Genes driving potato tuber initiation and growth: identification based on transcriptional changes using the POCI array

The increasing amount of available expressed gene sequence data makes whole-transcriptome analysis of certain crop species possible. Potato currently has the second largest number of publicly available expressed sequence tag (EST) sequences among the Solanaceae. Most of these ESTs, plus other proprietary sequences, were combined and used to generate a unigene assembly. The set of 246,182 sequences produced 46,345 unigenes, which were used to design a 44K 60-mer oligo array (Potato Oligo Chip Initiative: POCI). In this study, we attempt to identify genes controlling and driving the process of tuber initiation and growth by implementing large-scale transcriptional changes using the newly developed POCI array. Major gene expression profiles could be identified exhibiting differential expression at key developmental stages. These profiles were associated with functional roles in cell division and growth. A subset of genes involved in the regulation of the cell cycle, based on their Gene Ontology classification, exhibit a clear transient upregulation at tuber onset indicating increased cell division during these stages. The POCI array allows the study of potato gene expression on a much broader level than previously possible and will greatly enhance analysis of transcriptional control mechanisms in a wide range of potato research areas. POCI sequence and annotation data are publicly available through the POCI database (http://pgrc.ipk-gatersleben.de/poci).

Controlled adhesion and growth of long term glial and neuronal cultures on Parylene-C

This paper explores the long term development of networks of glia and neurons on patterns of Parylene-C on a SiO2 substrate. We harvested glia and neurons from the Sprague-Dawley (P1–P7) rat hippocampus and utilized an established cell patterning technique in order to investigate cellular migration, over the course of 3 weeks. This work demonstrates that uncontrolled glial mitosis gradually disrupts cellular patterns that are established early during culture. This effect is not attributed to a loss of protein from the Parylene-C surface, as nitrogen levels on the substrate remain stable over 3 weeks. The inclusion of the anti-mitotic cytarabine (Ara-C) in the culture medium moderates glial division and thus, adequately preserves initial glial and neuronal conformity to underlying patterns. Neuronal apoptosis, often associated with the use of Ara-C, is mitigated by the addition of brain derived neurotrophic factor (BDNF). We believe that with the right combination of glial inhibitors and neuronal promoters, the Parylene-C based cell patterning method can generate structured, active neural networks that can be sustained and investigated over extended periods of time. To our knowledge this is the first report on the concurrent application of Ara-C and BDNF on patterned cell cultures.

On the F-word: a corpus-based analysis of the media representation of Feminism in British and German press discourse,1990-2009

Research in social psychology has shown that public attitudes towards feminism are mostly based on stereotypical views linking feminism with leftist politics and lesbian orientation. It is claimed that such attitudes are due to the negative and sexualised media construction of feminism. Studies concerned with the media representation of feminism seem to confirm this tendency. While most of this research provides significant insights into the representation of feminism, the findings are often based on a small sample of texts. Also, most of the research was conducted in an Anglo-American setting. This study attempts to address some of the shortcomings of previous work by examining the discourse of feminism in a large corpus of German and British newspaper data. It does so by employing the tools of Corpus Linguistics. By investigating the collocation profiles of the search term feminism, we provide evidence of salient discourse patterns surrounding feminism in two different cultural contexts.

Array based detection of antibiotic resistance genes in Gram negative bacteria isolated from retail poultry meat in the UK and Ireland

The use of antibiotics in birds and animals intended for human consumption within the European Union (EU) and elsewhere has been subject to regulation prohibiting the use of antimicrobials as growth promoters and the use of last resort antibiotics in an attempt to reduce the spread of multi-resistant Gram negative bacteria. Given the inexorable spread of antibiotic resistance there is an increasing need for improved monitoring of our food. Using selective media, Gram negative bacteria were isolated from retail chicken of UK-Intensively reared (n = 27), Irish-Intensively reared (n = 19) and UK-Free range (n = 30) origin and subjected to an oligonucleotide based array system for the detection of 47 clinically relevant antibiotic resistance genes (ARGs) and two integrase genes. High incidences of β-lactamase genes were noted in all sample types, acc (67%), cmy (80%), fox (55%) and tem (40%) while chloramphenicol resistant determinants were detected in bacteria from the UK poultry portions and were absent in bacteria from the Irish samples. Denaturing Gradient Gel Electrophoresis (DGGE) was used to qualitatively analyse the Gram negative population in the samples and showed the expected diversity based on band stabbing and DNA sequencing. The array system proved to be a quick method for the detection of antibiotic resistance gene (ARG) burden within a mixed Gram negative bacterial population.

