New Observations of Balmer Continuum Flux in Solar Flares:Instrument Description and First Results

Increase in the Balmer continuum radiation during solar flares was predicted by various authors, but has never been firmly confirmed observationally using ground-based slit spectrographs. Here we describe a new post-focal instrument, the image selector, with which the Balmer continuum flux can be measured from the whole flare area, in analogy to successful detections of flaring dMe stars. The system was developed and put into operation at the horizontal solar telescope HSFA2 of the Ondřejov Observatory. We measure the total flux by a fast spectrometer from a limited but well-defined region on the solar disk. Using a system of diaphragms, the disturbing contribution of a bright solar disk can be eliminated as much as possible. Light curves of the measured flux in the spectral range 350 – 440 nm are processed, together with the Hα images of the flaring area delimited by the appropriate diaphragm. The spectral flux data are flat-fielded, calibrated, and processed to be compared with model predictions. Our analysis of the data proves that the described device is sufficiently sensitive to detect variations in the Balmer continuum during solar flares. Assuming that the Balmer-continuum kernels have at least a similar size as those visible in Hα, we find the flux increase in the Balmer continuum to reach 230 – 550 % of the quiet continuum during the observed X-class flare. We also found temporal changes in the Balmer continuum flux starting well before the onset of the flare in Hα.

The application of a novel, cell permeable activity-based probe for the detection of cysteine cathepsins.

Cysteine cathepsins, such as cathepsin S (CTSS), are implicated in the pathology of a wide range of diseases and are of potential utility as diagnostic and prognostic biomarkers. In previous work, we demonstrated the potency and efficiency of a biotinylated diazomethylketone (DMK)-based activity-based probe (ABP), biotin-PEG-LVG-DMK, for disclosure of recombinant CTSS and CTSS in cell lysates. However, the limited cell permeability of both the biotin and spacer groups restricted detection of CTSS to cell lysates. The synthesis and characterisation of a cell permeable ABP to report on intracellular CTSS activity is reported. The ABP, Z-PraVG-DMK, a modified peptidyl diazomethylketone, was based on the N-terminus of human cystatin motif (Leu-Val-Gly). The leucine residue was substituted for the alkyne-bearing proparcylglycine to facilitate conjugation of an azide-tagged reporter group using click chemistry, following irreversible inhibition of CTSS. When incubated with viable Human Embryonic Kidney 293 cells, Z-PraVG-DMK permitted disclosure of CTSS activity following cell lysis and rhodamine azide conjugation, by employing standard click chemistry protocols. Furthermore, the fluorescent tag facilitated direct detection of CTSS using in-gel fluorescent scanning, obviating the necessity for downstream biotin-streptavidin conjugation and detection procedures.

