The selective determination of sulfates, sulfonates and phosphates in urine by CE-MS

Metabolite identification and metabolite profiling are of major importance in the pharmaceutical and clinical context. However, highly polar and ionic substances are rarely included as analytical tools are missing. In this study, we present a new method for the determination of urinary sulfates, sulfonates, phosphates and other anions of strong acids. The method comprises a CE separation using an acidic BGE (pHmethod and, thus, CE-MS can be used for determination of this alcohol consumption marker. An SPE method was developed for the extraction of ethyl sulfate and other organic anions. Several additional compounds can be identified based on the accurate mass determined by the TOF MS in conjunction with databases. However, numerous detected compounds have not been reported in urinary metabolite databases so far. Thus, it is demonstrated that the presented method is complementary to the existing methods for metabolite characterization in urine.

Aberrant lipid metabolism in hepatocellular carcinoma revealed by plasma metabolomics and lipid profiling

There has been limited analysis of the effects of hepatocellular carcinoma (HCC) on liver metabolism and circulating endogenous metabolites. Here, we report the findings of a plasma metabolomic investigation of HCC patients by ultraperformance liquid chromatography-electrospray ionization-quadrupole time-of-flight mass spectrometry (UPLC-ESI-QTOFMS), random forests machine learning algorithm, and multivariate data analysis. Control subjects included healthy individuals as well as patients with liver cirrhosis or acute myeloid leukemia. We found that HCC was associated with increased plasma levels of glycodeoxycholate, deoxycholate 3-sulfate, and bilirubin. Accurate mass measurement also indicated upregulation of biliverdin and the fetal bile acids 7α-hydroxy-3-oxochol-4-en-24-oic acid and 3-oxochol-4,6-dien-24-oic acid in HCC patients. A quantitative lipid profiling of patient plasma was also conducted by ultraperformance liquid chromatography-electrospray ionization-triple quadrupole mass spectrometry (UPLC-ESI-TQMS). By this method, we found that HCC was also associated with reduced levels of lysophosphocholines and in 4 of 20 patients with increased levels of lysophosphatidic acid [LPA(16:0)], where it correlated with plasma α-fetoprotein levels. Interestingly, when fatty acids were quantitatively profiled by gas chromatography-mass spectrometry (GC-MS), we found that lignoceric acid (24:0) and nervonic acid (24:1) were virtually absent from HCC plasma. Overall, this investigation illustrates the power of the new discovery technologies represented in the UPLC-ESI-QTOFMS platform combined with the targeted, quantitative platforms of UPLC-ESI-TQMS and GC-MS for conducting metabolomic investigations that can engender new insights into cancer pathobiology.

Glacier mass balance reconstruction by sublimation induced enrichment of chemical species on Cerro Tapado (Chilean Andes)

A 36 m long ice core down to bedrock from the Cerro Tapado glacier (5536 m a.s.l, 30°08' S, 69°55' W) was analyzed to reconstruct past climatic conditions for Northern Chile. Because of the marked seasonality in the precipitation (short wet winter and extended dry summer periods) in this region, major snow ablation and related post-depositional processes occur on the glacier surface during summer periods. They include predominantly sublimation and dry deposition. Assuming that, like measured during the field campaign, the enrichment of chloride was always related to sublimation, the chemical record along the ice core may be applied to reconstruct the history of such secondary processes linked to the past climatic conditions over northern Chile. For the time period 1962–1999, a mean annual net accumulation of 316 mm water equivalent (weq) and 327 mm weq loss by sublimation was deduced by this method. This corresponds to an initial total annual accumulation of 539 mm weq. The annual variability of the accumulation and sublimation is related with the Southern Oscillation Index (SOI): higher net-accumulation during El-Niño years and more sublimation during La Niña years. The deepest part of the ice record shows a time discontinuity; with an ice body deposited under different climatic conditions: 290 mm higher precipitation but with reduced seasonal distribution (+470 mm in winter and –180 mm in summer) and –3°C lower mean annual temperature. Unfortunately, its age is unknown. The comparison with regional proxy data however let us conclude that the glacier buildup did most likely occur after the dry mid-Holocene.