Squeeze flow viscoelasticity of electrorheological fluids based on microcrystalline cellulose

Dynamic viscoelasticity of electrorheological fluids based on microcrystalline cellulose/castor oil suspensions was experimentally investigated in squeeze flow. The dependence of storage modulus G' and loss modulus G" parallel to external electric field on electric fields and strain amplitudes is presented. The experiments show that, when external electric field is higher than the critical field, the viscoelasticity of the ER fluids converts from linear to nonlinear, and the ER fluids transfer from solid-like state to fluid state with the growth of strain amplitude. The influences of strain amplitude and oscillatory frequency on the nonlinearity of viscoelasticity were also studied.

Growth factor receptor-bound protein 2 contributes to (hem)immunoreceptor tyrosine-based activation motif-mediated signaling in platelets

Rationale: Platelets are anuclear cell fragments derived from bone marrow megakaryocytes (MKs) that safeguard vascular integrity but may also cause pathological vessel occlusion. One major pathway of platelet activation is triggered by 2 receptors that signal through an (hem)immunoreceptor tyrosine-based activation motif (ITAM), the activating collagen receptor glycoprotein (GP) VI and the C-type lectin-like receptor 2 (CLEC-2). Growth factor receptor–bound protein 2 (Grb2) is a ubiquitously expressed adapter molecule involved in signaling processes of numerous receptors in different cell types, but its function in platelets and MKs is unknown. Objective: We tested the hypothesis that Grb2 is a crucial adapter protein in (hem)immunoreceptor tyrosine-based activation motif signaling in platelets. Methods and Results: Here, we show that genetic ablation of Grb2 in MKs and platelets did not interfere with MK differentiation or platelet production. However, Grb2-deficiency severely impaired glycoprotein VI–mediated platelet activation because of defective stabilization of the linker of activated T-cell (LAT) signalosome and activation of downstream signaling proteins that resulted in reduced adhesion, aggregation, and coagulant activity on collagen in vitro. Similarly, CLEC-2–mediated signaling was impaired in Grb2-deficient platelets, whereas the cells responded normally to stimulation of G protein–coupled receptors. In vivo, this selective (hem)immunoreceptor tyrosine-based activation motif signaling defect resulted in prolonged bleeding times but affected arterial thrombus formation only after concomitant treatment with acetylsalicylic acid, indicating that defective glycoprotein VI signaling in the absence of Grb2 can be compensated through thromboxane A2–induced G protein–coupled receptor signaling pathways. Conclusions: These results reveal an important contribution of Grb2 in (hem)immunoreceptor tyrosine-based activation motif signaling in platelets in hemostasis and thrombosis by stabilizing the LAT signalosome.

Salt and ionic cocrystalline forms of amides: protonation of carbamazepine in aqueous media

The products of reactions of the pharmaceutical amide carbamazepine (CBZ) with strong acids under aqueous conditions were investigated by both powder and single crystal X-ray diffraction. Despite previous claims to the contrary, it was found that salt forms with CBZ protonated at the amide O atom could be isolated from reactions with both HCl and HBr. These forms include the newly identified hydrate phase [CBZ(H)][Cl]·H O. Reactions with other mineral acids (HI and HBF ) gave ionic cocrystalline (ICC) forms (CBZ· [acridinium][I ]·2.5I and CBZ·[H O ] [BF ] ·H O) as well as the salt form CBZ·[CBZ(H)][BF ]·0.5H O. Reaction 2 4 3 2 5 2 0.25 4 0.25 2 4 2 of CBZ with a series of sulfonic acids also gave salt forms, namely, [CBZ(H)][O SC H ], [CBZ(H)][O SC H (OH)]· 3 6 5 3 6 4 0.5H O, [CBZ(H)] [O SCH CH SO ], and [CBZ(H)][O SC H (OH) (COOH)]·H O. CBZ and protonated CBZ(H) 2 2 3 2 2 3 3 6 3 2 moieties can be differentiated in the solid state both by changes to molecular geometry and by differing packing preferences

