From genotype to phenotype : diversity and population structure of Flavobacterium psychrophilum

Flavobacterium psychrophilum is the etiological agent of bacterial cold-water disease (BCWD) causing high fish mortalities and significant economic losses to the freshwater salmonid aquaculture industry around the world. Today BCWD outbreaks are mainly treated with environmentally hazardous antimicrobial agents and alternative preventative measures are urgently needed in order to ensure the well-being of animals and the sustainability of aquaculture. The diversity of pathogenic bacteria challenges the development of universal control strategies and in many cases the pathogen population structure, i.e. the total genetic diversity of the species must be taken into account. This work integrates the tools of modern molecular biology and conventional phenotypic microbiology to gain knowledge about the diversity and population structure of F. psychrophilum. The present work includes genetic characterization of a large collection of isolates collected from diverse origins and years, from aquaculture in a whole region including different countries, and provides the first international validation of a universal multilocus sequence typing (MLST) approach for unambiguous genetic typing of F. psychrophilum. Population structure analyses showed that the global F. psychrophilum population is subdivided into pathogenic species-specific clones, of which one particular genetic lineage, clonal complex CC-ST2, has been responsible for the majority of BCWD outbreaks in rainbow trout (Oncorhynchus mykiss) in European aquaculture facilities over several decades. Genotypic and phenotypic population heterogeneity affecting antimicrobial resistance in F. psychrophilum within BCWD outbreaks was discovered. Specific genotypes were associated with severe infections in farmed rainbow trout and Atlantic salmon (Salmo salar), and in addition to high adherence, antimicrobial resistance was strongly associated with outbreak strains. The study brought additional support for the hypothesis of an epidemic F. psychrophilum population structure, where recombination is an important force for the generation and maintenance of genetic diversity, and a significant contribution towards mapping the genetic diversity of this important fish pathogen. Evidence indicating dissemination of virulent strains with commercial movement of fish and fish products was strengthened.

Partial purification of tightly bound mitochondrial hexokinase from maize (Zea mays L.) root membranes

In mammals, hexokinase (HK) is strategically located at the outer membrane of mitochondria bound to the porin protein. The mitochondrial HK is a crucial modulator of apoptosis and reactive oxygen species generation. In plants, these properties related to HK are unknown. In order to better understand the physiological role of non-cytosolic hexokinase (NC-HK) in plants, we developed a purification strategy here described. Crude extract of 400 g of maize roots (230 mg protein) contained a specific activity of 0.042 µmol G6P min-1 mg PTN-1. After solubilization with detergent two fractions were obtained by DEAE column chromatography, NC-HK 1 (specific activity = 3.6 µmol G6P min-1 mg PTN-1 and protein recovered = 0.7 mg) and NC-HK 2. A major purification (yield = 500-fold) was obtained after passage of NC-HK 1 through the hydrophobic phenyl-Sepharose column. The total amount of protein and activity recovered were 0.04 and 18%, respectively. The NC-HK 1 binds to the hydrophobic phenyl-Sepharose matrix, as observed for rat brain HK. Mild chymotrypsin digestion did not affect adsorption of NC-HK 1 to the hydrophobic column as it does for rat HK I. In contrast to mammal mitochondrial HK, glucose-6-phosphate, clotrimazole or thiopental did not dissociate NC-HK from maize (Zea mays) or rice (Oryza sativa) mitochondrial membranes. These data show that the interaction between maize or rice NC-HK to mitochondria differs from that reported in mammals, where the mitochondrial enzyme can be displaced by modulators or pharmacological agents known to interfere with the enzyme binding properties with the mitochondrial porin protein.

