Conjugated polymer nanoparticles for effective siRNA delivery to tobacco BY-2 protoplasts

Background Post transcriptional gene silencing (PTGS) is a mechanism harnessed by plant biologists to knock down gene expression. siRNAs contribute to PTGS that are synthesized from mRNAs or viral RNAs and function to guide cellular endoribonucleases to target mRNAs for degradation. Plant biologists have employed electroporation to deliver artificial siRNAs to plant protoplasts to study gene expression mechanisms at the single cell level. One drawback of electroporation is the extensive loss of viable protoplasts that occurs as a result of the transfection technology. Results We employed fluorescent conjugated polymer nanoparticles (CPNs) to deliver siRNAs and knockdown a target gene in plant protoplasts. CPNs are non toxic to protoplasts, having little impact on viability over a 72 h period. Microscopy and flow cytometry reveal that CPNs can penetrate protoplasts within 2 h of delivery. Cellular uptake of CPNs/siRNA complexes were easily monitored using epifluorescence microscopy. We also demonstrate that CPNs can deliver siRNAs targeting specific genes in the cellulose biosynthesis pathway (NtCesA-1a and NtCesA-1b). Conclusions While prior work showed that NtCesA-1 is a factor involved in cell wall synthesis in whole plants, we demonstrate that the same gene plays an essential role in cell wall regeneration in isolated protoplasts. Cell wall biosynthesis is central to cell elongation, plant growth and development. The experiments presented here shows that NtCesA is also a factor in cell viability. We show that CPNs are valuable vehicles for delivering siRNAs to plant protoplasts to study vital cellular pathways at the single cell level.

Algal Calcification and Silicification

The algae represent major producers of calcium carbonate and silica among the world's biota. Calcification involves the precipitation of CaCO3 from Ca2+ and CO32− ions. Algal calcification by coccolithophores may account for up to half of global oceanic CaCO3 production. Silicification, the transformation of silicic acid into skeletal material, occurs in a few algal groups. The abundant diatoms represent the major silicifiers, playing a key role in marine silica cycling. Fossilised diatomaceous deposits have long been exploited for building and filling materials. Biomineralisation of calcium and silicon require homeostatic ion controls that are well characterised for Ca2+ and H+ in coccolithophores. Calcification occurs in an alkalinised vesicle, while silicification requires an acidic pH. Research on silicification remains focused upon cell wall development. Initiation and development of structures that are mineralised intracellularly requires initiation and regulation by organic components within the vesicles. Low-temperature, low-pressure biogenic formation of silica and calcite has potential for biotechnological application in novel industrial processes.

Algal Calcification and Silicification

The algae represent major producers of calcium carbonate and silica among the world's biota. Calcification involves the precipitation of CaCO3 from Ca2+ and CO32− ions. Algal calcification by coccolithophores may account for up to half of global oceanic CaCO3 production. Silicification, the transformation of silicic acid into skeletal material, occurs in a few algal groups. The abundant diatoms represent the major silicifiers, playing a key role in marine silica cycling. Fossilised diatomaceous deposits have long been exploited for building and filling materials. Biomineralisation of calcium and silicon require homeostatic ion controls that are well characterised for Ca2+ and H+ in coccolithophores. Calcification occurs in an alkalinised vesicle, while silicification requires an acidic pH. Research on silicification remains focused upon cell wall development. Initiation and development of structures that are mineralised intracellularly requires initiation and regulation by organic components within the vesicles. Low-temperature, low-pressure biogenic formation of silica and calcite has potential for biotechnological application in novel industrial processes.

Structure and lipid interactions of membrane-associated glycosyltransferases : Cationic patches and anionic lipids regulate biomembrane binding of both GT-A and GT-B enzymes

This thesis concerns work on structure and membrane interactions of enzymes involved in lipid synthesis, biomembrane and cell wall regulation and cell defense processes. These proteins, known as glycosyltransferases (GTs), are involved in the transfer of sugar moieties from nucleotide sugars to lipids or chitin polymers. Glycosyltransferases from three types of organisms have been investigated; one is responsible for vital lipid synthesis in Arabidopsis thaliana (atDGD2) and adjusts the lipid content in biomembranes if the plant experiences stressful growth conditions. This enzyme shares many structural features with another GT found in gram-negative bacteria (WaaG). WaaG is however continuously active and involved in synthesis of the protective lipopolysaccharide layer in the cell walls of Escherichia coli. The third type of enzymes investigated here are chitin synthases (ChS) coupled to filamentous growth in the oomycete Saprolegnia monoica. I have investigated two ChS-derived MIT domains that may be involved in membrane interactions within the endosomal pathway. From analysis of the three-dimensional structure and the amino-acid sequence, some important regions of these very large proteins were selected for in vitro studies. By the use of an array of biophysical methods (e.g. Nuclear Magnetic Resonance, Fluorescence and Circular Dichroism spectroscopy) and directed sequence analyses it was possible to shed light on some important details regarding the structure and membrane-interacting properties of the GTs. The importance of basic amino-acid residues and hydrophobic anchoring segments, both generally and for the abovementioned proteins specifically, is discussed. Also, the topology and amino-acid sequence of GT-B enzymes of the GT4 family are analyzed with emphasis on their biomembrane association modes. The results presented herein regarding the structural and lipid-interacting properties of GTs aid in the general understanding of glycosyltransferase activity. Since GTs are involved in a high number of biochemical processes in vivo it is of outmost importance to understand the underlying processes responsible for their activity, structure and interaction events. The results are likely to be useful for many applications and future experimental design within life sciences and biomedicine.