Sedimentology of sites 14-141, 41-366, 47-397 and 79-544B

Along the N-S-transect of DSDP-Sites 5446, 397, 141, and 366, oxygen and carbon isotopes, flux rates of calcium carbonate, terrigenous matter, and biogenic opal, clay minerals and the size distribution of terrigenous partictes were determined in order to assess the ties between atmospheric and oceanic surface and deep-water circulation off northwest Africa during the late Neogene. During the last 9 m.y., both the paleoceanography in the eastern Atlantic and west African paleodimates were intimately correlated with the evolution of the polar ice sheets as reflected in the benthos d18O curves of the 4 DSDP-Sites. These records make it possible to distinguish six major time intervals which were charaterized by long-term persistent regimes of climatic stability or climatic change. Short-term, "Milankovitch"-type cycles superimpose the long-term climatic evolution and may reflect the chronostratigraphic control fluctuations of the solar insolation persisting back to pre-Pleistocene times. Relatively stable, warm climates prevailed during the late Tortonian/early Messinean, 9 to 6 m.y., and the early Pliocene, 4.5 to 3.5 m.y. ago. Based on d18O curves, the amplitudes of short-term climatic variation were generally low, and the ice sheets were smaller than during peak Holocene time. Oceanic circulation and resulting paleoproductivity in upwelling zones were insignificant. The strength of dust supplying meridional trade winds was low (3 to 5 m/s), interglacial-style zonal winds near the ITCZ were dominant, as indicated by the high abundance of kaolinite. Phases of fluvial sediment supply were common. Humidity was characteristic of the climate in northwest Africa for the major part of this time. Major episodes of climatic deterioration in the subtropics occurred in the latest Miocene/early Pliocene, between some 5.6 and 5.2 and between 4.9 and 4.6 m.y. ago, in the late Pliocene, between 3.2 and 2.4 m.y. ago, and again in the Quaternary, near 1 m.y. ago. The episodes were correlated with marked increases of the global ice volume, as revealed by drastic increases of d18O values. They suggest sea-level falls of up to 70 m below the present sea level in the latest Miocene and earliest Pliocene and of 145 m in the latest Pliocene and Quaternary. The climatic changes resulted in strongly enhanced meridional trade winds as suggested by coarser terrigenous grain-sizes, increased mass accumulation rates of eolian dust, and changes in clay-mineral composition from dominantly kaolinite to illite and chlorite. The meridional trade winds reached speeds of 8 to 10 m/s with a maximum near 15 m/s. The enhanced winds probably led t o intensified coastal upwelling as shown by the contemporaneous local increase i n the deposition of biogenic silica and the local depletion of 13C at Site 397. The most drastic environmental changes near 2.4 and 1 m.y. ago coincide with hiatuses which may indicate phases of general erosion due to strongly enhanced deep-water circulation in the northeast At1antic along the northwest African continental margin. The occasional occurrence of quartz grains coarser than 250 µm may suggest ice-rafted debris in sediments off Morocco. During these time intervals the climate in NW-Africa was dominantly arid. Nevertheless, fluvial runoff (and humidity) continued to be important during intermittent warm phases of the short-term climatic cycles. During the end and the beginning of (inter-) glacial times, fluvial supply of nutrients seems to be the dominant factor, controling phases of enhanced paleoproductivity observed off northwest Africa, whereas during phases of glacial maximum strenger fertility of (increased) coastal upwelling becomes more important. A long-term evolution of paleoenvironments during the last 40 m.y. is depicted in the sediments of Site 366 and is clearly controlled by the plate tectonic route of this Site. During Oligocene times, Site 366 lay in the center of the equatorial upwelling, as shown by the high content of biogenic silica contributing up to 100 % of the carbonate-free sediment fraction >6 µm. The influence of equatorial upwelling abruptly terminated near 15 m.y. ago, a change in the record exaggerated by a hiatus of about 2 m.y. Prior to 25 m.y., the terrigenous input at the paleolatitude of Site 366 was restricted t o eolian sediment supply from South Africa by southeasterly trade winds, as shown by dominantly illite and chlorite in the clay fraction and extremely fine-grained terrigenous matter. Near the Oligocene/Miocene boundary, Site 366 drifted across the equator into the belt of the northeasterly trade winds, which is inferred from the increased content of kaolinite and coarser grain sizes of the terrigenous sediment fraction. The clay-mineral and grain-size compositions of Site 366 do not reflect a noteworthy northward shift of the ITCZ during late Miocene and early Pliocene times, i.e. no marked global circulation asymmetry due to the possible absence of a major Northern Hemisphere glaciation (Flohn 1981). This lack of a more northerly position of the ITCZ may result from a bipolar glaciation already existing during late Miocene times, such as also suggested by the evidence of tillites on Iceland and in southern Alaska during those intervals (e.g., Denton & Amstrong 1969, Mudie & Helgason 1983).