Oleaginous yeast Cryptococcus curvatus exhibits interplay between biosynthesis of intracellular sugars and lipids

Patterns of the biosynthesis ofmajor metabolites of the oleaginous yeast Cryptococcus curvatus NRRL Y-1511 were investigated during cultivation on sugar-based media. When lactose or sucrose was employed as substrate under nitrogen-limited conditions, the yeast strain accumulated high quantities of intra-cellular total sugars (ITS) at the beginning of fermentation (up to 68% w/w), with ITS values progressively decreasing to 20%, w/w, at the end of the fermentation. Decrease in ITS content and consumption of extracellular lactose led to a subsequent rise in lipid accumulation, reaching 29.8% in dry cell weight at 80 g/L of initial lactose concentration. Lactose was a more favorable substrate for lipid production than sucrose. In nitrogen-excess conditions, ITS were produced in significant quantities despite the continuous presence of nitrogen in the medium. Growth on lactose was not followed by secretion of extra-cellular b-galactosidase. High quantities of extra-cellular invertase were observed during growth on sucrose. The composition of ITS was highly influenced by the sugar used as substrate. Cellular lipids contained mainly palmitic and to lesser extent linoleic and stearic acids. This is the first report in the literature that demonstrates the interplay between the biosynthesis of intra-cellular total sugars and lipid synthesis for oleaginous yeast strains.

Pseudo-nonlinear and athermal lensing effects on transverse properties of Cr(3+) based solid-state lasers

Several experiments (time-resolved Z-scan experiments based on pulsed and CW pump lasers, time-resolved divergence diagnostics) have been performed to examine and clarify the question of the converging or diverging population lensing effect occurring in a Cr(3+):Al(2)O(3) ruby laser. The dynamics of the laser far-field divergence of such a laser indeed indicated initially a diverging effect while Z-scan measurements conclude to a converging one. The origin of this discrepancy is thus analysed and elucidated here by introducing the general concept of correlation collapse between the centre and the wings of a laser beam having some clipping. (C) 2010 Elsevier B.V. All rights reserved.

All solid-state electrochromic devices with gelatin-based electrolyte

6 x 8cm(2) electrochromic devices (ECDs) with the configuration K-glass/EC-layer/electrotype/ion-storage (IS) layer/K-glass, have been assembled using Nb2O5:Mo EC layers, a (CeO2)(0.81)-TiO2 IS-layer and a new gelatin electrolyte containing Li+ ions. The structure of the electrolyte is X-ray amorphous. Its ionic conductivity passed by a maximum of 1.5 x 10(-5) S/CM for a lithium concentration of 0.3g/15ml. The value increases with temperature and follows an Arrhenius law with an activation energy of 49.5 kJ/mol. All solid-state devices show a reversible gray coloration, a long-term stability of more than 25,000 switching cycles (+/- 2.0 V/90 s), a transmission change at 550 nm between 60% (bleached state) and 40% (colored state) corresponding to a change of the optical density (Delta OD = 0. 15) with a coloration efficiency increasing from 10cm(2)/C (initial cycle) to 23cm(2)/C (25,000th cycle). (c) 2007 Elsevier B.V. All rights reserved.

Dynamic Solid Phase DNA Extraction and PCR Amplification in Polyester-Toner Based Microchip