Development of Imaging Mass Spectrometry Analysis of Lipids in Biological and Clinically Relevant Applications

La spectrométrie de masse mesure la masse des ions selon leur rapport masse sur charge. Cette technique est employée dans plusieurs domaines et peut analyser des mélanges complexes. L’imagerie par spectrométrie de masse (Imaging Mass Spectrometry en anglais, IMS), une branche de la spectrométrie de masse, permet l’analyse des ions sur une surface, tout en conservant l’organisation spatiale des ions détectés. Jusqu’à présent, les échantillons les plus étudiés en IMS sont des sections tissulaires végétales ou animales. Parmi les molécules couramment analysées par l’IMS, les lipides ont suscité beaucoup d'intérêt. Les lipides sont impliqués dans les maladies et le fonctionnement normal des cellules; ils forment la membrane cellulaire et ont plusieurs rôles, comme celui de réguler des événements cellulaires. Considérant l’implication des lipides dans la biologie et la capacité du MALDI IMS à les analyser, nous avons développé des stratégies analytiques pour la manipulation des échantillons et l’analyse de larges ensembles de données lipidiques. La dégradation des lipides est très importante dans l’industrie alimentaire. De la même façon, les lipides des sections tissulaires risquent de se dégrader. Leurs produits de dégradation peuvent donc introduire des artefacts dans l’analyse IMS ainsi que la perte d’espèces lipidiques pouvant nuire à la précision des mesures d’abondance. Puisque les lipides oxydés sont aussi des médiateurs importants dans le développement de plusieurs maladies, leur réelle préservation devient donc critique. Dans les études multi-institutionnelles où les échantillons sont souvent transportés d’un emplacement à l’autre, des protocoles adaptés et validés, et des mesures de dégradation sont nécessaires. Nos principaux résultats sont les suivants : un accroissement en fonction du temps des phospholipides oxydés et des lysophospholipides dans des conditions ambiantes, une diminution de la présence des lipides ayant des acides gras insaturés et un effet inhibitoire sur ses phénomènes de la conservation des sections au froid sous N2. A température et atmosphère ambiantes, les phospholipides sont oxydés sur une échelle de temps typique d’une préparation IMS normale (~30 minutes). Les phospholipides sont aussi décomposés en lysophospholipides sur une échelle de temps de plusieurs jours. La validation d’une méthode de manipulation d’échantillon est d’autant plus importante lorsqu’il s’agit d’analyser un plus grand nombre d’échantillons. L’athérosclérose est une maladie cardiovasculaire induite par l’accumulation de matériel cellulaire sur la paroi artérielle. Puisque l’athérosclérose est un phénomène en trois dimension (3D), l'IMS 3D en série devient donc utile, d'une part, car elle a la capacité à localiser les molécules sur la longueur totale d’une plaque athéromateuse et, d'autre part, car elle peut identifier des mécanismes moléculaires du développement ou de la rupture des plaques. l'IMS 3D en série fait face à certains défis spécifiques, dont beaucoup se rapportent simplement à la reconstruction en 3D et à l’interprétation de la reconstruction moléculaire en temps réel. En tenant compte de ces objectifs et en utilisant l’IMS des lipides pour l’étude des plaques d’athérosclérose d’une carotide humaine et d’un modèle murin d’athérosclérose, nous avons élaboré des méthodes «open-source» pour la reconstruction des données de l’IMS en 3D. Notre méthodologie fournit un moyen d’obtenir des visualisations de haute qualité et démontre une stratégie pour l’interprétation rapide des données de l’IMS 3D par la segmentation multivariée. L’analyse d’aortes d’un modèle murin a été le point de départ pour le développement des méthodes car ce sont des échantillons mieux contrôlés. En corrélant les données acquises en mode d’ionisation positive et négative, l’IMS en 3D a permis de démontrer une accumulation des phospholipides dans les sinus aortiques. De plus, l’IMS par AgLDI a mis en évidence une localisation différentielle des acides gras libres, du cholestérol, des esters du cholestérol et des triglycérides. La segmentation multivariée des signaux lipidiques suite à l’analyse par IMS d’une carotide humaine démontre une histologie moléculaire corrélée avec le degré de sténose de l’artère. Ces recherches aident à mieux comprendre la complexité biologique de l’athérosclérose et peuvent possiblement prédire le développement de certains cas cliniques. La métastase au foie du cancer colorectal (Colorectal cancer liver metastasis en anglais, CRCLM) est la maladie métastatique du cancer colorectal primaire, un des cancers le plus fréquent au monde. L’évaluation et le pronostic des tumeurs CRCLM sont effectués avec l’histopathologie avec une marge d’erreur. Nous avons utilisé l’IMS des lipides pour identifier les compartiments histologiques du CRCLM et extraire leurs signatures lipidiques. En exploitant ces signatures moléculaires, nous avons pu déterminer un score histopathologique quantitatif et objectif et qui corrèle avec le pronostic. De plus, par la dissection des signatures lipidiques, nous avons identifié des espèces lipidiques individuelles qui sont discriminants des différentes histologies du CRCLM et qui peuvent potentiellement être utilisées comme des biomarqueurs pour la détermination de la réponse à la thérapie. Plus spécifiquement, nous avons trouvé une série de plasmalogènes et sphingolipides qui permettent de distinguer deux différents types de nécrose (infarct-like necrosis et usual necrosis en anglais, ILN et UN, respectivement). L’ILN est associé avec la réponse aux traitements chimiothérapiques, alors que l’UN est associé au fonctionnement normal de la tumeur.