Rheological Characterization of Bitumen and Asphalt including the effect of Added-recycled Material

This thesis evaluates the rheological behaviour of asphalt mixtures and the corresponding extracted binders from the mixtures containing different amounts of Reclaimed Asphalt (RA). Generally, the use of RA is limited to certain amounts. The study materials are Stone Mastic Asphalts including a control sample with 0% RA, and other samples with RA rates of 30%, 60% and 100%. Another set of studied mixtures are Asphalt Concretes (AC) types with again a control mix having 0% RA rate and the other mixtures designs containing 30%, 60% and 90% of reclaimed asphalt which also contain additives. In addition to the bitumen samples extracted from asphalt mixes, there are bitumen samples directly extracted from the original RA. To characterize the viscoelastic behaviour of the binders, Dynamic Shear Rheometer (DSR) tests were conducted on bitumen specimens. The resulting influence of the RA content in the bituminous binders are illustrated through master curves, black diagrams and Cole-Cole plots with regressing these experimental data by the application of the analogical 2S2P1D and the analytical CA model. The advantage of the CA model is in its limited number of parameters and thus is a simple model to use. The 2S2P1D model is an analogical rheological model for the prediction of the linear viscoelastic properties of both asphalt binders and mixtures. In order to study the influence of RA on mixtures, the Indirect Tensile Test (ITT) has been conducted. The master curves of different mixture samples are evaluated by regressing the test data points to a sigmoidal function and subsequently by comparing the master curves, the influence of RA materials is studied. The thesis also focusses on the applicability and also differences of CA model and 2S2P1D model for bitumen samples and the sigmoid function for the mixtures and presents the influence of the RA rate on the investigated model parameters.

Improving the Accuracy of 3-D Reconstruction in Robotic Vision Applications

Thesis (Ph.D.)--University of Washington, 2016-08

Main causes of death in Dande, Angola: results from verbal autopsies of deaths occurring during 2009–2012

bACKGROUND - The Dande Health and Demographic Surveillance System (HDSS) located in Bengo province, Angola, covers nearly 65,500 residents living in approximately 19,800 households. This study aims to describe the main causes of deaths (CoD) occurred within the HDSS, from 2009 to 2012, and to explore associations between demographic or socioeconomic factors and broad mortality groups (Group I-Communicable diseases, maternal, perinatal and nutritional conditions; Group II-Non-communicable diseases; Group III-Injuries; IND-Indeterminate). Methods - Verbal Autopsies (VA) were performed after death identification during routine HDSS visits. Associations between broad groups of CoD and sex, age, education, socioeconomic position, place of residence and place of death, were explored using chi-square tests and fitting logistic regression models. Results - From a total of 1488 deaths registered, 1009 verbal autopsies were performed and 798 of these were assigned a CoD based on the 10th revision of the International Classification of Diseases (ICD-10). Mortality was led by CD (61.0%), followed by IND (18.3%), NCD (11.6%) and INJ (9.1%). Intestinal infectious diseases, malnutrition and acute respiratory infections were the main contributors to under-five mortality (44.2%). Malaria was the most common CoD among children under 15 years old (38.6%). Tuberculosis, traffic accidents and malaria led the CoD among adults aged 15–49 (13.5%, 10.5 % and 8.0% respectively). Among adults aged 50 or more, diseases of the circulatory system (23.2%) were the major CoD, followed by tuberculosis (8.2%) and malaria (7.7%). CD were more frequent CoD among less educated people (adjusted odds ratio, 95% confidence interval for none vs. 5 or more years of school: 1.68, 1.04–2.72). Conclusion - Infectious diseases were the leading CoD in this region. Verbal autopsies proved useful to identify the main CoD, being an important tool in settings where vital statistics are scarce and death registration systems have limitations.

Evidence for different QTL underlying the immune and hypersensitive responses of Eucalyptus globulus to the rust pathogen Puccinia psidii