Prediction of whole-genome DNA-DNA similarity, determination of G+C content and phylogenetic analysis within the family Pasteurellaceae by multilocus sequence analysis (MLSA)

Genome predictions based on selected genes would be a very welcome approach for taxonomic studies, including DNA-DNA similarity, G+C content and representative phylogeny of bacteria. At present, DNA-DNA hybridizations are still considered the gold standard in species descriptions. However, this method is time-consuming and troublesome, and datasets can vary significantly between experiments as well as between laboratories. For the same reasons, full matrix hybridizations are rarely performed, weakening the significance of the results obtained. The authors established a universal sequencing approach for the three genes recN, rpoA and thdF for the Pasteurellaceae, and determined if the sequences could be used for predicting DNA-DNA relatedness within the family. The sequence-based similarity values calculated using a previously published formula proved most useful for species and genus separation, indicating that this method provides better resolution and no experimental variation compared to hybridization. By this method, cross-comparisons within the family over species and genus borders easily become possible. The three genes also serve as an indicator of the genome G+C content of a species. A mean divergence of around 1 % was observed from the classical method, which in itself has poor reproducibility. Finally, the three genes can be used alone or in combination with already-established 16S rRNA, rpoB and infB gene-sequencing strategies in a multisequence-based phylogeny for the family Pasteurellaceae. It is proposed to use the three sequences as a taxonomic tool, replacing DNA-DNA hybridization.

Gene transfer by viral vectors

To initiate our clinical trial for chemotherapy protection, I established the retroviral vector system for human MDR1 cDNA gene transfer. The human MDR1 cDNA continued to be expressed in the transduced bone marrow cells after four cohorts of serial transplants, 17 months after the initial transduction and transplant. In addition, we used this retroviral vector pVMDR1 to transduce human bone marrow and peripheral blood CD34$\sp+$ cells on stromal monolayer in the presence of hematopoietic growth factors. These data suggest that the retroviral vector pVMDR1 could modify hematopoietic precursor cells with a capacity for long-term self renewal. Thus, it may be possible to use the MDR1 retroviruses to confer chemotherapeutic protection on human normal hematopoietic precursor cells of ovarian and breast cancer patients in whom high doses of MDR drugs may be required to control the diseases.^ Another promising vector system is recombinant adeno-associated virus (rAAV) vector. An impediment to use rAAV vectors is that production of rAAV vectors for clinical use is extremely cumbersome and labor intensive. First I set up the rAAV vector system in our laboratory and then, I focused on studies related to the production of rAAV vectors for clinical use. By using a self-inactivating retroviral vector carrying a selection marker under the control of the CMV immediate early promoter and an AAV genome with the deletion of both ITRs, I have developed either a transient or a stable method to produce rAAV vectors. These methods involve infection only and can generate high-titer rAAV vectors (up to 2 x 10$\sp5$ cfu/ml of CVL) with much less work.^ Although recombinant adenoviral vectors hardly infect early hematopoietic precursor cells lacking $\alpha\sb v\beta\sb5$ or $\alpha\sb v\beta\sb3$ integrin on their surface, but efficiently infect other cells, we can use these properties of adenoviral vectors for bone marrow purging as well as for development of new viral vectors such as pseudotyped retroviral vectors and rAAV vectors. Replacement of self-inactivating retroviral vectors by recombinant adenoviral vectors will facilitate the above strategies for production of new viral vectors. In order to accomplish these goals, I developed a new method which is much more efficient than the current methods to construct adenoviral vectors. This method involves a cosmid vector system which is utilized to construct the full-length recombinant adenoviral vectors in vitro.^ First, I developed an efficient and flexible method for in vitro construction of the full-length recombinant adenoviral vectors in the cosmid vector system by use of a three-DNA fragment ligation. Then, this system was improved by use of a two-DNA fragment ligation. The cloning capacity of recombinant adenoviral vectors constructed by this method to develop recombinant adenoviral vectors depends on the efficiency of transfection only. No homologous recombination is required for development of infectious adenoviral vectors. Thus, the efficiency of generating the recombinant adenoviral vectors by the cosmid method reported here was much higher than that by the in vitro direct ligation method or the in vivo homologous recombination method reported before. This method of the in vitro construction of recombinant adenoviral vectors in the cosmid vector system may facilitate the development of adenoviral vector for human gene therapy. (Abstract shortened by UMI.) ^