Computer simulations of soft particles in flow

Understanding the dynamics of blood cells is a crucial element to discover biological mechanisms, to develop new efficient drugs, design sophisticated microfluidic devices, for diagnostics. In this work, we focus on the dynamics of red blood cells in microvascular flow. Microvascular blood flow resistance has a strong impact on cardiovascular function and tissue perfusion. The flow resistance in microcirculation is governed by flow behavior of blood through a complex network of vessels, where the distribution of red blood cells across vessel cross-sections may be significantly distorted at vessel bifurcations and junctions. We investigate the development of blood flow and its resistance starting from a dispersed configuration of red blood cells in simulations for different hematocrits, flow rates, vessel diameters, and aggregation interactions between red blood cells. Initially dispersed red blood cells migrate toward the vessel center leading to the formation of a cell-free layer near the wall and to a decrease of the flow resistance. The development of cell-free layer appears to be nearly universal when scaled with a characteristic shear rate of the flow, which allows an estimation of the length of a vessel required for full flow development, $l_c \approx 25D$, with vessel diameter $D$. Thus, the potential effect of red blood cell dispersion at vessel bifurcations and junctions on the flow resistance may be significant in vessels which are shorter or comparable to the length $l_c$. The presence of aggregation interactions between red blood cells lead in general to a reduction of blood flow resistance. The development of the cell-free layer thickness looks similar for both cases with and without aggregation interactions. Although, attractive interactions result in a larger cell-free layer plateau values. However, because the aggregation forces are short-ranged at high enough shear rates ($\bar{\dot{\gamma}} \gtrsim 50~\text{s}^{-1}$) aggregation of red blood cells does not bring a significant change to the blood flow properties. Also, we develop a simple theoretical model which is able to describe the converged cell-free-layer thickness with respect to flow rate assuming steady-state flow. The model is based on the balance between a lift force on red blood cells due to cell-wall hydrodynamic interactions and shear-induced effective pressure due to cell-cell interactions in flow. We expect that these results can also be used to better understand the flow behavior of other suspensions of deformable particles such as vesicles, capsules, and cells. Finally, we investigate segregation phenomena in blood as a two-component suspension under Poiseuille flow, consisting of red blood cells and target cells. The spatial distribution of particles in blood flow is very important. For example, in case of nanoparticle drug delivery, the particles need to come closer to microvessel walls, in order to adhere and bring the drug to a target position within the microvasculature. Here we consider that segregation can be described as a competition between shear-induced diffusion and the lift force that pushes every soft particle in a flow away from the wall. In order to investigate the segregation, on one hand, we have 2D DPD simulations of red blood cells and target cell of different sizes, on the other hand the Fokker-Planck equation for steady state. For the equation we measure force profile, particle distribution and diffusion constant across the channel. We compare simulation results with those from the Fokker-Planck equation and find a very good correspondence between the two approaches. Moreover, we investigate the diffusion behavior of target particles for different hematocrit values and shear rates. Our simulation results indicate that diffusion constant increases with increasing hematocrit and depends linearly on shear rate. The third part of the study describes development of a simulation model of complex vascular geometries. The development of the model is important to reproduce vascular systems of small pieces of tissues which might be gotten from MRI or microscope images. The simulation model of the complex vascular systems might be divided into three parts: modeling the geometry, developing in- and outflow boundary conditions, and simulation domain decomposition for an efficient computation. We have found that for the in- and outflow boundary conditions it is better to use the SDPD fluid than DPD one because of the density fluctuations along the channel of the latter. During the flow in a straight channel, it is difficult to control the density of the DPD fluid. However, the SDPD fluid has not that shortcoming even in more complex channels with many branches and in- and outflows because the force acting on particles is calculated also depending on the local density of the fluid.