The rust Puccinia psidii infects many species in the family Myrtaceae. Native to South America, the pathogen has recently entered Australia which has a rich Myrtaceous flora, including trees of the ecologically and economically important genus Eucalyptus. We studied the genetic basis of variation in rust resistance in Eucalyptus globulus, the main plantation eucalypt in Australia. Quantitative trait loci (QTL) analysis was undertaken using 218 genotypes of an outcross F2 mapping family, phenotyped by controlled inoculation of their open pollinated progeny with the strain of P. psidii found in Australia. QTL analyses were conducted using a binary classification of individuals with no symptoms (immune) versus those with disease symptoms, and in a separate analysis dividing plants with disease symptoms into those exhibiting the hypersensitive response versus those with more severe symptoms. Four QTL were identified, two influencing whether a plant exhibited symptoms (Ppr2 and Ppr3), and two influencing the presence or absence of a hypersensitive reaction (Ppr4 and Ppr5). These QTL mapped to four different linkage groups, none of which overlap with Ppr1, the major QTL previously identified for rust resistance in Eucalyptus grandis. Candidate genes within the QTL regions are presented and possible mechanisms discussed. Together with past findings, our results suggest that P. psidii resistance in eucalypts is quantitative in nature and influenced by the complex interaction of multiple loci of variable effect.

The grand challenge of food security - general lessons from a comprehensive approach to protecting stored grain from insect pests in Australia and India

We outline a philosophical approach to Grand Challenge projects, with particular reference to our experience in our food security project involving the protection of stored grain from insect attack in two countries on different continents. A key consideration throughout has been the management of resistance in these pests to the valuable fumigant phosphine. Emphasis is given to the chain of research issues that required solution and the assembly of a well-integrated team, overlapping in skills for effective communication, in each country to solve the problems identified along that chain. A crucial aspect to maintaining direction is the inclusion of key end users in all deliberations, as well as the establishment and maintenance of effective outlets for the dissemination of practical recommendations. We finish with a summary of our achievements with respect to our approach to this food security Grand Challenge.

Status of resistance to phosphine in insect pests of stored products in Vietnam

In response to numerous reports of failures to control insect pests of stored products with phosphine in Vietnam, a national survey for resistance to this key fumigant was undertaken in 2009–2011. Data from a more limited survey undertaken by the authors in 2002 in northern Vietnam are also presented. Samples collected in the 2002 survey (Sitophilus oryzae, n=8; Tribolium castaneum, n=8) were tested using a full dose- response assay, while for the 2009–11 survey, F1 generations were tested for resistance with two discriminating dosages of phosphine to detect frequency of weak and strong resistance phenotypes. Compared with a susceptible reference strain, in 2002, resistance to phosphine was indicated in six T. castaneum samples but only two of S. oryzae. Resistance factor, however, did not exceed 2.8-fold in T. castaneum and 1.7 in S. oryzae indicating relatively low frequency and weak expression of resistance. In 2009–11 survey, 176 samples were collected from a range of food and feed storages along the supply chain and from all major regions of Vietnam (125 sites). Rhyzopertha dominica and S. oryzae were the most common species found infesting stored commodities. Resistance was detected at high frequency in all the species. Weak and strong resistance phenotype frequencies were, respectively: Cryptolestes ferrugineus (37 and 58%, n=19), R. dominica (1.5 and 97%, n=65), S. oryzae (34 and 59%, n=82) and T. castaneum (70 and 30%, n=10). Strong resistance phenotype was detected in all the major regions and all parts of the supply chain but frequency was the highest in central storages and animal feed establishments. The increase in frequency and strength of resistance to phosphine in the eight years between the two surveys has been rapid and dramatic. The survey demonstrates the threat of resistance to grain protection in Vietnam and highlights the need for training of fumigators, and the development and adoption of phosphine resistance management tactics nationally.