Proteomic inventory of myocardial proteins from patients with chronic Chagas' cardiomyopathy

Chronic Chagas' disease cardiomyopathy (CCC) is an often fatal outcome of Trypanosoma cruzi infection, with a poorer prognosis than other cardiomyopathies. CCC is refractory to heart failure treatments, and is the major indication of heart transplantation in Latin America. A diffuse myocarditis, plus intense myocardial hypertrophy, damage and fibrosis, in the presence of very few T. cruzi forms, are the histopathological hallmarks of CCC. To gain a better understanding of the pathophysiology of CCC, we analyzed the protein profile in the affected CCC myocardium. Homogenates from left ventricular myocardial samples of end-stage CCC hearts explanted during heart transplantation were subjected to two-dimensional electrophoresis with Coomassie blue staining; protein identification was performed by MALDI-ToF mass spectrometry and peptide mass fingerprinting. The identification of selected proteins was confirmed by immunoblotting. We demonstrated that 246 proteins matched in gels from two CCC patients. They corresponded to 112 distinct proteins. Along with structural/contractile and metabolism proteins, we also identified proteins involved in apoptosis (caspase 8, caspase 2), immune system (T cell receptor ß chain, granzyme A, HLA class I) and stress processes (heat shock proteins, superoxide dismutases, and other oxidative stress proteins). Proteins involved in cell signaling and transcriptional factors were also identified. The identification of caspases and oxidative stress proteins suggests the occurrence of active apoptosis and significant oxidative stress in CCC myocardium. These results generated an inventory of myocardial proteins in CCC that should contribute to the generation of hypothesis-driven experiments designed on the basis of the classes of proteins identified here.

Learning about brain physiology and complexity from the study of the epilepsies

The brain is a complex system, which produces emergent properties such as those associated with activity-dependent plasticity in processes of learning and memory. Therefore, understanding the integrated structures and functions of the brain is well beyond the scope of either superficial or extremely reductionistic approaches. Although a combination of zoom-in and zoom-out strategies is desirable when the brain is studied, constructing the appropriate interfaces to connect all levels of analysis is one of the most difficult challenges of contemporary neuroscience. Is it possible to build appropriate models of brain function and dysfunctions with computational tools? Among the best-known brain dysfunctions, epilepsies are neurological syndromes that reach a variety of networks, from widespread anatomical brain circuits to local molecular environments. One logical question would be: are those complex brain networks always producing maladaptive emergent properties compatible with epileptogenic substrates? The present review will deal with this question and will try to answer it by illustrating several points from the literature and from our laboratory data, with examples at the behavioral, electrophysiological, cellular and molecular levels. We conclude that, because the brain is a complex system compatible with the production of emergent properties, including plasticity, its functions should be approached using an integrated view. Concepts such as brain networks, graphics theory, neuroinformatics, and e-neuroscience are discussed as new transdisciplinary approaches dealing with the continuous growth of information about brain physiology and its dysfunctions. The epilepsies are discussed as neurobiological models of complex systems displaying maladaptive plasticity.

Berberine induces apoptosis via ROS generation in PANC-1 and MIA-PaCa2 pancreatic cell lines

Pancreatic cancer is the fourth leading cause of cancer death. Gemcitabine is widely used as a chemotherapeutic agent for the treatment of pancreatic cancer, but the prognosis is still poor. Berberine, an isoquinoline alkaloid extracted from a variety of natural herbs, possesses a variety of pharmacological properties including anticancer effects. In this study, we investigated the anticancer effects of berberine and compared its use with that of gemcitabine in the pancreatic cancer cell lines PANC-1 and MIA-PaCa2. Berberine inhibited cell growth in a dose-dependent manner by inducing cell cycle arrest and apoptosis. After berberine treatment, the G1 phase of PANC-1 cells increased by 10% compared to control cells, and the G1 phase of MIA-PaCa2 cells was increased by 2%. Whereas gemcitabine exerts antiproliferation effects through S-phase arrest, our results showed that berberine inhibited proliferation by inducing G1-phase arrest. Berberine-induced apoptosis of PANC-1 and MIA-PaCa2 cells increased by 7 and 2% compared to control cells, respectively. Notably, berberine had a greater apoptotic effect in PANC-1 cells than gemcitabine. Upon treatment of PANC-1 and MIA-PaCa2 with berberine at a half-maximal inhibitory concentration (IC50), apoptosis was induced by a mechanism that involved the production of reactive oxygen species (ROS) rather than caspase 3/7 activation. Our findings showed that berberine had anti-cancer effects and may be an effective drug for pancreatic cancer chemotherapy.