Effets des procédés d’usinage de finition sur les propriétés de surface, la performance d’un vernis et l’émission de poussières du bois de chêne rouge

La performance d’un produit de finition sur le bois est influencée par la manière dont la surface est préparée. Le ponçage est très utilisé pour préparer les surfaces lors de la finition. Toutefois, ce procédé génère une grande quantité de poussières. Ainsi, les effets des procédés d’usinage sur les propriétés de surface, la performance d’un vernis et l’émission de poussières ont été étudiés dans le but de déterminer les modes de préparation des surfaces les plus adéquats pour le bois de chêne rouge. Dans un premier volet, les propriétés de surface et la performance d’un vernis ont été évaluées sur les surfaces préparées à l’aide du procédé traditionnel de ponçage et de trois procédés alternatifs de rabotage soit la coupe périphérique droite, la coupe hélicoïdale et la coupe oblique. La qualité de surface a été évaluée au moyen des caractéristiques de rugosité, d’endommagement cellulaire et de mouillabilité. Des essais de résistance à l’adhésion d’un vernis d’usage intérieur ont été effectués avant et après un traitement de vieillissement accéléré. Les résultats ont montré que le ponçage a induit une rugosité et un niveau de fibrillation supérieurs à ceux des autres procédés, ainsi qu’une mouillabilité et une adhésion du vernis après vieillissement accéléré élevées. Les surfaces rabotées avec la coupe périphérique droite ont présenté un certain niveau de fibrillation, une rugosité et une mouillabilité intermédiaires. Néanmoins, l’adhésion du vernis après vieillissement a été également inférieure par rapport aux autres procédés. La coupe hélicoïdale a produit une rugosité intermédiaire. D’autre part, la coupe oblique a été le procédé qui a présenté une perte d’adhésion après vieillissement similaire au ponçage. Ce procédé a généré des surfaces lisses avec rugosité et mouillabilité intermédiaires. Sur la base des résultats obtenus, le ponçage à l’aide d’un programme P100-grain et une vitesse d’avance de 7 m/min, la coupe périphérique droite avec un angle d’attaque de 25° et une onde d’usinage de 1,0 mm, la coupe hélicoïdale avec une onde d’usinage de 1,0 mm et la coupe oblique realisé avec un angle oblique de 15° ont permis d’obtenir les meilleures conditions d’usinage pour chaque procédé. Dans un deuxième volet, l’effet de différents paramètres de coupe sur l’émission de poussières et la rugosité de la surface a été étudié lors de la coupe hélicoïdale. Les émissions de poussières ont diminué avec la diminution de laprofondeur de coupe et l’augmentation de l’épaisseur moyenne du copeau. Cependant, les surfaces obtenues avec l’épaisseur moyenne du copeau plus élevée ont présenté une rugosité supérieure. Par contre, si une surface plus lisse est requise, une vitesse d’avance intermédiaire doit être utilisée afin de diminuer la rugosité des surfaces sans exposer les travailleurs à des niveaux élevés de poussière de bois. Par ailleurs, l’émission de poussières pour chaque fraction de particules peut être estimée à travers les modèles développés.

Whipple’s disease infection surgical treatment: presentation of a rare case and literature review