Hybrid mathematical and informational modeling of beam-to-column connections

The analysis of steel and composite frames has traditionally been carried out by idealizing beam-to-column connections as either rigid or pinned. Although some advanced analysis methods have been proposed to account for semi-rigid connections, the performance of these methods strongly depends on the proper modeling of connection behavior. The primary challenge of modeling beam-to-column connections is their inelastic response and continuously varying stiffness, strength, and ductility. In this dissertation, two distinct approaches—mathematical models and informational models—are proposed to account for the complex hysteretic behavior of beam-to-column connections. The performance of the two approaches is examined and is then followed by a discussion of their merits and deficiencies. To capitalize on the merits of both mathematical and informational representations, a new approach, a hybrid modeling framework, is developed and demonstrated through modeling beam-to-column connections. Component-based modeling is a compromise spanning two extremes in the field of mathematical modeling: simplified global models and finite element models. In the component-based modeling of angle connections, the five critical components of excessive deformation are identified. Constitutive relationships of angles, column panel zones, and contact between angles and column flanges, are derived by using only material and geometric properties and theoretical mechanics considerations. Those of slip and bolt hole ovalization are simplified by empirically-suggested mathematical representation and expert opinions. A mathematical model is then assembled as a macro-element by combining rigid bars and springs that represent the constitutive relationship of components. Lastly, the moment-rotation curves of the mathematical models are compared with those of experimental tests. In the case of a top-and-seat angle connection with double web angles, a pinched hysteretic response is predicted quite well by complete mechanical models, which take advantage of only material and geometric properties. On the other hand, to exhibit the highly pinched behavior of a top-and-seat angle connection without web angles, a mathematical model requires components of slip and bolt hole ovalization, which are more amenable to informational modeling. An alternative method is informational modeling, which constitutes a fundamental shift from mathematical equations to data that contain the required information about underlying mechanics. The information is extracted from observed data and stored in neural networks. Two different training data sets, analytically-generated and experimental data, are tested to examine the performance of informational models. Both informational models show acceptable agreement with the moment-rotation curves of the experiments. Adding a degradation parameter improves the informational models when modeling highly pinched hysteretic behavior. However, informational models cannot represent the contribution of individual components and therefore do not provide an insight into the underlying mechanics of components. In this study, a new hybrid modeling framework is proposed. In the hybrid framework, a conventional mathematical model is complemented by the informational methods. The basic premise of the proposed hybrid methodology is that not all features of system response are amenable to mathematical modeling, hence considering informational alternatives. This may be because (i) the underlying theory is not available or not sufficiently developed, or (ii) the existing theory is too complex and therefore not suitable for modeling within building frame analysis. The role of informational methods is to model aspects that the mathematical model leaves out. Autoprogressive algorithm and self-learning simulation extract the missing aspects from a system response. In a hybrid framework, experimental data is an integral part of modeling, rather than being used strictly for validation processes. The potential of the hybrid methodology is illustrated through modeling complex hysteretic behavior of beam-to-column connections. Mechanics-based components of deformation such as angles, flange-plates, and column panel zone, are idealized to a mathematical model by using a complete mechanical approach. Although the mathematical model represents envelope curves in terms of initial stiffness and yielding strength, it is not capable of capturing the pinching effects. Pinching is caused mainly by separation between angles and column flanges as well as slip between angles/flange-plates and beam flanges. These components of deformation are suitable for informational modeling. Finally, the moment-rotation curves of the hybrid models are validated with those of the experimental tests. The comparison shows that the hybrid models are capable of representing the highly pinched hysteretic behavior of beam-to-column connections. In addition, the developed hybrid model is successfully used to predict the behavior of a newly-designed connection.

Real-Time PCR Assays for the Detection of Puccinia psidii

Puccinia psidii (Myrtle rust) is an emerging pathogen that has a wide host range in the Myrtaceae family; it continues to show an increase in geographic range and is considered to be a significant threat to Myrtaceae plants worldwide. In this study, we describe the development and validation of three novel real-time polymerase reaction (qPCR) assays using ribosomal DNA and β-tubulin gene sequences to detect P. psidii. All qPCR assays were able to detect P. psidii DNA extracted from urediniospores and from infected plants, including asymptomatic leaf tissues. Depending on the gene target, qPCR was able to detect down to 0.011 pg of P. psidii DNA. The most optimum qPCR assay was shown to be highly specific, repeatable, and reproducible following testing using different qPCR reagents and real-time PCR platforms in different laboratories. In addition, a duplex qPCR assay was developed to allow coamplification of the cytochrome oxidase gene from host plants for use as an internal PCR control. The most optimum qPCR assay proved to be faster and more sensitive than the previously published nested PCR assay and will be particularly useful for high-throughput testing and to detect P. psidii at the early stages of infection, before the development of sporulating rust pustules.

