Mueller matrix measurements of algae with different shape and size distributions.

The full Mueller matrix was measured to obtain the polarization state of the scattered light for a variety of algae with different shapes, wall compositions, sizes, and refractive indices. The experimental setup was a multiple laser Mueller matrix ellipsometer, by which measurements were performed for scattering angles from 16° to 160° sampled at every second degree for wavelengths of 473 nm and 532 nm. Previously, the polarization of light scattered from microalgae was investigated only for a few species, and the Mueller matrix was found to have little variation between the species. In our work a total of 11 algal species were investigated, representing diatoms, dinoflagellates, coccolithophorids, green algae, and a cryptophyte. The selection of species was made to obtain high variability in shape, size, cell wall, and refractive index. As in previous investigations, very small variations were found between species for most of the Mueller matrix elements, but noticeable variations were found for M(11), (M(12)+M(21))/2 and (M(33)+M(44))/2.

Genetic diversity of root anatomy in wild and cultivated Manihot species.

An anatomical study of roots was conducted on two wild Manihot species, namely M. glaziovii and M. fortalezensis, and two cassava varieties, M. esculenta Crantz variety UnB 201 and M. esculenta variety UnB 122, to identify taxonomic differences in primary growth. Anatomical characters of cassava roots have been rarely investigated. Their study may help cassava breeders to identify varieties with economically important characters, such as tolerance to drought. We investigated tap and lateral adventitious roots of two specimens of each clone or species. Free-hand cross-sections of roots were drawn; these had been clarified with 20% sodium hypochlorite solution, stained with 1% safranin-alcian blue ethanolic solution, dehydrated in ethanol series and butyl acetate and mounted in synthetic resin. Anatomical differences among Manihot species and varieties were found in the epidermal and exodermal cell shape and wall thickness, content of cortical parenchyma, and number of xylem poles. Wall thickness of the epidermis and exodermis of tap root were similar in all species, while in the lateral root there were differences in cell shape and wall thickness. Epidermal cells with thick walls were found in the tap root of all species and in lateral roots of cassava varieties. This character is apparently associated with tolerance to drought and disease. The variation in the number of xylem poles of cassava varieties was larger (4-8) than in wild species (4-6), and appears to support the hybrid origin of cassava.

A phylum level perspective on bacterial cell envelope architecture.

Improved understanding of the bacterial phylogenetic tree has allowed the distinction of at least 25 phyla with cultured representatives. This review surveys the diversity of cell envelope types present in these phyla and emphasises that it is important to define bacterial cell envelopes according to whether they have one (monoderm) or two (diderm) cellular membranes and, in the latter case, lipopolysaccharide as well. A comparative genomics approach, facilitated by the recent vast expansion in genome sequence information, is used here to survey the distribution of key lipopolysaccharide biosynthesis enzymes across the bacterial world and to consider alternative diderm cell envelope architectures. These data add to our understanding of microbial diversity and it is notable that the majority of phyla are likely to comprise diderm, lipopolysaccharide containing bacteria. This analysis and a critical review of the literature also suggest that members of the phylum Chloroflexi are typically monoderm.

Lack of effect of cell-wall targeted antibacterials on biofilm formation and antifungal susceptibility of Candida species

The use of central venous catheters (CVC) and broad-spectrum antibacterials are among the main risk factors for the development of candidemia in patients admitted to intensive care units (ICU). It is known that some antibacterials increase the resistance of these yeasts to azole antifungals. Thus, the aim of this research was to determine whether yeast present in CVC colonizations previously exposed to cell-wall targeted antibacterials benefit from a reduction in susceptibility to fluconazole and voriconazole, facilitating their ability to form biofilms. Candida albicans, C. tropicalis, C. glabrata, C. parapsilosis and C. guilhermondii were seeded into antibacterial (cefepime, meropenem, vancomycin, and piperacillin-tazobactam) gradient plates produced in Mueller-Hinton Agar. The susceptibility to fluconazole and voriconazole and the biofilm formation of the yeasts were tested before and after exposure to the antibacterials. None of the antibacterials exerted a significant effect on the in vitro susceptibility of the yeasts to the antifungal agents or on their ability to form biofilms. These results suggest that increased candidemia in ICU patients is not attributable to possible alterations in the yeasts, but is more likely caused by a weakening of the patient's general condition after long exposure to infection.