Production of yeast extracts from whey for food use: market and technical considerations

Whey is produced in large amounts by cheese industries. This by-product can be used for biomass production by yeast cultivation, resulting in commercially attractive products. The use of yeast extracts as source of flavour enhancer consists of an expansible market, encouraged by costumer's choice for natural additives. The development of a suitable and economically viable project for the generation of valued-added by-products, may allow the dairy industry to diversify their portfolio and increase their rentability.

Developing novel one-step processes for obtaining food-grade O/W emulsions from pressurized fluid extracts: processes description, state of the art and perspectives

Abstract In this work, a novel on-line process for production of food-grade emulsions containing oily extracts, i.e. oil-in-water (O/W) emulsions, in only one step is presented. This process has been called ESFE, Emulsions from Supercritical Fluid Extraction. With this process, emulsions containing supercritical fluid extracts can be obtained directly from plant materials. The aim in the conception of this process is to propose a new rapid way to obtain emulsions from supercritical fluid extracts. Nowadays the conventional emulsion formulation method is a two-step procedure, i.e. first supercritical fluid extraction for obtaining an extract; secondly emulsion formulation using another device. Other variation of the process was tested and successfully validated originating a new acronymed process: EPFE (Emulsions from Pressurized Fluid Extractions). Both processes exploit the supercritical CO2-essential oils miscibility, in addition, EPFE process exploits the emulsification properties of saponin-rich pressurized aqueous plant extracts. The feasibility of this latter process was demonstrated using Pfaffia glomerata roots as source of saponin-rich extract, water as extracting solvent and clove essential oil, directly extracted using supercritical CO2, as a model dispersed phase. In addition, examples of pressurized fluid-based coupled processes applied for adding value to food bioactive compounds developed in the past five years are reviewed.

Monooxygenase Diversity and Oxygen Activation within Polyketide Antibiotic Biosynthesis

Molecular oxygen (O2) is a key component in cellular respiration and aerobic life. Through the redox potential of O2, the amount of free energy available to organisms that utilize it is greatly increased. Yet, due to the nature of the O2 electron configuration, it is non-reactive to most organic molecules in the ground state. For O2 to react with most organic compounds it must be activated. By activating O2, oxygenases can catalyze reactions involving oxygen incorporation into organic compounds. The oxygen activation mechanisms employed by many oxygenases to have been studied, and they often include transition metals and selected organic compounds. Despite the diversity of mechanisms for O2 activation explored in this thesis, all of the monooxygenases studied in the experimental part activate O2 through a transient carbanion intermediate. One of these enzymes is the small cofactorless monooxygenase SnoaB. Cofactorless monooxygenases are unusual oxygenases that require neither transition metals nor cofactors to activate oxygen. Based on our biochemical characterization and the crystal structure of this enzyme, the mechanism most likely employed by SnoaB relies on a carbanion intermediate to activate oxygen, which is consistent with the proposed substrate-assisted mechanism for this family of enzymes. From the studies conducted on the two-component system AlnT and AlnH, both the functions of the NADH-dependent flavin reductase, AlnH, and the reduced flavin dependent monooxygenase, AlnT, were confirmed. The unusual regiochemistry proposed for AlnT was also confirmed on the basis of the structure of a reaction product. The mechanism of AlnT, as with other flavin-dependent monooxygenases, is likely to involve a caged radical pair consisting of a superoxide anion and a neutral flavin radical formed from an initial carbanion intermediate. In the studies concerning the engineering of the S-adenosyl-L-methionine (SAM) dependent 4-O-methylase DnrK and the homologous atypical 10-hydroxylase RdmB, our data suggest that an initial decarboxylation of the substrate is catalyzed by both of these enzymes, which results in the generation of a carbanion intermediate. This intermediate is not essential for the 4-O-methylation reaction, but it is important for the 10-hydroxylation reaction, since it enables substrate-assisted activation of molecular oxygen involving a single electron transfer to O2 from a carbanion intermediate. The only role for SAM in the hydroxylation reaction is likely to be stabilization of the carbanion through the positive charge of the cofactor. Based on the DnrK variant crystal structure and the characterizations of several DnrK variants, the insertion of a single amino acid in DnrK (S297) is sufficient for gaining a hydroxylation function, which is likely caused by carbanion stabilization through active site solvent restriction. Despite large differences in the three-dimensional structures of the oxygenases and the potential for multiple oxygen activation mechanisms, all the enzymes in my studies rely on carbanion intermediates to activate oxygen from either flavins or their substrates. This thesis provides interesting examples of divergent evolution and the prevalence of carbanion intermediates within polyketide biosynthesis. This mechanism appears to be recurrent in aromatic polyketide biosynthesis and may reflect the acidic nature of these compounds, propensity towards hydrogen bonding and their ability to delocalize π-electrons.