The Whipple’ Disease (W.D.) is a very rare disease with an incidence of 1 per 1.000.000 inhabitants; it is a systemic infection that may mimic a wide spectrum of clinical disorders, which may have a fatal outcome and affects mainly male 40-50 years old. The infective agent is an actinomycete, Tropheryma Whipplei (T.W.) that was isolated 100 years after first description by Wipple, and identified in macrophages of mucosa of the small intestine by biopsy which is characterized by periodic acid-Schiff-positive, products of the inner membrane of his polysaccharide bacterial cell wall. The multisystemic clinical manifestations evolve rapidly towards an organic decay characterized by weight loss, malabsorption, diarrhea, polyathralgia, opthalmoplegia, neuro-psychiatric disorders and sometimes associated to endocarditis. Early antibiotic treatment with trimethoprim and sulfometathaxazole reduces the fatal evolution of the disease. The authors present a rare experience about a female subject in which the clinical gastrointestinal signs were preceded by neuro-psychiatric disorders, and evolved into obstruction and intestinal perforation which required an emergency surgery with temporary ileostomy, recanalized only after adequate medical treatment with a full dose of antibiotic and resolution of clinical disease for the high risks of fistulae for the edema and lymphadenopathy of mucosa. The diagnosis was histologically examined by intestinal biopsy performed during surgery, which showed PAS-positive histiocytes, while PRC polymerase RNA was negative, which confirms the high sensibility of PAS positive and low specificity of RNA polymerase for T.W.

Expression-based and co-localization detection of arabinogalactan protein 6 and arabinogalactan protein 11 interactors in Arabidopsis pollen and pollen tubes

Arabinogalactan proteins (AGPs) are cell wall proteoglycans that have been shown to be important for pollen development. An Arabidopsis double null mutant for two pollen-specific AGPs (agp6 agp11) showed reduced pollen tube growth and compromised response to germination cues in vivo. A microarray experiment was performed on agp6 agp11 pollen tubes to search for genetic interactions in the context of pollen tube growth. A yeast two-hybrid experiment for AGP6 and AGP11 was also designed.

Whole Genome Analysis of Gene Expression Reveals Coordinated Activation of Signaling and Metabolic Pathways during Pollen-Pistil Interactions in Arabidopsis

Plant reproduction depends on the concerted activation of many genes to ensure correct communication between pollen and pistil. Here, we queried the whole transcriptome of Arabidopsis (Arabidopsis thaliana) in order to identify genes with specific reproductive functions. We used the Affymetrix ATH1 whole genome array to profile wild-type unpollinated pistils and unfertilized ovules. By comparing the expression profile of pistils at 0.5, 3.5, and 8.0 h after pollination and applying a number of statistical and bioinformatics criteria, we found 1,373 genes differentially regulated during pollen-pistil interactions. Robust clustering analysis grouped these genes in 16 time-course clusters representing distinct patterns of regulation. Coregulation within each cluster suggests the presence of distinct genetic pathways, which might be under the control of specific transcriptional regulators. A total of 78% of the regulated genes were expressed initially in unpollinated pistil and/or ovules, 15% were initially detected in the pollen data sets as enriched or preferentially expressed, and 7% were induced upon pollination. Among those, we found a particular enrichment for unknown transcripts predicted to encode secreted proteins or representing signaling and cell wall-related proteins, which may function by remodeling the extracellular matrix or as extracellular signaling molecules. A strict regulatory control in various metabolic pathways suggests that fine-tuning of the biochemical and physiological cellular environment is crucial for reproductive success. Our study provides a unique and detailed temporal and spatial gene expression profile of in vivo pollen-pistil interactions, providing a framework to better understand the basis of the molecular mechanisms operating during the reproductive process in higher plants.

Intercepting Cyclic Dinucleotide Signaling with Small Molecules

Bacterial infections, especially the ones that are caused by multidrug-resistant strains, are becoming increasingly difficult to treat and put enormous stress on healthcare systems. Recently President Obama announced a new initiative to combat the growing problem of antibiotic resistance. New types of antibiotic drugs are always in need to catch up with the rapid speed of bacterial drug-resistance acquisition. Bacterial second messengers, cyclic dinucleotides, play important roles in signal transduction and therefore are currently generating great buzz in the microbiology community because it is believed that small molecules that inhibit cyclic dinucleotide signaling could become next-generation antibacterial agents. The first identified cyclic dinucleotide, c-di-GMP, has now been shown to regulate a large number of processes, such as virulence, biofilm formation, cell cycle, quorum sensing, etc. Recently, another cyclic dinucleotide, c-di-AMP, has emerged as a regulator of key processes in Gram-positive and mycobacteria. C-di-AMP is now known to regulate DNA damage sensing, fatty acid synthesis, potassium ion transport, cell wall homeostasis and host type I interferon response induction. Due to the central roles that cyclic dinucleotides play in bacteria, we are interested in small molecules that intercept cyclic dinucleotide signaling with the hope that these molecules would help us learn more details about cyclic dinucleotide signaling or could be used to inhibit bacterial viability or virulence. This dissertation documents the development of several small molecule inhibitors of a cyclic dinucleotide synthase (DisA from B. subtilis) and phosphodiesterases (RocR from P. aeruginosa and CdnP from M. tuberculosis). We also demonstrate that an inhibitor of RocR PDE can inhibit bacterial swarming motility, which is a virulence factor.

