North African populations carry the signature of admixture with Neandertals

One of the main findings derived from the analysis of the Neandertal genome was the evidence for admixture between Neandertals and non-African modern humans. An alternative scenario is that the ancestral population of non-Africans was closer to Neandertals than to Africans because of ancient population substructure. Thus, the study of North African populations is crucial for testing both hypotheses. We analyzed a total of 780,000 SNPs in 125 individuals representing seven different North African locations and searched for their ancestral/derived state in comparison to different human populations and Neandertals. We found that North African populations have a significant excess of derived alleles shared with Neandertals, when compared to sub-Saharan Africans. This excess is similar to that found in non-African humans, a fact that can be interpreted as a sign of Neandertal admixture. Furthermore, the Neandertal's genetic signal is higher in populations with a local, pre-Neolithic North African ancestry. Therefore, the detected ancient admixture is not due to recent Near Eastern or European migrations. Sub-Saharan populations are the only ones not affected by the admixture event with Neandertals.

The fusion protein SS18-SSX1 employs core Wnt pathway transcription factors to induce a partial Wnt signature in synovial sarcoma.

Expression of the SS18/SYT-SSX fusion protein is believed to underlie the pathogenesis of synovial sarcoma (SS). Recent evidence suggests that deregulation of the Wnt pathway may play an important role in SS but the mechanisms whereby SS18-SSX might affect Wnt signaling remain to be elucidated. Here, we show that SS18/SSX tightly regulates the elevated expression of the key Wnt target AXIN2 in primary SS. SS18-SSX is shown to interact with TCF/LEF, TLE and HDAC but not β-catenin in vivo and to induce Wnt target gene expression by forming a complex containing promoter-bound TCF/LEF and HDAC but lacking β-catenin. Our observations provide a tumor-specific mechanistic basis for Wnt target gene induction in SS that can occur in the absence of Wnt ligand stimulation.

Headspace needle-trap analysis of priority volatile organic compounds from aqueous samples: application to the analysis of natural and waste waters

Combining headspace (HS) sampling with a needle-trap device (NTD) to determine priority volatile organic compounds (VOCs) in water samples results in improved sensitivity and efficiency when compared to conventional static HS sampling. A 22 gauge stainless steel, 51-mm needle packed with Tenax TA and Carboxen 1000 particles is used as the NTD. Three different HS-NTD sampling methodologies are evaluated and all give limits of detection for the target VOCs in the ng L−1 range. Active (purge-and-trap) HS-NTD sampling is found to give the best sensitivity but requires exhaustive control of the sampling conditions. The use of the NTD to collect the headspace gas sample results in a combined adsorption/desorption mechanism. The testing of different temperatures for the HS thermostating reveals a greater desorption effect when the sample is allowed to diffuse, whether passively or actively, through the sorbent particles. The limits of detection obtained in the simplest sampling methodology, static HS-NTD (5 mL aqueous sample in 20 mL HS vials, thermostating at 50 °C for 30 min with agitation), are sufficiently low as to permit its application to the analysis of 18 priority VOCs in natural and waste waters. In all cases compounds were detected below regulated levels

Experimental Identification of Actinobacillus pleuropneumoniae Strains L20 and JL03 Heptosyltransferases, Evidence for a New Heptosyltransferase Signature Sequence.

We experimentally identified the activities of six predicted heptosyltransferases in Actinobacillus pleuropneumoniae genome serotype 5b strain L20 and serotype 3 strain JL03. The initial identification was based on a bioinformatic analysis of the amino acid similarity between these putative heptosyltrasferases with others of known function from enteric bacteria and Aeromonas. The putative functions of all the Actinobacillus pleuropneumoniae heptosyltrasferases were determined by using surrogate LPS acceptor molecules from well-defined A. hydrophyla AH-3 and A. salmonicida A450 mutants. Our results show that heptosyltransferases APL_0981 and APJL_1001 are responsible for the transfer of the terminal outer core D-glycero-D-manno-heptose (D,D-Hep) residue although they are not currently included in the CAZY glycosyltransferase 9 family. The WahF heptosyltransferase group signature sequence [S(T/S)(GA)XXH] differs from the heptosyltransferases consensus signature sequence [D(TS)(GA)XXH], because of the substitution of D(261) for S(261), being unique.

