Time of flight mass spectrometry for quantitative data analysis in fast transient studies using a Temporal Analysis of Products (TAP) reactor

A Time of flight (ToF) mass spectrometer suitable in terms of sensitivity, detector response and time resolution, for application in fast transient Temporal Analysis of Products (TAP) kinetic catalyst characterization is reported. Technical difficulties associated with such application as well as the solutions implemented in terms of adaptations of the ToF apparatus are discussed. The performance of the ToF was validated and the full linearity of the specific detector over the full dynamic range was explored in order to ensure its applicability for the TAP application. The reported TAP-ToF setup is the first system that achieves the high level of sensitivity allowing monitoring of the full 0-200 AMU range simultaneously with sub-millisecond time resolution. In this new setup, the high sensitivity allows the use of low intensity pulses ensuring that transport through the reactor occurs in the Knudsen diffusion regime and that the data can, therefore, be fully analysed using the reported theoretical TAP models and data processing.

Blue luminous stars in nearby galaxies: Quantitative spectral analysis of M33 B-type supergiant stars

We present the detailed spectral analysis of a sample of M33 B-type supergiant stars, aimed at the determination of their fundamental parameters and chemical composition. The analysis is based on a grid of non-LTE metal line-blanketed model atmospheres including the effects of stellar winds and spherical extension computed with the code FASTWIND. Surface abundance ratios of C, N, and O are used to discuss the chemical evolutionary status of each individual star. The comparison of observed stellar properties with theoretical predictions of massive star evolutionary models shows good agreement within the uncertainties of the analysis. The spatial distribution of the sample allows us to investigate the existence of radial abundance gradients in the disk of M33. The comparison of stellar and H II region O abundances ( based on direct determinations of the electron temperature of the nebulae) shows good agreement. Using a simple linear radial representation, the stellar oxygen abundances result in a gradient of -0.0145 +/- 0.005 dex arcmin(-1) (or -0.06 +/- 0.02 dex kpc(-1)) up to a distance equal to similar to 1.1 times the isophotal radius of the galaxy. A more complex representation cannot be completely discarded by our stellar sample. The stellar Mg and Si abundances follow the trend displayed by O abundances, although with shallower gradients. These differences in gradient slope cannot be explained at this point. The derived abundances of the three alpha-elements yield solar metallicity in the central regions of the disk of M33. A comparison with recent planetary nebula data from Magrini and coworkers indicates that the disk of M33 has not suffered from a significant O enrichment in the last 3 Gyr.

Review and quantitative meta-analysis of diet suggests the Eurasian otter (Lutra lutra) is likely to be a poor bioindicator

The Eurasian otter (Lutra lutra L.) is a top predator in aquatic systems and plays an important role in ecosystem functioning. However, it has undergone dramatic declines throughout Europe as a result of environmental degradation. We examine the putative role of the otter as a bioindicator in Ireland which remains a stronghold for the species and affords a unique opportunity to examine variation in its ecological niche. We describe diet, using spraint contents, along rivers during 2010 and conduct a review and quantitative meta-analysis of the results of a further 21 studies. We aimed to assess variation in otter diet in relation to river productivity, a proxy for natural nutrification and anthropogenic eutrophication, and availability of salmonid prey (Salmo trutta and Salmo salar), to test the hypothesis that otter diet is related to environmental quality. Otter diet did not vary with levels of productivity or availability of salmonids whilst Compositional Analysis suggested there was no selection of salmonid over non-salmonid fish. There was a distinct niche separation between riverine and lacustrine systems, the latter being dominated by Atlantic eel (Anguilla anguilla). Otters are opportunistic and may take insects, freshwater mussels, birds, mammals and even fruit. Otters living along coasts have a greatest niche breath than those in freshwater systems which encompasses a wide variety of intertidal prey though pelagic fish are rarely taken. It is concluded that the ability of the otter to feed on a wide diversity of prey taxa and the strong influence of habitat type, renders it a poor bioindicator of environmental water quality. It seems likely that the plasticity of the habitat and dietary niche of otters, and the extent of suitable habitat, may have sustained populations in Ireland despite intensification of agriculture during the 20th century.