Identification and Characterization of New Small Molecule Inhibitors of Picornavirus Replication

The Picornaviridae family consists of positive-strand RNA viruses that are the causative agents of a variety of diseases in humans and animals. Few drugs targeting picornaviruses are available, making the discovery of new antivirals a high priority. Here, we identified and characterized three compounds from a library of kinase inhibitors that block replication of poliovirus, coxsackievirus B3, and encephalomyocarditis virus. The antiviral effect of these compounds is not likely related to their known cellular targets because other inhibitors targeting the same pathways did not inhibit viral replication. Using an in vitro translation-replication system, we showed that these drugs inhibit different stages of the poliovirus life cycle. A4(1) inhibited the formation of a functional replication complex, while E5(1) and E7(2) affected replication after the replication complex had formed. A4(1) demonstrated partial protection from paralysis in a murine model of poliomyelitis. Poliovirus resistant to E7(2) had a single mutation in the 3A protein. This mutation was previously found to confer resistance to enviroxime-like compounds, which target either PI4KIIIβ (major enviroxime-like compounds) or OSBP (minor enviroxime-like compounds), cellular factors involved in lipid metabolism and shown to be important for replication of diverse positive-strand RNA viruses. We classified E7(2) as a minor enviroxime-like compound, because the localization of OSBP changed in the presence of this inhibitor. Interestingly, both E7(2) and major enviroxime-like compound GW5074 interfered with the viral polyprotein processing. Multiple attempts to isolate resistant mutants in the presence of A4(1) or E5(1) were unsuccessful, showing that effective broad-spectrum antivirals could be developed on the basis of these compounds. Studies with these compounds shed light on pathways shared by diverse picornaviruses that could be potential targets for the development of broad-spectrum antiviral drugs.

Does Fumigation of Durum Wheat and Semolina with Sulfuryl Fluoride affect Quality of the Grain, Semolina and derived Spaghetti and Bread?

There is no information on the effect of sulfuryl fluoride (SF) on durum wheat technological properties and products made from fumigated durum wheat. Durum wheat and semolina were exposed to a range of SF applications under conditions that might be typically encountered in bulk storage facilities used in many countries. SF greatly reduced the germination percentage of fumigated durum wheat with increasing impact under higher SF concentration, grain moisture content, and fumigation temperature. SF greatly reduced seed germination percentage impacting more the higher the SF concentration. SF had little to no effects on grain test weight, 1000 grain weight, hardness, protein content, semolina ash content and mixograph properties. At the highest SF concentration (31.25 mg/L for 48 h) there was a tendency for pasta cooking loss to be increased but still acceptable while other pasta properties were largely unaffected. Fumigation with SF did not have any impact on the baking properties of a wholemeal durum flour-commercial flour mix. Therefore, SF is not recommended if the grains are to be used as seeds for agricultural production but for the production of semolina, pasta and bread, SF used under typical fumigation conditions has little to no impact on technological properties of durum wheat.

Microfluidic platforms for the characterization of in meso membrane protein crystallization

