastoris.

Antibiotics resistance of Stenotrophomonas maltophilia strains isolated from various clinical specimens.

Background: A limited number of antibiotics are recommended for the therapy of Stenotrophomonas maltophilia infections due to therapy difficulties caused by its numerous mechanisms of resistance. Objectives: In this study conducted over a period of approximately 5 years we aimed to determine resistance rates of S. maltphilia based on drug classification recommended by Clinical and Laboratory Standards Institute. Methods: A total of 118 S. maltphilia strains isolated from various clinical specimens between January 2006 and June 2012 were included in the study. BD Phoenixautomated microbiology system (Becton Dickinson, USA) was utilized for species level identification and antibiotic susceptibility testing. Results: Sixty seven of S. maltphilia strains were isolated from tracheal aspirate isolates, 17 from blood, 10 from sputum, 10 from wound and 14 from other clinical specimens. Levofloxacin was found to be the most effective antibiotic against S. maltphilia strains with resistance rate of 7.6%. The resistance rates to other antibiotics were as follows: chloramphenicol 18.2%, trimethoprim-sulfamethoxazole 20.3% and ceftazidime 72%. Conclusion: The study revealed that S. maltphilia is resistant to many antibiotics. The treatment of infections caused by S. maltphilia should be preferred primarily as levofloxacin, chloramphenicol, and TMP-SXT, respectively.

Molecular Profiling of Shiga Toxin-Producing Escherichia coli and Enteropathogenic E. coli Strains Isolated from French Coastal Environments

Shiga toxin-producing Escherichia coli (STEC) and enteropathogenic E. coli (EPEC) strains may be responsible for food-borne infections in humans. Twenty-eight STEC and 75 EPEC strains previously isolated from French shellfish-harvesting areas and their watersheds and belonging to 68 distinguishable serotypes were characterized in this study. High-throughput real-time PCR was used to search for the presence of 75 E. coli virulence-associated gene targets, and genes encoding Shiga toxin (stx) and intimin (eae) were subtyped using PCR tests and DNA sequencing, respectively. The results showed a high level of diversity between strains, with 17 unique virulence gene profiles for STEC and 56 for EPEC. Seven STEC and 15 EPEC strains were found to display a large number or a particular combination of genetic markers of virulence and the presence of stx and/or eae variants, suggesting their potential pathogenicity for humans. Among these, an O26:H11 stx1a eae-β1 strain was associated with a large number of virulence-associated genes (n = 47), including genes carried on the locus of enterocyte effacement (LEE) or other pathogenicity islands, such as OI-122, OI-71, OI-43/48, OI-50, OI-57, and the high-pathogenicity island (HPI). One O91:H21 STEC strain containing 4 stx variants (stx1a, stx2a, stx2c, and stx2d) was found to possess genes associated with pathogenicity islands OI-122, OI-43/48, and OI-15. Among EPEC strains harboring a large number of virulence genes (n, 34 to 50), eight belonged to serotype O26:H11, O103:H2, O103:H25, O145:H28, O157:H7, or O153:H2.