Label-free based quantitative proteomics analysis of primary neonatal porcine Leydig cells exposed to the persistent contaminant 3-methylsulfonyl-DDE

Evidence that persistent environmental pollutants may target the male reproductive system is increasing. The male reproductive system is regulated by secretion of testosterone by testicular Leydig cells, and perturbation of Leydig cell function may have ultimate consequences. 3-Methylsulfonyl-DDE (3-MeSO₂-DDE) is a potent adrenal toxicants formed from the persistent insecticide DDT. Although studies have revealed the endocrine disruptive effect of 3-MeSO₂-DDE, the underlying mechanisms at cellular level in steroidogenic Leydig cells remains to be established. The current study addresses the effect of 3-MeSO₂-DDE on viability, hormone production and proteome response of primary neonatal porcine Leydig cells. The AlamarBlue™ assay was used to evaluate cell viability. Solid phase radioimmunoassay was used to measure concentration of hormones produced by both unstimulated and Luteinizing hormone (LH)-stimulated Leydig cells following 48h exposure. Protein samples from Leydig cells exposed to a non-cytotoxic concentration of 3-MeSO₂-DDE (10μM) were subjected to nano-LC-MS/MS and analyzed on a Q Exactive mass spectrometer and quantified using label-free quantitative algorithm. Gene Ontology (GO) and Ingenuity Pathway Analysis (IPA) were carried out for functional annotation and identification of protein interaction networks. 3-MeSO₂-DDE regulated Leydig cell steroidogenesis differentially depending on cell culture condition. Whereas its effect on testosterone secretion at basal condition was stimulatory, the effect on LH-stimulated cells was inhibitory. From triplicate experiments, a total of 6804 proteins were identified in which the abundance of 86 proteins in unstimulated Leydig cells and 145 proteins in LH-stimulated Leydig cells was found to be significantly regulated in response to 3-MeSO₂-DDE exposure. These proteins not only are the first reported in relation to 3-MeSO₂-DDE exposure, but also display small number of proteins shared between culture conditions, suggesting the action of 3-MeSO₂-DDE on several targeted pathways, including mitochondrial dysfunction, oxidative phosphorylation, EIF2-signaling, and glutathione-mediated detoxification. Further identification and characterization of these proteins and pathways may build our understanding to the molecular basis of 3-MeSO₂-DDE induced endocrine disruption in Leydig cells.

Rapid, quantitative analysis of ppm/ppb nicotine using surface-enhanced Raman scattering from polymer-encapsulated Ag nanoparticles (gel-colls)

Rapid, quantitative SERS analysis of nicotine at ppm/ppb levels has been carried out using stable and inexpensive polymer-encapsulated Ag nanoparticles (gel-colls). The strongest nicotine band (1030 cm(-1)) was measured against d(5)-pyridine internal standard (974 cm(-1)) which was introduced during preparation of the stock gel-colls. Calibration plots of I-nic/I-pyr against the concentration of nicotine were non-linear but plotting I-nic/I-pyr against [nicotine](x) (x = 0.6-0.75, depending on the exact experimental conditions) gave linear calibrations over the range (0.1-10 ppm) with R-2 typically ca. 0.998. The RMS prediction error was found to be 0.10 ppm when the gel-colls were used for quantitative determination of unknown nicotine samples in 1-5 ppm level. The main advantages of the method are that the gel-colls constitute a highly stable and reproducible SERS medium that allows high throughput (50 sample h(-1)) measurements.

Quantitative surface-enhanced Raman spectroscopy of dipicolinic acid - towards rapid anthrax endospore detection

Dipicolinic acid (DPA) is an excellent marker compound for bacterial spores, including those of Bacillus anthracis ( anthrax). Surface-enhanced Raman spectroscopy (SERS) potentially has the sensitivity and discrimination needed for trace DPA analysis, but mixing DPA solutions with citrate-reduced silver colloid only yielded measurable SERS spectra at much higher (> 80 ppm) concentrations than would be desirable for anthrax detection. Aggregation of the colloid with halide salts eliminated even these small DPA bands but aggregation with Na2SO4(aq) resulted in a remarkable increase in the DPA signals. With sulfate aggregation even 1 ppm solutions gave detectable signals with 10 s accumulation times, which is in the sensitivity range required. Addition of CNS- as an internal standard allowed quantitative DPA analysis, plotting the intensity of the strong DPA 1010 cm(-1) band (normalised to the ca. 2120 cm(-1) CNS- band) against DPA concentration gave a linear calibration (R-2 = 0.986) over the range 0 - 50 ppm DPA. The inclusion of thiocyanate also allows false negatives due to accidental deactivation of the enhancing medium to be detected.