Flow injection analysis (FIA) determination of lead by hydride generation in banded coral skeletons /

A flow injection hydride generation direct current plasma atomic emission spectrometric (FI-HG-DCP-AES) method was developed for the determination of lead at ng.ml-l level. Potassium ferricyanide (K3Fe(CN)6) was used along with sodium tetrahydroborate(III) (NaBH4) to produce plumbane (PbH4) in an acid medium. The design of a gas-liquid separator (hydride generator) was tested and the parameters of the flow injection system were optimized to achieve a good detection limit and sample throughput. The technique developed gave a detection limit of 0.7 ng.ml-l(3ob). The precision at 20 ng.ml"* level was 1.6 % RSD with 1 1 measurements (n=l 1). Volume of sample loop was 500 |J.l. A sample throughput of 120 h"^ was achieved. The transition elements, Fe(II), FeOH), Cd(n), Co(II), Mn(n), Ni(II) and Zn(n) do not interfere in this method but 1 mg,l'l Cu(II) will suppress 50 % of the signal from a sample containing 20 ng.ml'l Pb. This method was successfully applied to determine lead in a calcium carbonate (CaC03) matrix of banded coral skeletons from Si-Chang Island in Thailand.

ESL students' perceptions of web-based prewriting activities /

Although much research has explored computer mediated communication for its application in second language instruction, there still exists a need for empirical results from research to guide practitioners who wish to introduce web-based activities into their instruction. This study was undertaken to explore collaborative online task-based activities for the instruction of ESL academic writing. Nine ESL students in their midtwenties, enrolled at a community college in Ontario, engaged in two separate online prewriting activities in both a synchronous and an asynchronous environment. The students were interviewed in order to explore their perceptions of how the activities affected the generation and organization of ideas for academic essays. These interviews were triangulated with examples of the students' online writing, nonparticipatory observations of the students' interactions, and a discussion with the course instructor. The results of the study reveal that a small majority of students felt that brainstorming in writing with their peers in an asynchronous online discussion created a grammatical and lexical framework that supported idea generation and organization. The students did not feel that the synchronous chat activity was as successful. Although they felt that this activity also contributed to the generation of ideas, synchronous chat introduced a level of difficulty in communication that hindered the students' engagement in the task and failed to assist them with the organization of their ideas. The students also noted positive aspects of the web-based activities that were not related to prewriting tasks, for example, improved typing and word processing skills. Directions for future research could explore whether online prewriting activities can assist students in the creation of essays that are syntactically or lexically complex.