Functional studies of lignin biosynthesis genes and putative flowering gene in Miscanthus x giganteus and studies on indolyl glucosinolate biosynthesis and translocation in Brassica oleracea

The first topic area of this thesis involved studies on the accumulation and translocation of glucosinolates (GSs), bioactive secondary plant compounds, in broccoli plants. Changes in GS accumulation and gene expression levels in response to exogeneous methyl jasmonate (MeJA) treatment were analyzed in different tissue types at different developmental stages of broccoli. Greater accumulation of GSs with MeJA treatment was observed in apical leaves of broccoli seedlings and florets of plants at harvest maturity. Increases in indolyl GS in apical leaves of seedlings and florets were coupled with the up-regulation of indolyl GS biosynthesis genes. The accumulation of indolyl GSs appears to be modulated by MeJA treatment in an organ-specific manner for optimal distribution of defense substances in the plant. Metabolic profiling of hydrophilic metabolites using GC-MS demonstrated increased accumulation of various phenolics, ascorbates and amino acids in broccoli tissues after MeJA treatment. Distinct changes in carbohydrate levels observed between different tissues (vegetative leaves and floret tissues) of broccoli plants after treatment suggest that carbon metabolism is differentially modulated by MeJA treatment in different tissue types depending on sink-source relationships. Reduced levels of hexose sugars and tricarboxylic acid intermediates after MeJA treatment may reflect the increased requirement for carbon and energy needed to drive secondary product biosynthesis to accumulate metabolites for defense against insects and other herbivores. Substantial increases of indolyl and aromatic GSs after exogenous treatment with MeJA in stem and petioles of seedlings and the existence of intact indolyl-GS forms in phloem exudates suggest enhanced de novo synthesis in combination with active transport. Indoly GSs share structural similarities with the auxin, IAA, and may interact with components of the auxin transport system for intra- and extra-cellular transport or translocation. Application of the auxin efflux inhibitor, 1-naphthylphthalamic acid (NPA) reduced MeJA-mediated accumulation of indolyl GSs in broccoli florets and seedling tissues. NPA did not inhibit expression of indolyl GS biosynthesis genes shown to be upregulated by MeJA treatment or the accumulation of tryptophan, the amino acid precursor of indolyl GSs. Exogenous application of benzyl GS to Arabidopsis roots induced ectopic expression of the PIN1 protein associated with the auxin transport system similar to treatment with NPA, again suggesting GS interaction with the auxin efflux carrier system. The inhibitory effect of NPA on MeJA-mediated accumulation of GS may be due to competitive binding of NPA to auxin efflux carrier components and that GS transport is mediated by the auxin transport system. The inhibitory effect of NPA on indolyl and aromatic GS accumulation and the bioactivity of exogenous treatment of these GS compounds in PIN1 localization, Arabidopsis root growth, and gravitrophic response suggest that indolyl and aromatic GSs may be antagonistic to IAA transport and biosynthesis. Indolyl and aromatic GSs can also be potentially converted into IAA by hydrolysis. This intrinsic feature of GSs may be the part of a sophisticated regulatory process where the metabolic pathways in the plant shift from active growth to a reversible defense posture in response to biotic or abiotic stress. It seems likely that indolyl and aromatic GSs are important compounds that provide connections between jasmonate and auxin signaling. Further studies are required to reveal the regulatory mechanism for crosstalk between the two hormones. The third part of this research was to investigate effect of selenium fertilization and MeJA treatment on accumulation of GSs in broccoli florets. Increasing dietary intake of the element selenium (Se) has been shown to reduce the risk of cancer. Simultaneous enhancement of both Se and GS concentrations in broccoli floret tissue were conducted through the combined treatment of MeJA with Se fertilization. A low level of Se fertilization (concentration) with MeJA treatment displayed no significant changes in total aliphatic GS concentrations with 90% and 50% increases in indolyl and total GSs concentrations, respectively. This result suggests that Se- and GS-enriched broccoli with improved health-promoting properties can be generated by this combined treatment. The second topic of this thesis was conducted to provide basic information required to improve biomass quality and productivity and develop tools for gene transformation in Miscanthus x giganteus. The perennial rhizomatous grass, Miscanthus x giganteus is an ideal biomass crop due to its rapid vegetative growth and high biomass yield potential. As a naturally occurring sterile hybrid, M. x giganteus must be propagated vegetatively by mechanicalling divided rhizomes or from micropropagated plantlets. The effect of callus type, age and culture methods on regeneration competence was studied to improve regeneration efficiency and shorten the period of tissue culture in M. x giganteus propagation. Seven lignin biosynthesis genes and one putative flowering gene were isolated from M. x giganteus by PCR reactions using maize othologous sequences. Southern hybridization and nuclear DNA content analysis indicated that the genes isolated from M. x giganteus exist in the genome of other Miscanthus species as multiple copies. Analysis of lignin content and histological staining of lignin deposition indicated that higher lignin content is found in mature stem node tissues compared to young leaves and apical stem nodal tissues. Cell wall lignification is associated with increasing tissue maturity in Miscanthus species. RNAi and antisense constructs harboring sequences of these genes were developed to generate Miscanthus transgenic plants with suppressed of lignin biosynthesis and delayed flowering.