CD14-Dependent Monocyte Isolation Enhances Phagocytosis of Listeria monocytogenes by Proinflammatory, GM-CSF-Derived Macrophages

Macrophages are an important line of defence against invading pathogens. Human macrophages derived by different methods were tested for their suitability as models to investigate Listeria monocytogenes (Lm) infection and compared to macrophage-like THP-1 cells. Human primary monocytes were isolated by either positive or negative immunomagnetic selection and differentiated in the presence of granulocyte macrophage colony-stimulating factor (GM-CSF) or macrophage colony-stimulating factor (M-CSF) into pro- or anti-inflammatory macrophages, respectively. Regardless of the isolation method, GM-CSF-derived macrophages (GM-Mφ) stained positive for CD206 and M-CSF-derived macrophages (M-Mφ) for CD163. THP-1 cells did not express CD206 or CD163 following incubation with PMA, M- or GM-CSF alone or in combination. Upon infection with Lm, all primary macrophages showed good survival at high multiplicities of infection whereas viability of THP-1 was severely reduced even at lower bacterial numbers. M-Mφ generally showed high phagocytosis of Lm. Strikingly, phagocytosis of Lm by GM-Mφ was markedly influenced by the method used for isolation of monocytes. GM-Mφ derived from negatively isolated monocytes showed low phagocytosis of Lm whereas GM-Mφ generated from positively selected monocytes displayed high phagocytosis of Lm. Moreover, incubation with CD14 antibody was sufficient to enhance phagocytosis of Lm by GM-Mφ generated from negatively isolated monocytes. By contrast, non-specific phagocytosis of latex beads by GM-Mφ was not influenced by treatment with CD14 antibody. Furthermore, phagocytosis of Lactococcus lactis, Escherichia coli, human cytomegalovirus and the protozoan parasite Leishmania major by GM-Mφ was not enhanced upon treatment with CD14 antibody indicating that this effect is specific for Lm. Based on these observations, we propose macrophages derived by ex vivo differentiation of negatively selected human primary monocytes as the most suitable model to study Lm infection of macrophages.

Towards Faster Method Search Through Static Ecosystem Analysis

Software developers are often unsure of the exact name of the method they need to use to invoke the desired behavior in a given context. This results in a process of searching for the correct method name in documentation, which can be lengthy and distracting to the developer. We can decrease the method search time by enhancing the documentation of a class with the most frequently used methods. Usage frequency data for methods is gathered by analyzing other projects from the same ecosystem - written in the same language and sharing dependencies. We implemented a proof of concept of the approach for Pharo Smalltalk and Java. In Pharo Smalltalk, methods are commonly searched for using a code browser tool called "Nautilus", and in Java using a web browser displaying HTML based documentation - Javadoc. We developed plugins for both browsers and gathered method usage data from open source projects, in order to increase developer productivity by reducing method search time. A small initial evaluation has been conducted showing promising results in improving developer productivity.

Concentration of trace elements in samples of sea water determined by use of two methods of concentrating

A device and a specific procedure for simultaneous concentration of trace ele¬ments from sea water by co-precipitating them in precipitate of magnesium hydroxide obtained by electrolytic alkalization of samples in a two-chamber electrolyzer are described. Analyses of sea water samples for zinc, iron, copper, nickel and lead demonstrate that the method produces a thousand-fold concentration and gives results that agree well with those obtained by extractive concentration using diethyldithiocarbamate and 8-hydroxyquinoline in chloroform. Extracts were analyzed by flame atomic absorption. Correlation coefficients of results obtained with use of these two methods of concentration were 0.76-0.87 for zinc, iron, and copper at confidence levels of 0.05-0.07. Average zinc and iron concentrations determined by the method differed by less than 10%.