How trophic interaction strength depends on traits

A key problem in community ecology is to understand how individual-level traits give rise to population-level trophic interactions. Here, we propose a synthetic framework based on ecological considerations to address this question systematically. We derive a general functional form for the dependence of trophic interaction coefficients on trophically relevant quantitative traits of consumers and resources. The derived expression encompasses-and thus allows a unified comparison of-several functional forms previously proposed in the literature. Furthermore, we show how a community's, potentially low-dimensional, effective trophic niche space is related to its higher-dimensional phenotypic trait space. In this manner, we give ecological meaning to the notion of the "dimensionality of trophic niche space." Our framework implies a method for directly measuring this dimensionality. We suggest a procedure for estimating the relevant parameters from empirical data and for verifying that such data matches the assumptions underlying our derivation. © Springer Science+Business Media B.V. 2009.


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Clinical features of psychotic disorders and polymorphisms in HT2A, DRD2, DRD4, SLC6A3 (DAT1), and BDNF:a family based association study

Schizophrenia is clinically heterogeneous and multidimensional, but it is not known whether this is due to etiological heterogeneity. Previous studies have not consistently reported association between any specific polymorphisms and clinical features of schizophrenia, and have primarily used case-control designs. We tested for the presence of association between clinical features and polymorphisms in the genes for the serotonin 2A receptor (HT2A), dopamine receptor types 2 and 4, dopamine transporter (SLC6A3), and brain-derived neurotrophic factor (BDNF). Two hundred seventy pedigrees were ascertained on the basis of having two or more members with schizophrenia or poor outcome schizoaffective disorder. Diagnoses were made using a structured interview based on the SCID. All patients were rated on the major symptoms of schizophrenia scale (MSSS), integrating clinical and course features throughout the course of illness. Factor analysis revealed positive, negative, and affective symptom factors. The program QTDT was used to implement a family-based test of association for quantitative traits, controlling for age and sex. We found suggestive evidence of association between the His452Tyr polymorphism in HT2A and affective symptoms (P = 0.02), the 172-bp allele of BDNF and negative symptoms (P = 0.04), and the 480-bp allele in SLC6A3 (= DAT1) and negative symptoms (P = 0.04). As total of 19 alleles were tested, we cannot rule out false positives. However, given prior evidence of involvement of the proteins encoded by these genes in psychopathology, our results suggest that more attention should be focused on the impact of these alleles on clinical features of schizophrenia.

In silico analysis and DHPLC screening strategy identifies novel apoptotic gene targets of aberrant promoter hypermethylation in prostate cancer

BACKGROUND: Aberrant DNA methylation has been implicated as a key survival mechanism in cancer, whereby promoter hypermethylation silences genes essential for many cellular processes including apoptosis. Limited data is available on the methylation profile of apoptotic genes in prostate cancer (CaP). The aim of this study was to profile methylation of apoptotic-related genes in CaP using denaturing high performance liquid chromatography (DHPLC).

METHODS: Based on an in silico selection process, 13 genes were screened for methylation in CaP cell lines using DHPLC. Quantitative methylation specific PCR was employed to determine methylation levels in prostate tissue specimens (n = 135), representing tumor, histologically benign prostate, high-grade prostatic intraepithelial neoplasia and benign prostatic hyperplasia. Gene expression was measured by QRT-PCR in cell lines and tissue specimens.

RESULTS: The promoters of BIK, BNIP3, cFLIP, TMS1, DCR1, DCR2, and CDKN2A appeared fully or partially methylated in a number of malignant cell lines. This is the first report of aberrant methylation of BIK, BNIP3, and cFLIP in CaP. Quantitative methylation analysis in prostate tissues identified 5 genes (BNIP3, CDKN2A, DCR1, DCR2 and TMS1) which were frequently methylated in tumors but were unmethylated in 100% of benign tissues. Furthermore, 69% of tumors were methylated in at least one of the five-gene panel. In the case of all genes, except BNIP3, promoter hypermethylation was associated with concurrent downregulation of gene expression.