Improvement of the yeast slide culture technique

Este trabalho tem como objetivo melhorar a técnica de cultura em lâmina para ser usada na avaliação da viabilidade de leveduras sob diferentes condições fisiológicas. Inicialmente, foram otimizadas as condições ideais para o cultivo em lâmina de uma estirpe laboratorial (BY4741) e de uma estirpe industrial (NCYC 1214) da levedura Saccharomyces cerevisiae. O melhor protocolo foi obtido utilizando: YEPD agar com uma espessura de cerca de 2 mm; 20 μL de uma suspensão de 1 x 105 células/mL para a estirpe BY4741 ou de 5 x 104 células/mL para a estirpe NCYC 1214; uma câmara de humedecimento com 100 μL de água desionizada e um tempo de incubação de 24 h, a 25 ° C. Com o objetivo de facilitar a contagem das microcolónias, foi adicionado um corante (calcofluor white, CFW) ao meio YEPD agar. Ensaios preliminares, em YEPD líquido, contendo diferentes concentrações de CFW, permitiram verificar que o corante, até 5,0 μg/L, não inibe o crescimento da levedura. Uma concentração de 2,5 μg/L de CFW permitiu a coloração da parede das leveduras, não se observando células com morfologia alterada, sendo esta a concentração de CFW selecionado nos estudos subsequentes. A técnica de cultura em lâmina, com ou sem CFW, foi aplicada para avaliar a viabilidade de células saudáveis (células em fase exponencial de crescimento), células submetidas a stress de etanol [células expostas a 20% (v/v) de etanol, a 25 ºC, durante 2 h] e células envelhecidas (células incubadas em água, a 25 ° C, durante 48 h), da estirpe laboratorial. A percentagem de células viáveis não foi significativamente diferente entre as duas técnicas (com ou sem CFW), após uma incubação de 24 horas. Finalmente, a técnica de cultura de lâmina, contendo CFW, foi comparada com duas técnicas habitualmente usadas na indústria cervejeira: fermentação de curta duração e determinação da percentagem de células gemuladas. Os resultados obtidos através da técnica de cultura de lâmina, desenvolvida, seguem um padrão similar aos obtidos nos ensaios de fermentação de curta duração e aos da determinação da percentagem de células gemuladas. Os resultados obtidos sugerem que a técnica de cultura em lâmina, combinada com CFW, parece ser uma alternativa, fácil, rápida (em 24 h) e reprodutível, relativamente ao método convencional (técnica de plaqueamento), para a avaliação da viabilidade de células de levedura. Deverá ser realizado trabalho adicional a fim de validar o método com estirpes industriais.

Recuperação de carotenóides microbianos por diferentes técnicas de ruptura celular