A Headspace needle-trap method for the analysis of volatile organic compounds in whole blood

Needle trap devices (NTDs) are a relatively new and promising tool for headspace (HS) analysis. In this study, a dynamic HS sampling procedure is evaluated for the determination of volatile organic compounds (VOCs) in whole blood samples. A full factorial design was used to evaluate the influence of the number of cycles and incubation time and it is demonstrated that the controlling factor in the process is the number of cycles. A mathematical model can be used to determine the most appropriate number of cycles required to adsorb a prefixed amount of VOCs present in the HS phase whenever quantitative adsorption is reached in each cycle. Matrix effect is of great importance when complex biological samples, such as blood, are analyzed. The evaluation of the salting out effect showed a significant improvement in the volatilization of VOCs to the HS in this type of matrices. Moreover, a 1:4 (blood:water) dilution is required to obtain quantitative recoveries of the target analytes when external calibration is used. The method developed gives detection limits in the 0.020–0.080 μg L−1 range (0.1–0.4 μg L−1 range for undiluted blood samples) with appropriate repeatability values (RSD < 15% at high level and <23% at LOQ level). Figure of merits of the method can be improved by using a smaller phase ratio (i.e., an increase in the blood volume and a decrease in the HS volume), which lead to lower detection limits, better repeatability values and greater sensibility. Twenty-eight blood samples have been evaluated with the proposed method and the results agree with those indicated in other studies. Benzene was the only target compound that gave significant differences between blood levels detected in volunteer non-smokers and smokers

Seasonal variation in the composition of volatile oils from Schinus terebinthifolius raddi

Essential oils from leaves, ripe and unripe fruits of Schinus terebinthifolius growing in Brazil were investigated. Oil content from either ripe or unripe fruits was similar (4.65% and 3.98%, respectively). Sesquiterpenes (from 78.0% to 90.4%) dominated the oil content of both leaves and unripe fruit. The essential oils were tested in vitro for their allelopathic activity on germination and radicle growth of Lactuca sativa and Cucumis sativus at 1,000 and 10,000 µg mL-1concentrations. The three samples tested were more active in inhibiting the radicle growth for L. sativa (88.6-92.4%) than for C. sativus (50.5-84.5%) at 10,000 µg mL-1 concentration.

Volatile constituents of the oils from Povedadaphne Quadriporata (lauraceae) from "Alberto M. Brenes" biological preserve, Costa Rica

The composition of the leaf, bark and wood oils of Povedadaphne quadriporata W. Burger from Costa Rica were analyzed by capillary GC/FID and GC/MS. One hundred and sixty-three compounds were identified. The major components from the leaf oil were a-pinene (21.2%), germacrene D (18.1%), b-pinene (14.8%), a-phellandrene (7.8%), a-copaene (6.6%), b-caryophyllene (6.1%) and d-cadinene (3.5%). From bark oil, the main constituents were a-pinene (27.7%), p-cymene (7.8%), b-pinene (7.4%), camphene (3.6%), a-copaene (3.5%) and limonene (3.3%). From wood oil, 1,10-di-epi-cubenol (8.0%), a-eudesmol (3.4%), cadalene (3.4%) and d-cadinene (3.0%) were the major compounds identified. This paper describes for the first time the composition of essential oils in this unique species and genus.

Plasma polymerized acetaldehyde thin films for retention of volatile organic compounds

The aim of this work is the production and characterization of plasma polymerized acetaldehyde thin films. These films show highly polar species, are hydrophilic, organophilic and easily adsorb organic reactants with CO radicals but only allow permeation of reactants with OH radicals. The good step coverage of films deposited on aluminum trenches is useful for sensor development. Films deposited on hydrophobic substrates may result in a discontinued layer, which allows the use of preconcentration in sample pretreatment. Deposition on microchannels showed the possibility of chromatographic columns and/or retention system production to selectively detect or remove organic compounds from gas flows.

Volatile compounds in the thermoplastic extrusion of bovine rumen

The volatile compounds of raw and extruded bovine rumen, extracted by dynamic headspace, were separated by gas chromatography and analyzed by GC-MS. Raw and extruded materials presented thirty-two volatile compounds. The following compounds were identified in raw bovine rumen: heptane, 1-heptene, 4-methyl-2-pentanone, toluene, hexanal, ethyl butyrate, o-xylene, m-xylene, p-xylene, heptanal, limonene, nonanal, dodecane, tridecane, tetradecane, pentadecane, hexadecane, heptadecane and octadecane. The following compounds were identified in the extruded material: 1-heptene, 2,4-dimethylhexane, toluene, limonene, undecane, tetradecane, pentadecane, hexadecane, heptadecane, octadecane and nonadecane. Mass spectra of some unidentified compounds indicated the presence of hydrocarbons with branched chains or cyclic structure.