Learning and healing: a wellness pedagogy for Aboriginal teacher education /

During the last 30 years Aboriginal peoples in Canada have made steady progress in reclaiming the responsibility for the education of their young people, especially in primary and secondary school. In comparison the education and or training of adult populations has not kept pace and many socioeconomic and sociocultural indicators demonstrate a ' , continued confinement of those populations to the margins of the dominant society of Canada. It is the adults, the mothers and the fathers, the grandmothers and grandfathers, the aunties and uncles that are the first teachers of the next generation and the nature of these relationships replicates the culture of unwellness in each subsequent generation through those teachers. There are few examples in the Aboriginal adult education literatures that give voice to the educational experience of the Learner. This study addresses that gap by exploring the perspectives embedded in the stories of a Circle of Learners who are, or were enrolled in the Bachelor of Education in Aboriginal Adult Education program at Brock University. That Circle of 1 participants included 9 women and 1 man, 6 of whom were from various i Anishinabek nations while 4 represented the Hotinonshd:ni nations in southern Ontario. They are an eclectic group, representing many professions, age groups, spiritual traditions, and backgrounds. This then is their story, the story of the heaming and Healing pedagogy and an expanded vision of Aboriginal education and research at Brock University.

Implementing a question-generation strategy with bilingual students: exploring the perspectives of a beginning teacher /

This study examined the challenges associated with the explicit delivery of questiongeneration strategy with 8 Arab Canadian students from the perspective of a bilingual beginning teacher. This study took place in a private school and involved 2 stages consisting of 9 instructional sessions, and individual interviews with the students. Data gathered from these interviews and the researcher's field notes from the sessions were used to gain insights about the participants' understanding and use of explicit instruction. The themes that emerged from the data included "teacher attitude," "students' enhanced metacognitive awareness and strategy use," "listening skills," and "instructional challenges." Briefly, teacher's attitude demonstrated how teacher's beliefs and knowledge influenced her willingness and perseverance to teach explicitly. Students' enhanced metacognitive awareness and strategy use included students' understanding and use of the question-generation strategy. The students' listening skills suggested that culture may influence their response to the delivery of explicit instruction. Here, the cultural expectations associated with being a good listener reinforced students' willingness to engage in this strategy. Students' prior knowledge also influenced their interaction with the question-generation strategy. Time for process versus covering content was a dominant instructional challenge. This study provides first hand information for teachers when considering how students' cultural backgrounds may affect their reactions to explicit strategy instruction.

Arsenic and germanium determination by hydride generation in the D.C. plasma optical emission spectrometer

Modifications to the commercial hydride generator, manufactured by Spectrametrics, resulted in improved operating procedure and enhancement of the arsenic and germanium signals. Experiments with arsenic(III) and arsenic(V) showed that identical reiults could be produced from both oxidation states. However, since arsenic(V) is reduced more slowly than arsenic(III), peak areas and not peak heights must be measured when the arsine is immediately stripped from the system (approximately 5 seconds reaction). When the reduction is allowed to proceed for 20 seconds before the arsine is stripped, peak heights may be used. For a 200 ng/mL solution, the relative standard deviation is 2.8% for As(III) and 3.8% for As(V). The detection limit for arsenic using the modified system is 0.50 ng/mL. Studies performed on As(V) standards show that the interferences from 1000 mg/L of nickel(II), cobalt(II), iron(III), copper(II), cadmium(II), and zinc(II) can be eliminated with the aid of 5 M Hel and 3% L-cystine. Conditions for the reduction of germanium to the corresponding hydride were investigated. The effect of different concentrations of HCl on the reduction of germanium to the covalent hydride in aqueous media by means of NaBH 4 solutions was assessed. Results show that the best response is accomplished at a pH of 1.7. The use of buffer solutions was similarly characterized. In both cases, results showed that the element is best reduced when the final pH of the solution after reaction is almost neutral. In addition, a more sensitive method, which includes the use of (NH4)2S208' has been developed. A 20% increase in the germanium signal is registered when compared to the signal achieved with Hel alone. Moreover, under these conditions, reduction of germanium could be accomplished, even when the solution's pH is neutral. For a 100 ng/mL germanium standard the rsd is 3%. The detection limit for germanium in 0.05 M Hel medium (pH 1.7) is 0.10 ng/mL and 0.09 ng/mL when ammonium persulphate is used in conjunction with Hel. Interferences from 1000 mg/L of iron(III), copper(II), cobalt(II), nickel(II), cadmium(II), lead(II), mercury(II), aluminum(III), tin(IV), arsenic(III), arsenic(V) and zinc(II) were studied and characterized. In this regard, the use of (NH4)ZS20S and Hel at a pH of 1.7 proved to be a successful mixture in the sbppression of the interferences caused by iron, copper, aluminum, tin, lead, and arsenic. The method was applied to the determination of germanium in cherts and iron ores. In addition, experiments with tin(IV) showed that a 15% increase in the tin signal can be accomplished in the presence of 1 mL of (NH4)2S20S 10% (m/V).