A variety of substrates have been used for fabrication of microchips for DNA extraction, PCR amplification, and DNA fragment separation, including the more conventional glass and silicon as well as alternative polymer-based materials. Polyester represents one such polymer, and the laser-printing of toner onto polyester films has been shown to be effective for generating polyester-toner (PeT) microfluidic devices with channel depths on the order of tens of micrometers. Here, we describe a novel and simple process that allows for the production of multilayer, high aspect-ratio PeT microdevices with substantially larger channel depths. This innovative process utilizes a CO(2) laser to create the microchannel in polyester sheets containing a uniform layer of printed toner, and multilayer devices can easily be constructed by sandwiching the channel layer between uncoated cover sheets of polyester containing precut access holes. The process allows the fabrication of deep channels, with similar to 270 mu m, and we demonstrate the effectiveness of multilayer PeT microchips for dynamic solid phase extraction (dSPE) and PCR amplification. With the former, we found that (i) more than 65% of DNA from 0.6 mu L of blood was recovered, (ii) the resultant DNA was concentrated to greater than 3 ng/mu L., (which was better than other chip-based extraction methods), and (iii) the DNA recovered was compatible with downstream microchip-based PCR amplification. Illustrative of the compatibility of PeT microchips with the PCR process, the successful amplification of a 520 bp fragment of lambda-phage DNA in a conventional thermocycler is shown. The ability to handle the diverse chemistries associated with DNA purification and extraction is a testimony to the potential utility of PeT microchips beyond separations and presents a promising new disposable platform for genetic analysis that is low cost and easy to fabricate.

Media piracy in emerging economies

Media Piracy in Emerging Economies is the first independent, large-scale study of music, film and software piracy in the developing world, with a focus on Brazil, India, Russia, South Africa, Mexico and Bolivia. Based on three years of work by some thirty-five researchers, the study tells two overarching stories: one tracing the explosive growth of piracy as digital technologies became cheap and ubiquitous around the world, and another following the growth of industry lobbies that have reshaped laws and law enforcement around copyright protection. The report argues that enforcement efforts have largely failed, and that the problem of piracy is better addressed as a failure of affordable access to media in legal markets.

Comparative study of the whisky aroma profile based on headspace solid phase microextraction using different fibre coatings

A dynamic headspace solid-phase microextraction (HS-SPME) and gas chromatography coupled to ion trap mass spectrometry (GC–ITMS) method was developed and applied for the qualitative determination of the volatile compounds present in commercial whisky samples which alcoholic content was previously adjusted to 13% (v/v). Headspace SPME experimental conditions, such as fibre coating, extraction temperature and extraction time, were optimized in order to improve the extraction process. Five different SPME fibres were used in this study, namely, poly(dimethylsiloxane)(PDMS),poly(acrylate)(PA),Carboxen-poly(dimethylsiloxane)(CAR/PDMS),Carbowax-divinylbenzene(CW/DVB)and Carboxen-poly(dimethylsiloxane)-divinylbenzene (CAR/PDMS/DVB). The best results were obtained using a 75 m CAR/PDMS fibre during headspace extraction at 40◦C with stirring at 750rpm for 60min, after saturating the samples with salt. The optimised methodology was then appliedtoinvestigatethevolatilecompositionprofileofthreeScotchwhiskysamples—BlackLabel,BallantinesandHighlandClan.Approximately seventy volatile compounds were identified in the these samples, pertaining at several chemical groups, mainly fatty acids ethyl esters, higher alcohols, fatty acids, carbonyl compounds, monoterpenols, C13 norisoprenoids and some volatile phenols. The ethyl esters form an essential group of aroma components in whisky, to which they confer a pleasant aroma, with “fruity” odours. Qualitatively, the isoamyl acetate, with “banana” aroma,wasthemostinteresting.Quantitatively,significantcomponentsareethylestersofcaprilic,capricandlauricacids.Thehighestconcentration of fatty acids, were observed for caprilic and capric acids. From the higher alcohols the fusel oils (3-methylbutan-1-ol and 2.phenyletanol) are the most important ones.

Profiling allergic asthma volatile metabolic patterns using a headspace-solid phase microextraction/gas chromatography based methodology