Atmospheric Propagation at 100 and 300 GHz: Assessment of a Method to Identify Rainy Conditions during Radiosoundings

The influence of atmospheric gases and tropospheric phenomena becomes more relevant at frequencies within the THz band (100 GHz to 10 THz), severely affecting the propagation conditions. The use of radiosoundings in propagation studies is a well established measurement technique in order to collect information about the vertical structure of the atmosphere, from which gaseous and cloud attenuation can be estimated with the use of propagation models. However, some of these prediction models are not suitable to be used under rainy conditions. In the present study, a method to identify the presence of rainy conditions during radiosoundings is introduced, with the aim of filtering out these events from yearly statistics of predicted atmospheric attenuation. The detection procedure is based on the analysis of a set of parameters, some of them extracted from synoptical observations of weather (SYNOP reports) and other derived from radiosonde observations (RAOBs). The performance of the method has been evaluated under different climatic conditions, corresponding to three locations in Spain, where colocated rain gauge data were available. Rain events detected by the method have been compared with those precipitations identified by the rain gauge. The pertinence Received 26 June 2012, Accepted 31 July 2012, Scheduled 15 August 2012 * Corresponding author: Gustavo Adolfo Siles Soria (gsiles@grc.ssr.upm.es). 258 Siles et al. of the method is discussed on the basis of an analysis of cumulative distributions of total attenuation at 100 and 300 GHz. This study demonstrates that the proposed method can be useful to identify events probably associated to rainy conditions. Hence, it can be considered as a suitable algorithm in order to filter out this kind of events from annual attenuation statistics.

Comments and remarks over classic linear loop-gain method for oscillator design and analysis. New proposed method based on NDF/RRT

Abstract. This paper describes a new and original method for designing oscillators based on the Normalized Determinant Function (NDF) and Return Relations (RRT)- Firstly, a review of the loop-gain method will be performed. The loop-gain method pros, cons and some examples for exploring wrong solutions provided by this method will be shown. This method produces in some cases wrong solutions because some necessary conditions have not been fulfilled. The required necessary conditions to assure a right solution will be described. The necessity of using the NDF or the Transpose Return Relations (RRT), which are related with the True Loop-Gain, to test the additional conditions will be demonstrated. To conclude this paper, the steps for oscillator design and analysis, using the proposed NDF/RRj method, will be presented. The loop-gain wrong solutions will be compared with the NDF/RRj and the accuracy of this method to estimate the oscillation frequency and QL will be demonstrated. Some additional examples of plane reference oscillators (Z/Y/T), will be added and they will be analyzed with the new NDF/RRj proposed method, even these oscillators cannot be analyzed using the classic loop gain method.

Accurate characterization of multi-resonant reflectarray cells by artificial neural networks

This paper describes the accurate characterization of the reflection coefficients of a multilayered reflectarray element by means of artificial neural networks. The procedure has been tested with different RA elements related to actual specifications. Up to 9 parameters were considered and the complete reflection coefficient matrix was accurately obtained, including cross polar reflection coefficients. Results show a good agreement between simulations carried out by the Method of Moments and the ANN model outputs at RA element level, as well as with performances of the complete RA antenna designed.

A quantitative method for evaluating the stabilities of nucleic acids

We report a general method for screening, in solution, the impact of deviations from canonical Watson-Crick composition on the thermodynamic stability of nucleic acid duplexes. We demonstrate how fluorescence resonance energy transfer (FRET) can be used to detect directly free energy differences between an initially formed “reference” duplex (usually a Watson-Crick duplex) and a related “test” duplex containing a lesion/alteration of interest (e.g., a mismatch, a modified, a deleted, or a bulged base, etc.). In one application, one titrates into a solution containing a fluorescently labeled, FRET-active, reference duplex, an unlabeled, single-stranded nucleic acid (test strand), which may or may not compete successfully to form a new duplex. When a new duplex forms by strand displacement, it will not exhibit FRET. The resultant titration curve (normalized fluorescence intensity vs. logarithm of test strand concentration) yields a value for the difference in stability (free energy) between the newly formed, test strand-containing duplex and the initial reference duplex. The use of competitive equilibria in this assay allows the measurement of equilibrium association constants that far exceed the magnitudes accessible by conventional titrimetric techniques. Additionally, because of the sensitivity of fluorescence, the method requires several orders of magnitude less material than most other solution methods. We discuss the advantages of this method for detecting and characterizing any modification that alters duplex stability, including, but not limited to, mutagenic lesions. We underscore the wide range of accessible free energy values that can be defined by this method, the applicability of the method in probing for a myriad of nucleic acid variations, such as single nucleotide polymorphisms, and the potential of the method for high throughput screening.

Redirecting the specificity of ubiquitination by modifying ubiquitin-conjugating enzymes.