Membrane proteins, which reside in the membranes of cells, play a critical role in many important biological processes including cellular signaling, immune response, and material and energy transduction. Because of their key role in maintaining the environment within cells and facilitating intercellular interactions, understanding the function of these proteins is of tremendous medical and biochemical significance. Indeed, the malfunction of membrane proteins has been linked to numerous diseases including diabetes, cirrhosis of the liver, cystic fibrosis, cancer, Alzheimer's disease, hypertension, epilepsy, cataracts, tubulopathy, leukodystrophy, Leigh syndrome, anemia, sensorineural deafness, and hypertrophic cardiomyopathy.1-3 However, the structure of many of these proteins and the changes in their structure that lead to disease-related malfunctions are not well understood. Additionally, at least 60% of the pharmaceuticals currently available are thought to target membrane proteins, despite the fact that their exact mode of operation is not known.4-6 Developing a detailed understanding of the function of a protein is achieved by coupling biochemical experiments with knowledge of the structure of the protein. Currently the most common method for obtaining three-dimensional structure information is X-ray crystallography. However, no a priori methods are currently available to predict crystallization conditions for a given protein.7-14 This limitation is currently overcome by screening a large number of possible combinations of precipitants, buffer, salt, and pH conditions to identify conditions that are conducive to crystal nucleation and growth.7,9,11,15-24 Unfortunately, these screening efforts are often limited by difficulties associated with quantity and purity of available protein samples. While the two most significant bottlenecks for protein structure determination in general are the (i) obtaining sufficient quantities of high quality protein samples and (ii) growing high quality protein crystals that are suitable for X-ray structure determination,7,20,21,23,25-47 membrane proteins present additional challenges. For crystallization it is necessary to extract the membrane proteins from the cellular membrane. However, this process often leads to denaturation. In fact, membrane proteins have proven to be so difficult to crystallize that of the more than 66,000 structures deposited in the Protein Data Bank,48 less than 1% are for membrane proteins, with even fewer present at high resolution (< 2Å)4,6,49 and only a handful are human membrane proteins.49 A variety of strategies including detergent solubilization50-53 and the use of artificial membrane-like environments have been developed to circumvent this challenge.43,53-55 In recent years, the use of a lipidic mesophase as a medium for crystallizing membrane proteins has been demonstrated to increase success for a wide range of membrane proteins, including human receptor proteins.54,56-62 This in meso method for membrane protein crystallization, however, is still by no means routine due to challenges related to sample preparation at sub-microliter volumes and to crystal harvesting and X-ray data collection. This dissertation presents various aspects of the development of a microfluidic platform to enable high throughput in meso membrane protein crystallization at a level beyond the capabilities of current technologies. Microfluidic platforms for protein crystallization and other lab-on-a-chip applications have been well demonstrated.9,63-66 These integrated chips provide fine control over transport phenomena and the ability to perform high throughput analyses via highly integrated fluid networks. However, the development of microfluidic platforms for in meso protein crystallization required the development of strategies to cope with extremely viscous and non-Newtonian fluids. A theoretical treatment of highly viscous fluids in microfluidic devices is presented in Chapter 3, followed by the application of these strategies for the development of a microfluidic mixer capable of preparing a mesophase sample for in meso crystallization at a scale of less than 20 nL in Chapter 4. This approach was validated with the successful on chip in meso crystallization of the membrane protein bacteriorhodopsin. In summary, this is the first report of a microfluidic platform capable of performing in meso crystallization on-chip, representing a 1000x reduction in the scale at which mesophase trials can be prepared. Once protein crystals have formed, they are typically harvested from the droplet they were grown in and mounted for crystallographic analysis. Despite the high throughput automation present in nearly all other aspects of protein structure determination, the harvesting and mounting of crystals is still largely a manual process. Furthermore, during mounting the fragile protein crystals can potentially be damaged, both from physical and environmental shock. To circumvent these challenges an X-ray transparent microfluidic device architecture was developed to couple the benefits of scale, integration, and precise fluid control with the ability to perform in situ X-ray analysis (Chapter 5). This approach was validated successfully by crystallization and subsequent on-chip analysis of the soluble proteins lysozyme, thaumatin, and ribonuclease A and will be extended to microfluidic platforms for in meso membrane protein crystallization. The ability to perform in situ X-ray analysis was shown to provide extremely high quality diffraction data, in part as a result of not being affected by damage due to physical handling of the crystals. As part of the work described in this thesis, a variety of data collection strategies for in situ data