O uso de cateter venoso central (CVC) e antibióticos de amplo espectro estão entre os principais fatores de risco para o desenvolvimento da candidemia em pacientes internados em unidades de terapia intensiva (UTI). É conhecido que alguns antibióticos aumentam a resistência das leveduras aos antifúngicos azólicos. Assim, o objetivo deste estudo foi avaliar se leveduras presentes em colonização de CVC expostas a antibióticos que atuam em parede celular se beneficiam de uma redução na suscetibilidade ao fluconazol e voriconazol e se obtêm maior capacidade de formar biofilme. Candida albicans, C. tropicalis, C. glabrata,C. parapsilosis e C. guilhermondii foram semeadas em placas de Mueller-Hinton Agar, com gradientes de antibióticos (cefepima, meropenem, vancomicina e piperacilina-tazobactam). A suscetibilidade e a formação de biofilme das leveduras foram testadas antes e após a exposição aos antibióticos. Nenhum dos antibióticos provocou alterações detectáveis in vitro sobre a suscetibilidade das leveduras aos antifúngicos ou à capacidade de formar biofilme. Estes resultados sugerem que o aumento da candidemia na UTI não seria atribuído a possíveis alterações provocadas nas leveduras e sim pelo enfraquecimento da condição geral do paciente após longa exposição à infecção.

Structural-dependent effects of dietary fibers in colon cancer: Focus on dietary fiber naturally changed by the papaya ripening / Efeitos estrutura-dependente das fibras alimentares no câncer de cólon: foco na fibra alimentar naturalmente modificada durante o amadurecimento do mamão papaia

ietary fiber (DF) consumption is related with several healthy benefits such as the decreasing risk of colon cancer development. The DF is not digested by the digestive enzymes and reach to colon where is fermented by the colonic microbiota. The fermentation process releases metabolites as short chain fatty acids (SCFA) such as butyrate, propionate and acetate. Besides the fermentation process, the DF can directly interact with intestinal epithelial cells inducing mechanism that can also be related with the associated DF consumption benefits. The lack of information regarding DF and colon cancer are due to the complexity of both the cancer and the DF structure. The papayas DF are derived from the fruit cell wall, and they are probably naturally modified during ripening through a massive polysaccharide hydrolysis, because papayas show a very fast pulp softening. Due to the lack of information about DF and their beneficial effects to human health as well as the possibility of the natural papaya ripening to modifying the DF presented in the fruit pulp, the present thesis had as the primary objectives: 1) to evaluate how the cell-wall degrading enzymes affect the fruit cell wall solubilization and molecular weight; 2) to investigate the direct effects of the papaya pectin derived from unripe to ripe papayas in cancer cell lines, in galectin-3 interaction and in HEK cells expressing pattern recognition receptors (PRR); 3) to evaluate the human colonic in vitro fermentation using DF from unripe and ripe papayas as substrates; 4) to conduct an in vivo experiment using rats with pre-neoplastic colon lesions while receiving a diet with DF from unripe and ripe papayas. The endopolygalacturonases were the main enzymes acting on the solubilizing papaya cell wall pectin affecting both the papaya firmness and pectin structure. Overall, the papayas DF showed a ripening dependent structureeffects. In the cancer cell lines experiments, the ripe papayas pectin showed a more pronounced effects in inducing cancer cell death, inhibiting cancer cells migration and aggregation, activating PRR as toll-like receptors and inhibiting the pro-metastatic protein galectin-3. The DF from papayas also showed different aspects in colonic in vitro fermentation regarding the DF utilization by the bacteria and the bacteria abundance profile. Lastly, the animals receiving the diet with the DF from ripe papayas had less aberrant crypt foci in colon than the animals that received the DF from unripe papayas or cellulose (AIN-93G DF). Therefore, the study of papaya DF was carried out both during papaya ripening and its biological effects in vitro and in vivo, generating unprecedented results relating the endogenous biochemical changes of the fruits during maturation with the possible beneficial effects of their ingestion for health human