Depletion of specific cellular proteins is a powerful tool in biological research and has many medical and agricultural benefits. In contrast to genetic methods currently available to attenuate protein levels, we describe an alternative approach that redirects the ubiquitin-dependent proteolytic pathway to facilitate specific proteolytic removal. Degradation via the ubiquitin pathway requires the prior attachment of multiple ubiquitins to the target protein. This attachment is accomplished, in part, by a family of enzymes designated E2s (or ubiquitin-conjugating enzymes), some of which use domains near their C termini for target recognition. Here, we demonstrate that E2 target recognition can be redefined by engineering E2s to contain appropriate protein-binding peptides fused to their C termini. In five dissimilar examples, chimeric E2s were created that recognized and ubiquitinated their respective binding partners with high specificity. We also show that ubiquitination of one protein targeted by this method led to its ATP-dependent degradation in vitro. Thus, by exploiting interacting domains derived from natural and synthetic ligands, it may be possible to design E2s capable of directing the selective removal of many intracellular proteins.

Acceptability of pandemic A(H1N1) influenza vaccination by Essential Community Workers in 2010 Alicante (Spain), perceived seriousness and sources of information

Objective. Describe acceptability of pandemic A(H1N1) influenza vaccination by Essential Community Workers (ECWs) from Alicante province (Spain) in January 2010. Evaluate the correlation with attitudes, beliefs, professional advice and information broadcasted by media. Method. In this cross-sectional study, face-to-face interviews were conducted with 742 ECWs to assess their attitudes towards vaccination against the pandemic influenza strain. A multivariable regression model was made to adjust the Odds Ratios (ORs). Results. Some ECWs reported having been vaccinated with seasonal vaccine, 21.5% (95%IC 18.6–24.9); only 15.4% (95%IC 12.8–18.4) with the pandemic one. ECWs vaccinated regularly against seasonal flu (OR 5.1; 95%IC 2.9–9.1), those who considered pandemic influenza as a severe or more serious disease than seasonal flu (OR 3.8; 95%IC 2.1–6.7) and those who never had doubts about vaccine safety (OR 3.7; 95%IC2.1–6.7) had a better acceptance of pandemic vaccine. Finally, 78.7% (95%IC 75.1–81.4) had doubts about pandemic vaccine's effectiveness. Conclusion. The vast amount of information provided by the media did not seem to be decisive to prevent doubts or to improve the acceptability of the vaccine in ECWs. Professional advice should be the focus of interest in future influenza vaccination campaigns. These results should be taken into account by health authorities.

Photocatalytic oxidation of propene in gas phase at low concentration by optimized TiO2 nanoparticles

In the present study, nanocrystalline titanium dioxide (TiO2) was prepared by sol–gel method at low temperature from titanium tetraisopropoxide (TTIP) and characterized by different techniques (gas adsorption, XRD, TEM and FTIR). Variables of the synthesis, such as the hydrolyzing agent (acetic acid or isopropanol) and calcination temperatures (300–800 °C), were analyzed to get uniform size TiO2 nanoparticles. The effect that these two variables have on the structure of the resultant TiO2 nanoparticles and on their photocatalytic activity is investigated. The photocatalytic activities of TiO2 nanoparticles were evaluated for propene oxidation at low concentration (100 ppmv) under two different kinds of UV light (UV-A ∼ 365 nm and UV-C ∼ 257.7 nm) and compared with Degussa TiO2 P-25, used as reference sample. The results show that both hydrolyzing agents allow to prepare TiO2 nanoparticles and that the hydrolyzing agent influences the crystalline structure and its change with the thermal treatments. Interestingly, the prepared TiO2 nanoparticles possess anatase phase with small crystalline size, high surface area and higher photocatalytic activity for propene oxidation than commercial TiO2 (Degussa P-25) under UV-light. Curiously, these prepared TiO2 nanoparticles are more active with the 365 nm source than with the 257.7 nm UV-light, which is a remarkable advantage from an application point of view. Additionally, the obtained results are particularly good when acetic acid is the hydrolyzing agent at both wavelengths used, possibly due to the high crystallinity, low anatase phase size and high surface oxygen groups’ content in the nanoparticles prepared with it, in comparison to those prepared using isopropanol.