analysis were also tested, including merging of small slices of data from a large number of crystals grown on a single chip, to allow for diffraction analysis at biologically relevant temperatures. While such strategies have been applied previously,57,59,61,67 they are potentially challenging when applied via traditional methods due to the need to grow and then mount a large number of crystals with minimal crystal-to-crystal variability. The integrated nature of microfluidic platforms easily enables the generation of a large number of reproducible crystallization trials. This, coupled with in situ analysis capabilities has the potential of being able to acquire high resolution structural data of proteins at biologically relevant conditions for which only small crystals, or crystals which are adversely affected by standard cryocooling techniques, could be obtained (Chapters 5 and 6). While the main focus of protein crystallography is to obtain three-dimensional protein structures, the results of typical experiments provide only a static picture of the protein. The use of polychromatic or Laue X-ray diffraction methods enables the collection of time resolved structural information. These experiments are very sensitive to crystal quality, however, and often suffer from severe radiation damage due to the intense polychromatic X-ray beams. Here, as before, the ability to perform in situ X-ray analysis on many small protein crystals within a microfluidic crystallization platform has the potential to overcome these challenges. An automated method for collecting a "single-shot" of data from a large number of crystals was developed in collaboration with the BioCARS team at the Advanced Photon Source at Argonne National Laboratory (Chapter 6). The work described in this thesis shows that, even more so than for traditional structure determination efforts, the ability to grow and analyze a large number of high quality crystals is critical to enable time resolved structural studies of novel proteins. In addition to enabling X-ray crystallography experiments, the development of X-ray transparent microfluidic platforms also has tremendous potential to answer other scientific questions, such as unraveling the mechanism of in meso crystallization. For instance, the lipidic mesophases utilized during in meso membrane protein crystallization can be characterized by small angle X-ray diffraction analysis. Coupling in situ analysis with microfluidic platforms capable of preparing these difficult mesophase samples at very small volumes has tremendous potential to enable the high throughput analysis of these systems on a scale that is not reasonably achievable using conventional sample preparation strategies (Chapter 7). In collaboration with the LS-CAT team at the Advanced Photon Source, an experimental station for small angle X-ray analysis coupled with the high quality visualization capabilities needed to target specific microfluidic samples on a highly integrated chip is under development. Characterizing the phase behavior of these mesophase systems and the effects of various additives present in crystallization trials is key for developing an understanding of how in meso crystallization occurs. A long term goal of these studies is to enable the rational design of in meso crystallization experiments so as to avoid or limit the need for high throughput screening efforts. In summary, this thesis describes the development of microfluidic platforms for protein crystallization with in situ analysis capabilities. Coupling the ability to perform in situ analysis with the small scale, fine control, and the high throughput nature of microfluidic platforms has tremendous potential to enable a new generation of crystallographic studies and facilitate the structure determination of important biological targets. The development of platforms for in meso membrane protein crystallization is particularly significant because they enable the preparation of highly viscous mixtures at a previously unachievable scale. Work in these areas is ongoing and has tremendous potential to improve not only current the methods of protein crystallization and crystallography, but also to enhance our knowledge of the structure and function of proteins which could have a significant scientific and medical impact on society as a whole. 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Comparison of host range and pathogenicity of isolates of Pythium myriotylum and Pythium zingiberis

Apart from morphology and genetic characteristics, species status of Pythium zingiberis and P. myriotylum may also be confirmed based on their pathogenicity and host range. An Australian putative P. zingiberis isolate and imported type isolates of P. myriotylum and P. zingiberis were subject to both in vitro and in vivo pathogenicity tests. In vitro tests were carried out on excised carrot, ginger, potato, radish, and sweet potato tuber/root sections, and on seeds and seedlings of cucumber, cauliflower, millet, rye, sweet corn, tomato, and wheat. In all assays conducted, the Australian isolate was found to be the most pathogenic, followed by type specimen of P. zingiberis (UOP 275), and then the type specimen P. myriotylum (CBS 254.70). An in vivo experiment on ginger plants at 35°C (with 10 h day light) in quarantine conditions showed that the ginger plants inoculated with the Australian isolate and also the type specimen of P. zingiberis died at 21 days after inoculation, whereas those inoculated with P. myriotylum CBS 254.70 were still green and healthy. Along with cardinal growth rate, the Australian isolate was confirmed to be closely related to P. zingiberis. This is also the first direct comparison in pathogenicity of P. zingiberis and P. myriotylum.