Ambiental volatile organic compounds in the megacity of São Paulo

In order to characterize the composition of the main urban air organic compounds in the megacity of Sao Paulo, analysis of samples collected during the winter of 2003 downtown was carried out. The samplings were performed on the roof of a building in the commercial center of São Paulo. Hydrocarbons and carbonyls compounds were collected on August 4, 5 and 6. Comparing to previous data, the concentration of hydrocarbons presented no decrease in the concentration, except for the aldehydes, which decreased when compared to previous data. Among the HCs species analyzed, the highest concentrations observed were those of toluene (7.5 ± 3.4 ppbv), n-decane (3.2 ± 2.0 ppbv), benzene (2.7 ± 1.4 ppbv) and 1,3,5-trimethylbenzene (2.2 ± 1.5 ppbv).

Volatile compounds of Nectandra salicina (lauraceae) from Costa Rica and their cytotoxic activity on cell lines

The chemical composition of the volatiles of Nectandra salicina growing wild in Costa Rica was determined by capillary GC/FID and GC/MS. Thirty-seven and forty-two compounds were identified in the leaf and branch oils respectively corresponding to about 92.6 and 86.2% of the total amount of the oils. The major components of the leaf oil were: atractylone (14.6%), viridiflorene (10.1%), α-pinene (9.4%), β-caryophyllene (7.2%), α-humulene (7.0%), δ-cadinene (6.1%), β-pinene (6.0%) and germacrene D (5.8%). The major components of the branch oil were: atractylone (21.1%), germacrene D (10.7%), viridiflorene (7.9%) and 7-epi-α-selinene (5.0%). When the oils were tested on different cell lines, all the LD50 values were higher than 150 µg/mL, with values very similar for the leaf and branch oils. Low toxicity could be explained by antagonistic effects among the main compounds present in the oils.

Volatile compounds from Rosmarinus officinalis L. and Baccharis dracunculifolia DC. Growing in southeast coast of Brazil

Chemical composition of leaf volatiles of Rosmarinus officinalis and Baccharis dracunculifolia cultured in Southeast of Brazil has been characterized by GC/MS after simultaneous distillation-extraction. The main components in volatiles of these species showed in common α-pinene, myrcene, 1,8 cineole and camphor. Camphor was the major component among volatiles of B. dracunculifolia and R. officinalis with concentrations exceeding 25%. B. dracunculifolia volatiles possessed more sesquiterpenes (21.4%) than R. officinalis (16.7%), such as caryophyllene (1.9%) and α-humulene (0.4%). Lower concentrations of nerolidol and spathulenol were achieved in volatiles of B. dracunculifolia. Considering both species, there was a predominance of monoterpenes.

Chemical composition of volatile oils from leaves of Nectandra megapotamica Spreng. (Lauraceae)

The volatile oils from Nectandra megapotamica Spreng. leaves, collected in February and August of 2007 and at 7:00 and 12:00 h (samples A - D), were extracted by hydrodistillation and the chemical composition was analyzed by GC-FID and GC/MS. A total of nineteen compounds were identified with predominance of oxygenated sesquiterpenes, among them, α-bisabolol, was the main constituent (62.3-69.4 %). After chromatographic separation procedures, this compound was purified from crude oil and its structure was confirmed by analysis of NMR data. This paper describes for the first time the composition of the leaves volatile oil from N. megapotamica.

Interespecific variation in the composition of volatile oils from the leaves of Swietenia macrophylla King (Meliaceae)

The volatile oils from leaves of five Brazilian specimens of Swietenia macrophylla King (Meliaceae) collected in three different Amazon Rainforest Conservation Areas in the States of Mato Grosso, Pará, and Rondônia were extracted and analyzed by GC and GC/MS. The oils showed to be composed by terpenoids, majority hydrocarbon sesquiterpenes, being germacrene D (20.5-46.8%) and bicyclogermacrene (8.3-11.1%) the main components. Besides these derivatives, only α-cubebene, β-caryophyllene, β-gurjunene and γ-cadinene were detected in all of the analyzed samples. This analysis indicated a great diversity of constituents in the oils obtained from specimens collected in these regions, which could be associated to the different susceptibility in the attack of H. grandella in S. macrophylla cultures.