O consumo de fibras alimentares (FA) está relacionado com vários benefícios à saúde como a diminuição no risco do desenvolvimento de câncer de cólon. A FA não é digerida pelas enzimas digestivas do trato gastrointestinal sendo fermentada pela microbiota intestinal do cólon. Como subproduto do processo de fermentação há a liberação de ácidos graxos de cadeia curta (SCFA) - como o butirato, o propionato e o acetato. Além do processo de fermentação, a FA pode interagir diretamente com as células epiteliais do intestino, induzindo mecanismos que também podem estar relacionados com os benefícios associados ao consumo de FA. A falta de informação sobre a FA e o câncer de cólon é, em partes, devido à complexidade de ambos, tanto do câncer quanto da estrutura da FA. As FA do mamão papaia são derivadas da parede celular da fruta apresentando diferentes estruturas dependendo do ponto de amadurecimento do fruto. Esse fato ocorre, pois, durante o amadurecimento do mamão papaia, existe uma extensa hidrólise dos polissacarídeos presentes na parede celular, diminuindo rapidamente a firmeza da polpa do fruto. Devido à falta de informações sobre FA e seus efeitos benéficos à saúde humana que são dependentes da sua estrutura, bem como a possibilidade do amadurecimento do mamão papaia naturalmente modificar as FA presentes na polpa dos frutos, a presente tese teve como principais objetivos: 1) avaliar como as enzimas que degradam a parede celular do mamão papaia afetam a solubilização e o peso molecular da parede celular do fruto; 2) investigar os efeitos diretos da pectina derivada de mamões verdes e maduros em linhagens de células de câncer, na interação com a galectina-3, e em células do tipo HEK que expressam receptores de reconhecimento de padrões (RRP); 3) avaliar a fermentação colônica humana in vitro utilizando as FA de mamões verdes e maduros; 4) avaliar em ratos com lesões pré-neoplásicas no cólon o efeito do consumo de ração com ou sem FA de mamões papaias verdes e maduros. As endopoligalacturonases foram relacionadas como as principais enzimas que atuam solubilizando a pectina da parede celular do mamão, afetando tanto a firmeza da polpa do fruto quanto a solubilização da pectina durante o amadurecimento. De modo geral, as FA dos mamões exerceram um efeito estruturadependente de acordo com a maturação do fruto. Nos experimentos utilizando linhagens de células de câncer, a pectina do mamão papaia maduro apresentou efeitos mais pronunciados na indução da morte e na inibição da migração e da agregação das células, bem como ativando os RRP, como por exemplo, os receptores do tipo toll-like, além de inibir a proteína pró-metastática galectina-3. As FA dos mamões também apresentaram diferentes resultados na fermentação colônica in vitro quanto à utilização das FA pelas bactérias do intestino, e também no perfil de crescimento dessas bactérias. Por fim, os animais que receberam a dieta com as FA dos mamões maduros apresentaram menor incidência de focos de criptas aberrantes do que os animais que receberam as FA provenientes de mamões verdes ou de celulose (FA da ração AIN-93G). Portanto, o estudo das FA dos mamões foi efetuado tanto durante o amadurecimento dos mamões quanto dos seus efeitos biológicos in vitro e in vivo, tendo gerado resultados inéditos relacionando as alterações bioquímicas endógenas dos frutos durante o amadurecimento com os possíveis efeitos benéficos da sua ingestão para a saúde humana

Neural network analyses of infrared spectra for classifying cell wall architectures.

About 10% of plant genomes are devoted to cell wall biogenesis. Our goal is to establish methodologies that identify and classify cell wall phenotypes of mutants on a genome-wide scale. Toward this goal, we have used a model system, the elongating maize (Zea mays) coleoptile system, in which cell wall changes are well characterized, to develop a paradigm for classification of a comprehensive range of cell wall architectures altered during development, by environmental perturbation, or by mutation. Dynamic changes in cell walls of etiolated maize coleoptiles, sampled at one-half-d intervals of growth, were analyzed by chemical and enzymatic assays and Fourier transform infrared spectroscopy. The primary walls of grasses are composed of cellulose microfibrils, glucuronoarabinoxylans, and mixed-linkage (1 --> 3),(1 --> 4)-beta-D-glucans, together with smaller amounts of glucomannans, xyloglucans, pectins, and a network of polyphenolic substances. During coleoptile development, changes in cell wall composition included a transient appearance of the (1 --> 3),(1 --> 4)-beta-D-glucans, a gradual loss of arabinose from glucuronoarabinoxylans, and an increase in the relative proportion of cellulose. Infrared spectra reflected these dynamic changes in composition. Although infrared spectra of walls from embryonic, elongating, and senescent coleoptiles were broadly discriminated from each other by exploratory principal components analysis, neural network algorithms (both genetic and Kohonen) could correctly classify infrared spectra from cell walls harvested from individuals differing at one-half-d interval of growth. We tested the predictive capabilities of the model with a maize inbred line, Wisconsin 22, and found it to be accurate in classifying cell walls representing developmental stage. The ability of artificial neural networks to classify infrared spectra from cell walls provides a means to identify many possible classes of cell wall phenotypes. This classification can be broadened to phenotypes resulting from mutations in genes encoding proteins for which a function is yet to be described.

Reconstructing the evolution of agarics from nuclear gene sequences and basidiospore ultrastructure.