CONCLUSION: Future examination of this "CaP apoptotic methylation signature" in a larger cohort of patients is justified to further evaluate its value as a diagnostic and prognostic marker.

Effects of vasectomy on spermatogenesis and fertility outcomes after assisted conception

Abstract BACKGROUND: Each year 40,000 men have a vasectomy in the UK whilst another 2400 request a reversal to begin a second family. Sperm can now be obtained by testicular biopsy and subsequently used in assisted conception with intracytoplasmic sperm injection (ICSI). The study aims were to compare sperm yields of men post-vasectomy or with obstructive azoospermia (OA) of unknown aetiology with fertile men and to assess any alteration in the clinical pregnancy rates after ICSI. METHODS: Testicular tissue was obtained by Trucut needle from men who had undergone a vasectomy >5yrs previously, had OA from other causes and from fertile men during vasectomy. Seminiferous tubules were milked to measure sperm yields. Numbers of Sertoli cells, spermatids and thickness of the seminiferous tubule walls were assessed using quantitative computerized analysis. RESULTS and CONCLUSIONS: Sperm yields/g testis were significantly decreased in men post-vasectomy and in men with OA, relative to fertile men. Significant reductions were also observed in early (40%) and mature (29%) spermatid numbers and an increase of 31% was seen in the seminiferous tubule wall (basal membrane and collagen thickness) of vasectomised men compared to fertile men. Clinical pregnancy rates in couples who had had a vasectomy were also significantly reduced.

Development of composite tissue scaffolds containing naturally sourced mircoporous hydroxyapatite

The aims of this work were to investigate the conversion of a marine alga into hydroxyapatite (HA), and furthermore to design a composite bone tissue engineering scaffold comprising the synthesised HA within a porous bioresorbable polymer. The marine alga Phymatolithon calcareum, which exhibits a calcium carbonate honeycomb structure, with a natural architecture of interconnecting permeable pores (microporosity 4-11 mu m), provided the initial raw material for this study. The objective was to convert the alga into hydroxyapatite while maintaining its porous morphology using a sequential pyrolysis and chemical synthesis processes. Semi-quantitative XRD analysis of the post-hydrothermal material (pyrolised at 700-750 degrees C), indicated that the calcium phosphate (CaP) ceramic most likely consisted of a calcium carbonate macroporous lattice, with hydroxyapatite crystals on the surface of the macropores. Cell visibility (cytotoxicity) investigations of osteogenic cells were conducted on the CaP ceramic (i.e., the material post-hydrothermal analysis) which was found to be non-cytotoxic and displayed good biocompatibility when seeded with MG63 cells. Furthermore, a hot press scaffold fabrication technique was developed to produce a composite scaffold of CaP (derived from the marine alga) in a polycaprolactone (PCL) matrix. A salt leaching technique was further explored to introduce macroporosity to the structure (50-200 mu m). Analysis indicated that the scaffold contained both micro/macroporosity and mechanical strength, considered necessary for bone tissue engineering applications. (C) 2008 Published by Elsevier B.V.

Using XPS to determine solute solubility in room temperature ionic liquids

X-Ray Photoelectron Spectroscopy (XPS) was used to quantify the amount of bromide ions present in two samples of [C(4)mpyrr]Br dissolved in the room temperature ionic liquid (RTIL) [C(4)mpyrr][N(Tf)(2)]. One sample was of a known concentration (0.436 Br atom%); the other was a saturated solution. The results obtained from quantitative XPS analysis indicated that the saturated sample had a concentration, or solubility, of 0.90 Br atom% (746 mM) at 298 K, which was then independently confirmed by potential-step chronoamperometry of the same solution.

Rigorous conditions for food-web intervality in high-dimensional trophic niche spaces

Food webs represent trophic (feeding) interactions in ecosystems. Since the late 1970s, it has been recognized that food-webs have a surprisingly close relationship to interval graphs. One interpretation of food-web intervality is that trophic niche space is low-dimensional, meaning that the trophic character of a species can be expressed by a single or at most a few quantitative traits. In a companion paper we demonstrated, by simulating a minimal food-web model, that food webs are also expected to be interval when niche-space is high-dimensional. Here we characterize the fundamental mechanisms underlying this phenomenon by proving a set of rigorous conditions for food-web intervality in high-dimensional niche spaces. Our results apply to a large class of food-web models, including the special case previously studied numerically.