O objetivo deste trabalho foi utilizar diferentes técnicas químicas (dimetilsulfóxido, ácido clorídrico, acético e lático), técnicas mecânicas (banho ultrassônico, abrasão com pérolas de vidro, maceração com terra diatomácea, ruptor ultrassônico e imersão em nitrogênio líquido) e técnica enzimática (preparado enzimático comercial Glucanex®) para a recuperação de carotenoides a partir da ruptura da parede celular das leveduras Sporidiobolus pararoseus e Rhodotorula mucilaginosa isoladas de amostras ambientais. Para isso a obtenção de biomassa foi realizada através de cultivos submersos no meio YM, a 25 °C, 180 rpm por 168 h. Para a ruptura celular, a operação de congelamento da biomassa (-18°C por 48 h) foi estudada. Os métodos de secagem convencional por ar forçado (35°C/48h) e liofilização (-80°C/48h, em ultrafreezer, seguido de liofilizador até alcançar 2% de umidade da amostra) também foram avaliados. Nas técnicas químicas aplicadas, o dimetilsulfóxido apresentou os melhores resultados para as duas leveduras, porém o seu uso é limitado devido a sua toxicidade. Para S. pararoseus, os maiores valores encontrados foram para o ácido clorídrico, seguido do acético e do lático, sendo detectada diferença entre eles quando aplicado o congelamento. Com R. mucilaginosa, os maiores valores foram encontrados para os ácidos acético e lático, seguido do ácido clorídrico, no qual o congelamento da biomassa também não influenciou a recuperação dos carotenoides. Dentre as técnicas mecânicas estudadas, para a levedura S. pararoseus, o banho ultrassônico e a abrasão com pérolas de vidro apresentaram os resultados mais promissores comparados ao DMSO (84,79±2,34 e 76,87±2,06 μg/g respectivamente), onde o processo de congelamento da biomassa não influenciou positivamente no percentual de extratibilidade e na concentração específica dos carotenoides quando utilizada estas técnicas. Com Rhodotorula mucilaginosa, o banho ultrassônico propiciou a recuperação da maior concentração específica de carotenoides (193,5±25,8 μg/g), sendo que o processo de congelamento também não influenciou positivamente no percentual de extratibilidade e na concentração específica dos carotenoides. Através do Delineamento Central Composto Rotacional (DCCR) 23 foi possível avaliar que a levedura S. pararoseus não demonstrou nenhum efeito sob as variáveis pH, temperatura e concentração de enzima. Assim, a melhor condição de trabalho escolhida foi pH 7,4, 30 ºC e concentração de enzima de 1,0 g/gcs, onde apresentou a concentração específica de 42,6 μg/g e volumétrica de 308 μg/L de carotenoides. Para R. mucilaginosa, a condição ótima foi definida como 1,0 g/gcs, pH 5,0 e temperatura de 30 ºC, onde foi encontrado 115,1±8,1 μg/g e 470,1±38,8 μg/L para a concentração específica e volumétrica de carotenoides, respectivamente. A utilização de técnicas combinadas empregando banho ultrassônico e lise enzimática não proporcionou melhorias nos resultados para ambas as leveduras. A liofilização provocou um ganho de 20% e 13,7% na concentração específica dos carotenoides das leveduras S. pararoseus e R. mucilaginosa, respectivamente, onde o congelamento da biomassa não influenciou significativamente (p<0,05) a recuperação de carotenoides provenientes das duas leveduras, podendo ser eliminada do processo. Assim, para S. pararoseus o banho ultrassônico e as pérolas de vidro apresentaram os melhores resultados na recuperação de carotenoides, e para R. mucilaginosa o melhor resultado foi alcançado com o banho ultrassônico.

The cellular and mechanistic study of nisin inhibition of bacillus anthracis spore outgrowth, nisin alteration of infection, and native producer immunity

A critical step during Bacillus anthracis infection is the outgrowth of germinated spores into vegetative bacilli that proliferate and disseminate rapidly within the host. An important challenge exists for developing chemotherapeutic agents that act upon and kill B. anthracis immediately after germination initiation when antibiotic resistance is lost, but prior to the outgrowth into vegetative bacilli, which is accompanied by toxin production. Chemical agents must also function in a manner refractive to the development of antimicrobial resistance. In this thesis we have identified the lantibiotics as a class of chemotherapeutics that are predicted to satisfy these two criteria. The objective of this thesis was to evaluate the efficacy of nisin, a prototypical lantibiotic, in prevention of outgrowth of germinated B. anthracis spores. Like all lantibiotics, nisin is a ribosomally translated peptide that undergoes post-translational modification to form (methyl)lanthionine rings that are critical for antimicrobial activity. Our studies indicate that nisin rapidly inhibits the in vitro outgrowth of germinated B. anthracis Sterne 7702 spores. Although germination initiation was shown to be essential for nisin-dependent antimicrobial activity, nisin did not inhibit or promote germination initiation. Nisin irreversibly killed germinated spores by blocking the establishment of a membrane potential and oxidative metabolism, while not affecting the dissolution of the outer spore structures. The membrane permeability of the spore was increased by nisin, but germinated spores did not undergo full lysis. Nisin was demonstrated to localize to lipid II, which is the penultimate precursor for cell wall biogenesis. This localization suggests two possible independent mechanisms of action, membrane pore formation and inhibition of peptidoglycan synthesis. Structure-activity studies with a truncated form of nisin lacking the two C-terminal (methyl)lanthionine rings and with non-pore forming mutants indicated that membrane disruption is essential for nisin-dependent inhibition of spore outgrowth to prevent membrane potential establishment. Finally, utilizing an in vitro infection model, it was shown that nisin reduced the viability of B. anthracis spores within an infection resulting in increased survival of immune cells while reducing infection-mediated cytokine expression. Fluorescence microscopy indicated that nisin localizes with spores within phagosomes of peritioneal macrophages in germinating conditions. These data demonstrate the effectiveness of nisin, as a model lantibiotic, for preventing spore outgrowth. It is speculated that nisin targeting of lipid II, resulting in membrane perturbations, may be effective at inhibiting the outgrowth of spores prepared from bacteria across a number of species.