Atomic scale characterization of Mn doped InAs/GaAs quantum dots

Several growth procedures for doping InAs/GaAs quantum dots (QDs) with manganese (Mn) have been investigated with cross-sectional scanning tunneling microscopy. It is found that expulsion of Mn out of the QDs and subsequent segregation makes it difficult to incorporate Mn in the QDs even at low growth temperatures of T=320 degrees C and high Mn fluxes. Mn atoms in and around QDs have been observed with strain and potential confinement changing the appearance of the Mn features.

Surface characterization of absorbing polymer films deposited on transparent glasses

PANI films were deposited on glass substrates by in-situ polymerization and characterized by UV-VIS spectroscopy and atomic force microscopy. A method is developed to accurately analyze ellipsometric data obtained for transparent glass substrates before and after modification with absorbing polymer films. Surface modification was made with an overlayer such as polyaniline ( PANI), which exhibits different optical properties by varying its oxidation state. First, the issue of using transparent substrates for ellipsometry studies was examined and then, spectroscopic ellipsometry was used to characterize absorbing overlayers on transparent glasses. The same methodologies of data analysis can be also applied to other absorbing films on transparent substrates, and deposited by different techniques.

Quantitative determination of optical transmission through subwavelength slit arrays in Ag films: Role of surface wave interference and local coupling between adjacent slits

Measurement of the transmitted intensity from a coherent monomode light source through a series of subwavelength slit arrays in Ag films, with varying array pitch and number of slits, demonstrates enhancement (suppression) by factors of as much as 6 (9) when normalized to the transmission efficiency of an isolated slit. Pronounced minima in the transmitted intensity are observed at array pitches corresponding to lambda(SPP), 2 lambda(SPP), and 3 lambda(SPP), where lambda(SPP) is the wavelength of the surface plasmon polariton (SPP). The position of these minima arises from destructive interference between incident propagating waves and pi-phase-shifted SPP waves. Increasing the number of slits to four or more does not increase appreciably the per-slit transmission intensity. A simple interference model fits well the measured transmitted intensity profile.

Characterization of global transcription profile of normal and HPV-immortalized keratinocytes and their response to TNF treatment

Background: Persistent infection by high risk HPV types (e.g. HPV-16, -18, -31, and -45) is the main risk factor for development of cervical intraepithelial neoplasia and cervical cancer. Tumor necrosis factor (TNF) is a key mediator of epithelial cell inflammatory response and exerts a potent cytostatic effect on normal or HPV16, but not on HPV18 immortalized keratinocytes. Moreover, several cervical carcinoma-derived cell lines are resistant to TNF anti-proliferative effect suggesting that the acquisition of TNF-resistance may constitute an important step in HPV-mediated carcinogenesis. In the present study, we compared the gene expression profiles of normal and HPV16 or 18 immortalized human keratinocytes before and after treatment with TNF for 3 or 60 hours. Methods: In this study, we determined the transcriptional changes 3 and 60 hours after TNF treatment of normal, HPV16 and HPV18 immortalized keratinocytes by microarray analysis. The expression pattern of two genes observed by microarray was confirmed by Northern Blot. NF-kappa B activation was also determined by electrophoretic mobility shift assay (EMSA) using specific oligonucleotides and nuclear protein extracts. Results: We observed the differential expression of a common set of genes in two TNF-sensitive cell lines that differs from those modulated in TNF-resistant ones. This information was used to define genes whose differential expression could be associated with the differential response to TNF, such as: KLK7 (kallikrein 7), SOD2 (superoxide dismutase 2), 100P (S100 calcium binding protein P), PI3 (protease inhibitor 3, skin-derived), CSTA (cystatin A), RARRES1 (retinoic acid receptor responder 1), and LXN (latexin). The differential expression of the KLK7 and SOD2 transcripts was confirmed by Northern blot. Moreover, we observed that SOD2 expression correlates with the differential NF-kappa B activation exhibited by TNF-sensitive and TNF-resistant cells. Conclusion: This is the first in depth analysis of the differential effect of TNF on normal and HPV16 or HPV18 immortalized keratinocytes. Our findings may be useful for the identification of genes involved in TNF resistance acquisition and candidate genes which deregulated expression may be associated with cervical disease establishment and/or progression.