Arsenic speciation by ion-exchange chromatography with on- line determination by hydride generation: electronic modification of the D.C. plasma by photon counting

A method using L-cysteine for the determination of arsenous acid (As(III)), arsenic acid (As(V)), monomethylarsonic acid (MMAA), and dimethylarsinic acid (DMAA) by hydride generation was demonstrated. The instrument used was a d.c. plasma atomic emission spectrometer (OCP-AES). Complete recovery was reported for As(III), As(V), and DMAA while 86% recovery was reported for MMAA. Detection limits were determined, as arsenic for the species listed previously, to be 1.2, 0.8, 1.1, and 1.0 ngemL-l, respectively. Precision values, at 50 ngemL-1 arsenic concentration, were f.80/0, 2.50/0, 2.6% and 2.6% relative standard deviation, respectively. The L-cysteine reagent was compared directly with the conventional hydride generation technique which uses a potassium iodide-hydrochloric acid medium. Recoveries using L-cysteine when compared with the conventional method provided the following results: similar recoveries were obtained for As(III), slightly better recoveries were obtained for As(V) and MMAA, and significantly better recoveries for DMAA. In addition, tall and sharp peak shapes were observed for all four species when using L-cysteine. The arsenic speciation method involved separation by ion exchange .. high perfonnance liquid chromatography (HPLC) with on-line hydride generation using the L.. cysteine reagent and measurement byOCP-AES. Total analysis time per sample was 12 min while the time between the start of subsequent runs was approximately 20 min. A binary . gradient elution program, which incorporated the following two eluents: 0.01 and 0.5 mM tri.. sodium citrate both containing 5% methanol (v/v) and both at a pH of approximately 9, was used during the separation by HPLC. Recoveries of the four species which were measured as peak area, and were normalized against As(III), were 880/0, 290/0, and 40% for DMAA, MMAA and As(V), respectively. Resolution factors between adjacent analyte peaks of As(III) and DMAA was 1.1; DMAA and MMAA was 1.3; and MMAA and As(V) was 8.6. During the arsenic speciation study, signals from the d.c. plasma optical system were measured using a new photon-signal integrating device. The_new photon integrator developed and built in this laboratory was based on a previously published design which was further modified to reflect current available hardware. This photon integrator was interfaced to a personal computer through an AID convertor. The .photon integrator has adjustable threshold settings and an adjustable post-gain device.

Continuous hydride generation in the presence of L- cysteine for the determination of arsenic, bismuth, antimony and tin in steels by inductively coupled plasma atomic emission spectrometry

Arsenic, bismuth, germanium, antimony and tin were simultaneously determined by continuous hydride generation and inductively coupled plasma-atomic emission spectrometry . I Hydrides were introduced into four different types of gas-liquid separators. Two of the gas-liquid separators were available in-house. A third was developed for this project and a fourth was based on a design used by CET AC. The best signal intensity was achieved by the type II frit-based gas-liquid separator, but the modified Cetac design gave promise for the future, due to low relative standard deviation. A method was developed for the determination of arsenic, bismuth, antimony and tin in low-alloy steels. Four standard reference materials from NIST were dissolved in 10 mL aqua regia without heat. Good agreement was obtained between experimental values and certified values for arsenic, bismuth, antimony and tin. The method was developed to provide the analyst with the opportunity to determine the analytes by using simple aqueous standards to prepare calibration lines. Within the limits of the samples analyzed, the method developed is independent of matrix.