Traditional classifications of agaric fungi involve gross morphology of their fruit bodies and meiospore print-colour. However, the phylogeny of these fungi and the evolution of their morphological and ecological traits are poorly understood. Phylogenetic analyses have already demonstrated that characters used in traditional classifications of basidiomycetes may be heavily affected by homoplasy, and that non-gilled taxa evolved within the agarics several times. By integrating molecular phylogenetic analyses including domains D1-D3 and D7-D8 of nucLSU rDNA and domains A-C of the RPB1 gene with morphological and chemical data from representative species of 88 genera, we were able to resolve higher groups of agarics. We found that the species with thick-walled and pigmented basidiospores constitute a derived group, and hypothesize that this specific combination of characters represents an evolutionary advantage by increasing the tolerance of the basidiospores to dehydration and solar radiation and so opened up new ecological niches, e.g. the colonization of dung substrates by enabling basidiospores to survive gut passages through herbivores. Our results confirm the validity of basidiospore morphology as a phylogenetic marker in the agarics.

Cell wall proteome in the maize primary root elongation zone. I. Extraction and identification of water-soluble and lightly ionically bound proteins.

Cell wall proteins (CWPs) play important roles in various processes, including cell elongation. However, relatively little is known about the composition of CWPs in growing regions. We are using a proteomics approach to gain a comprehensive understanding of the identity of CWPs in the maize (Zea mays) primary root elongation zone. As the first step, we examined the effectiveness of a vacuum infiltration-centrifugation technique for extracting water-soluble and loosely ionically bound (fraction 1) CWPs from the root elongation zone. The purity of the CWP extract was evaluated by comparing with total soluble proteins extracted from homogenized tissue. Several lines of evidence indicated that the vacuum infiltration-centrifugation technique effectively enriched for CWPs. Protein identification revealed that 84% of the CWPs were different from the total soluble proteins. About 40% of the fraction 1 CWPs had traditional signal peptides and 33% were predicted to be nonclassical secretory proteins, whereas only 3% and 11%, respectively, of the total soluble proteins were in these categories. Many of the CWPs have previously been shown to be involved in cell wall metabolism and cell elongation. In addition, maize has type II cell walls, and several of the CWPs identified in this study have not been identified in previous cell wall proteomics studies that have focused only on type I walls. These proteins include endo-1,3;1,4-beta-D-glucanase and alpha-L-arabinofuranosidase, which act on the major polysaccharides only or mainly present in type II cell walls.

Comparative degradation of oomycete, ascomycete, and basidiomycete cell walls by mycoparasitic and biocontrol fungi.

Fourteen fungi (primarily representing mycoparasitic and biocontrol fungi) were tested for their ability to grow on and degrade cell walls (CWs) of an oomycete (Pythium ultimum), ascomycete (Fusarium equisetii), and basidiomycete (Rhizoctonia solani), and their hydrolytic enzymes were characterized. Protein was detected in the cultural medium of eleven of the test isolates, and these fungi significantly degraded CWs over the 14-day duration of the experiment. In general, a greater level of CW degradation occurred for F. equisetii and P. ultimum than for R. solani. Fungi that degraded F. equisetii CWs were Coniothyrium minitans, Gliocladium roseum, Myrothecium verrucaria, Talaromyces flavus, and Trichoderma harzianum. Taxa degrading P ultimum CWs included Chaetomium globosum, Coniothyrium minitans, M. verrucaria, Seimatosporium sp., Talaromyces flavus, Trichoderma hamatum, Trichoderma harzianum, and Trichoderma viride. Production of extracellular protein was highly correlated with CW degradation. Considerable variation in the molecular weights of CW-degrading enzymes were detected among the test fungi and the CW substrates in zymogram electrophoresis. Multivariate analysis between CW degradation and hydrolysis of barley beta-glucan (beta1,3- and beta1,4-glucanases), laminarin (beta1,3- and beta1,6-glucanases), carboxymethyl cellulose (endo-beta1,4-glucanases), colloidal chitin (chitinases), and chitosan (chitosanases) was conducted. For F. equisetii CWs, the regression model accounted for 80% of the variability, and carboxymethyl cellulases acting together with beta-glucanases contributed an R2 of 0.52, whereas chitinases and beta-glucanases alone contributed an R2 of 0.11 and 0.12, respectively. Only 61% of the variability observed in the degradation of P. ultimum CWs was explained by the enzyme classes tested, and primarily beta-glucanases (R2 of 0.53) and carboxymethyl cellulases (R2 of 0.08) alone contributed to CW break down. Too few of the test fungi degraded R. solani CWs to perform multivariate analysis effectively. This study identified several fungi that degraded ascomyceteous and oomyceteous, and to a lesser extent, basidiomycetous CWs. An array of enzymes were implicated in CW degradation.