Generation and characterization of human insulin-releasing cell lines

Background: The in vitro culture of insulinomas provides an attractive tool to study cell proliferation and insulin synthesis and secretion. However, only a few human beta cell lines have been described, with long-term passage resulting in loss of insulin secretion. Therefore, we set out to establish and characterize human insulin-releasing cell lines. Results: We generated ex-vivo primary cultures from two independent human insulinomas and from a human nesidioblastosis, all of which were cultured up to passage number 20. All cell lines secreted human insulin and C-peptide. These cell lines expressed neuroendocrine and islets markers, confirming the expression profile found in the biopsies. Although all beta cell lineages survived an anchorage independent culture, none of them were able to invade an extracellular matrix substrate. Conclusion: We have established three human insulin-releasing cell lines which maintain antigenic characteristics and insulin secretion profiles of the original tumors. These cell lines represent valuable tools for the study of molecular events underlying beta cell function and dysfunction.

Spectroscopic, structural, and functional characterization of the alternative low-spin state of horse heart cytochrome c

The alternative low-spin states of Fe3+ and Fe2+ cytochrome c induced by SDS or AOT/hexane reverse micelles exhibited the heme group in a less rhombic symmetry and were characterized by electron paramagnetic resonance, UV-visible, CD, magnetic CD, fluorescence, and Raman resonance. Consistent with the replacement of Met 80 by another strong field ligand at the sixth heme iron coordination position, Fe3+ ALSScytc exhibited 1-nm Soret band blue shift and e enhancement accompanied by disappearance of the 695-nm charge transfer band. The Raman resonance, CD, and magnetic CD spectra of Fe3+ and Fe2+ ALSScytc exhibited significant changes suggestive of alterations in the heme iron microenvironment and conformation and should not be assigned to unfold because the Trp(59) fluorescence remained quenched by the neighboring heme group. ALSScytc was obtained with His(33) and His(26) carboxyethoxylated horse cytochrome c and with tuna cytochrome c (His(33) replaced by Asn) pointing out Lys(79) as the probable heme iron ligand. Fe3+ ALSScytc retained the capacity to cleave tert-butylhydroperoxide and to be reduced by dithiothreitol and diphenylacetaldehyde but not by ascorbate. Compatible with a more open heme crevice, ALSScytc exhibited a redox potential similar to 200 mV lower than the wild-type protein (1220 mV) and was more susceptible to the attack of free radicals.

Instantaneous characterization of vegetable oils via TAG and FFA profiles by easy ambient sonic-spray ionization mass spectrometry

A fast and reliable method is presented for the analysis of vegetable oils. Easy ambient sonic-spray ionization mass spectrometry (EASI-MS) is shown to efficiently desorb and ionize the main oil constituents from an inert surface under ambient conditions and to provide comprehensive triacylglyceride (TAG) and free fatty acid (FFA) profiles detected mainly as either [ TAG + Na](+) or [FFA - H](-) ions. EASI(+/-)-MS analysis is simple, easily implemented, requires just a tiny droplet of the oil and is performed without any pre-separation or chemical manipulation. It also causes no fragmentation of TAG ions hence diacylglyceride (DAG) and monoacylglyceride (MAG) profiles and contents can also be measured. The EASI(+/-)-MS profiles of TAG and FFA permit authentication and quality control and can be used, for instance, to access levels of adulteration, acidity, oxidation or hydrolysis of vegetable oils in general.