Allergicasthmarepresentsanimportantpublichealthissuewithsignificantgrowthovertheyears,especially in the paediatric population. Exhaled breath is a non-invasive, easily performed and rapid method forobtainingsamplesfromthelowerrespiratorytract.Inthepresentmanuscript,themetabolicvolatile profiles of allergic asthma and control children were evaluated by headspace solid-phase microextraction combined with gas chromatography–quadrupole mass spectrometry (HS-SPME/GC–qMS). The lack ofstudiesinbreathofallergicasthmaticchildrenbyHS-SPMEledtothedevelopmentofanexperimental design to optimize SPME parameters. To fulfil this objective, three important HS-SPME experimental parameters that influence the extraction efficiency, namely fibre coating, temperature and time extractions were considered. The selected conditions that promoted higher extraction efficiency corresponding to the higher GC peak areas and number of compounds were: DVB/CAR/PDMS coating fibre, 22◦C and 60min as the extraction temperature and time, respectively. The suitability of two containers, 1L Tedlar® bags and BIOVOC®, for breath collection and intra-individual variability were also investigated. The developed methodology was then applied to the analysis of children exhaled breath with allergicasthma(35),fromwhich13hadalsoallergicrhinitis,andhealthycontrolchildren(15),allowing to identify 44 volatiles distributed over the chemical families of alkanes (linear and ramified) ketones, aromatic hydrocarbons, aldehydes, acids, among others. Multivariate studies were performed by Partial LeastSquares–DiscriminantAnalysis(PLS–DA)usingasetof28selectedmetabolitesanddiscrimination between allergic asthma and control children was attained with a classification rate of 88%. The allergic asthma paediatric population was characterized mainly by the compounds linked to oxidative stress, such as alkanes and aldehydes. Furthermore, more detailed information was achieved combining the volatile metabolic data, suggested by PLS–DA model, and clinical data.

Effectiveness of different solid-phase microextraction fibres for differentiation of selected Madeira island fruits based on their volatile metabolite profile: identification of novel compounds

A headspace solid-phase microextraction (HS-SPME) procedure based on five commercialised fibres (85 μm polyacrylate – PA, 100 μm polydimethylsiloxane – PDMS, 65 μm polydimethylsiloxane/divinylbenzene – PDMS/DVB, 70 μm carbowax/divinylbenzene – CW/DVB and 85 μm carboxen/polydimethylsiloxane – CAR/PDMS) is presented for the characterization of the volatile metabolite profile of four selected Madeira island fruit species, lemon (Citrus limon), kiwi (Actinidia deliciosa), papaya (Carica papaya L.) and Chickasaw plum (Prunus angustifolia). The isolation of metabolites was followed by thermal desorption gas chromatography–quadrupole mass spectrometry (GC–qMS) methodology. The performance of the target fibres was evaluated and compared. The SPME fibre coated with CW/DVB afforded the highest extraction efficiency in kiwi and papaya pulps, while in lemon and plum the same was achieved with PMDS/DVB fibre. This procedure allowed for the identification of 80 compounds, 41 in kiwi, 24 in plums, 23 in papaya and 20 in lemon. Considering the best extraction conditions, the most abundant volatiles identified in kiwi were the intense aldehydes and ethyl esters such as (E)-2-hexenal and ethyl butyrate, while in Chicasaw plum predominate 2-hexenal, 2-methyl-4-pentenal, hexanal, (Z)-3-hexenol and cyclohexylene oxide. The major compounds identified in the papaya pulp were benzyl isothiocyanate, linalool oxide, furfural, hydroxypropanone, linalool and acetic acid. Finally, lemon was shown to be the most divergent of the four fruits, being its aroma profile composed almost exclusively by terpens, namely limonene, γ-terpinene, o-cymene and α-terpinolene. Thirty two volatiles were identified for the first time in the fruit or close related species analysed and 14 volatiles are reported as novel volatile metabolites in fruits. This includes 5 new compounds in kiwi (2-cyclohexene-1,4-dione, furyl hydroxymethyl ketone, 4-hydroxydihydro-2(3H)-furanone, 5-acetoxymethyl-2-furaldehyde and ethanedioic acid), 4 in plum (4-hydroxydihydro-2(3H)-furanone, 5-methyl-2-pyrazinylmethanol, cyclohexylene oxide and 1-methylcyclohexene), 4 in papaya (octaethyleneglycol, 1,2-cyclopentanedione, 3-methyl-1,2-cyclopentanedione and 2-furyl methyl ketone) and 2 in lemon (geranyl farnesate and safranal). It is noteworthy that among the 15 volatile metabolites identified in papaya, 3-methyl-1,2-cyclopentanedione was previously described as a novel PPARγ (peroxisome proliferator-activated receptor γ) agonist, having a potential to minimize inflammation.