CHEMICAL AND PHYSICO-CHEMICAL CHARACTERIZATION OF LIGNINS OBTAINED FROM ETHANOL-WATER FRACTIONATION OF BAGASSE

Organosolv lignins can replace petroleum chemicals such as phenol either partially or totally in various applications. Eight lignins, seven of which corresponded to the ethanol-water fractionation of bagasse and the other to a reference lignin (Alcell (R)) were analyzed with the aim to evaluate their chemical and physicochemical characteristics. The purity of the lignin fractions was determined by high pressure liquid chromatography (HPLC) and by ash content. Fourier Transform-Infrared Spectroscopy (FTIR) techniques and differential UV spectroscopy were applied to identify the chemical groups in the lignin samples. The molecular weight distribution was determined by size exclusion chromatography (HPSEC). Thermogravimetric analysis (TGA) and differential scanning calorimetry (DSC) techniques were used to determine the mass loss due to the high temperature treatment. The lignins studied showed the presence of p-hydroxyphenyl (H unit) and a greater proportion of guaiacyl (G unit) moieties, lower purity, similar or greater amount of phenolic hydroxyl groups, and higher degradation temperatures, than the Alcell (R) lignin.

Characterization of dynamic solid phase DNA extraction from blood with magnetically controlled silica beads

A novel solid phase extraction technique is described where DNA is bound and eluted from magnetic silica beads in a manner where efficiency is dependent on the magnetic manipulation of the beads and not on the flow of solution through a packed bed. The utility of this technique in the isolation of reasonably pure, PCR-amplifiable DNA from complex samples is shown by isolating DNA from whole human blood, and subsequently amplifying a fragment of the beta-globin gene. By effectively controlling the movement of the solid phase in the presence of a static sample, the issues associated with reproducibly packing a solid phase in a microchannel and maintaining consistent flow rates are eliminated. The technique described here is rapid, simple, and efficient, allowing for recovery of more than 60% of DNA from 0.6 mu L of blood at a concentration which is suitable for PCR amplification. In addition, the technique presented here requires inexpensive, common laboratory equipment, making it easily adopted for both clinical point-of-care applications and on-site forensic sample analysis.

Molecular and morphological characterization of Amathia distans Busk and Amathia brasiliensis Busk (Bryozoa: Ctenostomata) from the tropical and subtropical Western Atlantic

Morphological and molecular analyses have proven to be complementary tools of taxonomic information for the redescription of the ctenostome bryozoans Amathia brasiliensis Busk, 1886 and Amathia distans Busk, 1886. The two species, originally described from material collected by the `Challenger` expedition but synonymized by later authors, now have their status fixed by means of the selection of lectotypes, morphological observations and analyses of DNA sequences described here. The morphological characters allowing the identification of living and/or preserved specimens are (1) A. brasiliensis: whitish-pale pigment spots in the frontal surface of stolons and zooids, and a wide stolon with biserial zooid clusters growing in clockwise and anti-clockwise spirals along it, the spirality direction being maintained from maternal to daughter stolons; and (2) A. distans: bright yellow pigment spots in stolonal and zooidal surfaces including lophophores, and a slender stolon, thickly cuticularized, with biserial zooid clusters growing in clockwise and anti-clockwise spirals along it and the spirality direction not maintained from maternal to daughter stolons. Pairwise comparisons of DNA sequences of the mitochondrial genes cytochrome c oxidase subunit I and large ribosomal RNA subunit revealed deep genetic divergence between A. brasiliensis and A. distans. Finally, analyses of those sequences within a Bayesian phylogenetic context recovered their genealogical species status.

Characterization of feather-degrading bacteria from Brazilian soils

Studies on keratinolytic microorganisms have been mainly related to their biotechnological applications and association with animal pathologies. However, these organisms have an ecological relevance to recycling keratinous residues in nature. This work aimed to select and identify new culturable feather-degrading bacteria isolated from soils of Brazilian Amazon forest and Atlantic forest. Bacteria that were isolated from temperate soils and bacteria from Amazonian basin soil were tested for their capability to grow on feather meal agar (FMA). Proteolytic bacteria were tested for feather degradation and were further identified according to their morphological and biochemical characteristics. Also, molecular identification based on 165 rDNA gene sequencing was carried out. A total of 24 proteolytic and 20 feather-degrading isolates were selected; Most of the isolates were from the Bacillus genus (division Firmicutes), but one Aeromonas, two Serratia (gamma-Proteobacteria), and one Chryseobacterium (Cytophaga-Flavobacterium group). (C) 2010 Elsevier Ltd. All rights reserved.

Purification and characterization of an antimicrobial peptide produced by Pseudomonas sp strain 4B

An antimicrobial peptide produced by a bacterium isolated from the effluent pond of a bovine abattoir was purified and characterized. The strain was characterized by biochemical profiling and 16S rDNA sequencing as Pseudomonas sp. The antimicrobial peptide was purified by ammonium sulfate precipitation, gel filtration, and ion exchange chromatography. Direct activity on sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) was observed. A major band on SDS-PAGE suggested that the antimicrobial peptide has a molecular mass of about 30 kDa. The substance was inhibitory to a broad range of indicator strains, including pathogenic and food spoilage bacteria such as Listeria monocytogenes, Bacillus cereus, Staphylococcus aureus, among other. The partially purified antimicrobial substance remained active over a wide temperature range and was resistant to all proteases tested. This substance showed different properties than other antimicrobials from Pseudomonas species, suggesting a novel antimicrobial peptide was characterized.

A Morphological and Histological Characterization of Bisexual and Male Flower Types in Pomegranate

Pomegranate [Punica granatum (Punicaceae)] is characterized by having two types of flowers on the same tree: hermaphroditic bisexual flowers and functionally male flowers. This condition, defined as functional andromonoecy, can result in decreased yields resulting from the inability of male flowers to set fruit. Morphological and histological analyses of bisexual and male flowers were conducted using light and scanning electron microscopy (SEM) to characterize the different flower types observed in pomegranate plants and to better understand their developmental differences. Bisexual flowers had a discoid stigma covered with copious exudate, elongated stigmatic papillae, a single elongate style, and numerous stamens inserted on the inner wall of the calyx tube. Using fluorescence staining, high numbers of pollen tubes were observed growing through a central stylar canal. Ovules were numerous, elliptical, and anatropous. In contrast, male flowers had reduced female parts and exhibited shortened pistils of variable heights. Stigmatic papillae of male flowers had little exudate yet supported pollen germination. However, pollen tubes were rarely observed in styles. Ovules in male flowers were rudimentary and exhibited various stages of degeneration. Pollen from both types of flowers was of similar size, approximate to 20 mu m, and exhibited similar percent germination using in vitro germination assays. Pollen germination was strongly influenced by temperature. Maximal germination (greater than 74%) was obtained at 25 and 35 degrees C; pollen germination was significantly lower at 15 degrees C (58%) and 5 degrees C (10%).

Chemical characterization of agricultural supplies applied to organic tomato cultivation

The agricultural supplies used in the organic system to control pests and diseases as well as to fertilize soil are claimed to be beneficial to plants and innocuous to human health and to the environment. The chemical composition of six agricultural supplies commonly used in the organic tomato culture, was evaluated by instrumental neutron activation analysis (INAA). Results were compared to the maximum limits established by the Environment Control Agency of the Sao Paulo State (CETESB) and the Guidelines for Organic Quality Standard of Instituto Biodinamico (IBD). Concentrations above reference values were found for Co, Cr and Zn in compost, Cr and Zn in cattle manure and Zn in rice bran.

Characterization of Brazilian commercial milks by instrumental neutron activation analysis

Aiming at the determination of toxic and essential elements in Brazilian commercial bovine milk, 25 ultra high temperature (UHT) milk samples were acquired in the local market of Piracicaba, SP. The samples were freeze-dried and analyzed by instrumental neutron activation analysis (INAA) allowing the determination of Br, Ca, Co, Cs, Fe, K, Na, Rb and Zn. When the results were expressed as concentration (mg.l(-1)) no significant differences were found. However, considering the dry matter, results showed a clear difference between the mass fractions (mg.kg(-1) d.w.) of skim milk and whole milk for the elements Br, Ca, K, Na, Rb and Zn, indicating that the removal of fat caused a concentration effect in the dry matter of skim milks. Discrepancies were found between the concentrations of Ca and Na measured by INAA and the values informed in the labels. Ca showed variations within 30% for most samples, while concentrations of Na were up to 190% higher than informed values. The sample preparation and the LNAA procedure were appropriate for the determination of Br, Ca, Co, Cs, Fe, K, Na, Rb and Zn in milk samples.