Analyses of six homologous proteins of Protochlamydia amoebophila UWE25 encoded by large GC-rich genes (lgr): a model of evolution and concatenation of leucine-rich repeats.

BACKGROUND: Along the chromosome of the obligate intracellular bacteria Protochlamydia amoebophila UWE25, we recently described a genomic island Pam100G. It contains a tra unit likely involved in conjugative DNA transfer and lgrE, a 5.6-kb gene similar to five others of P. amoebophila: lgrA to lgrD, lgrF. We describe here the structure, regulation and evolution of these proteins termed LGRs since encoded by "Large G+C-Rich" genes. RESULTS: No homologs to the whole protein sequence of LGRs were found in other organisms. Phylogenetic analyses suggest that serial duplications producing the six LGRs occurred relatively recently and nucleotide usage analyses show that lgrB, lgrE and lgrF were relocated on the chromosome. The C-terminal part of LGRs is homologous to Leucine-Rich Repeats domains (LRRs). Defined by a cumulative alignment score, the 5 to 18 concatenated octacosapeptidic (28-meric) LRRs of LGRs present all a predicted alpha-helix conformation. Their closest homologs are the 28-residue RI-like LRRs of mammalian NODs and the 24-meres of some Ralstonia and Legionella proteins. Interestingly, lgrE, which is present on Pam100G like the tra operon, exhibits Pfam domains related to DNA metabolism. CONCLUSION: Comparison of the LRRs, enable us to propose a parsimonious evolutionary scenario of these domains driven by adjacent concatenations of LRRs. Our model established on bacterial LRRs can be challenged in eucaryotic proteins carrying less conserved LRRs, such as NOD proteins and Toll-like receptors.

Initial Results on the Composition of Fingerprints and its Evolution as a Function of Time by GC/MS Analysis

Determining the time since deposition of fingermarks may prove necessary to assess their relevance to criminal investigations. The crucial factor is the initial composition of fingermarks, because it represents the starting point of any aging model. This study mainly aimed to characterize the initial composition of fingerprints, which show a high variability between donors (inter-variability), but also to investigate the variations among fingerprints from the same donor (intra-variability). Solutions to reduce this initial variability using squalene and cholesterol as target compounds are proposed and should be further investigated. The influence of substrates was also evaluated, and the initial composition was observed to be larger on porous surface than nonporous surfaces. Preliminary aging of fingerprints over 30 days was finally studied on a porous and a nonporous substrate to evaluate the potential for dating of fingermarks. Squalene was observed to decrease in a faster rate on a nonporous substrate.

Características estruturais de ácidos húmicos isolados de solos com adição de resíduos orgânicos de origem urbana: composição elementar, análise de RMN 13C e Pi-CG/EM

Foram avaliadas as alterações nas características estruturais de ácidos húmicos (AH) decorrentes da adição de matéria orgânica de resíduos urbanos. Os AH foram extraídos da camada superficial (0-20 cm) de um Argissolo Vermelho-Amarelo (Seropédica, RJ) e de um Latossolo Vermelho Amarelo (Piraí, RJ), ambos tratados com o equivalente a 80 t ha-1 (em base seca) de composto de lixo urbano e lodo de estação de tratamento de esgotos. O tempo de incubação em laboratório foi de 24 semanas à temperatura ambiente e umidade mantida na capacidade de campo. Para caracterizar os AH, foram utilizadas a análise elementar, a ressonância magnética nuclear (RMN) de 13C e Pirólise acoplada à cromatografia gasosa e a espectrometria de massas (Pi-CG/EM). A análise de RMN 13C permitiu observar alterações na composição molecular dos AH de forma clara, principalmente, pelo aumento do teor de C mono e di oxigenados (δC 50-110) e pela diminuição dos teores de grupos CH2 e CH3 (δC 50-110). O aumento no teor de carboidratos evidencia a presença de estruturas mais lábeis nos AH com adição dos resíduos. Em adição, a técnica de Pi-CG/EM permitiu verificar diferenças qualitativas significativas nos compostos orgânicos, provenientes da fragmentação térmica dos AH com incorporação de novas estruturas, sobretudo da fração lipídica e de derivados de carboidratos (furanos), nas amostras de solos tratados com ambos os resíduos orgânicos. O uso em conjunto das técnicas analíticas de RMN 13C e de Pi-CG/EM foi eficiente para avaliar as mudanças na composição molecular de ácidos húmicos decorrentes da adição de resíduos orgânicos de origem urbana.

Quantification of brain glycogen concentration and turnover through localized 13C NMR of both the C1 and C6 resonances.

We have recently shown that at isotopic steady state (13)C NMR can provide a direct measurement of glycogen concentration changes, but that the turnover of glycogen was not accessible with this protocol. The aim of the present study was to design, implement and apply a novel dual-tracer infusion protocol to simultaneously measure glycogen concentration and turnover. After reaching isotopic steady state for glycogen C1 using [1-(13)C] glucose administration, [1,6-(13)C(2)] glucose was infused such that isotopic steady state was maintained at the C1 position, but the C6 position reflected (13)C label incorporation. To overcome the large chemical shift displacement error between the C1 and C6 resonances of glycogen, we implemented 2D gradient based localization using the Fourier series window approach, in conjunction with time-domain analysis of the resulting FIDs using jMRUI. The glycogen concentration of 5.1 +/- 1.6 mM measured from the C1 position was in excellent agreement with concomitant biochemical determinations. Glycogen turnover measured from the rate of label incorporation into the C6 position of glycogen in the alpha-chloralose anesthetized rat was 0.7 micromol/g/h.

Hydrogen sulfide measurement by headspace-gas chromatography-mass spectrometry (HS-GC-MS): application to gaseous samples and gas dissolved in muscle.

The aim of our study was to present a new headspace-gas chromatography-mass spectrometry (HS-GC-MS) method applicable to the routine determination of hydrogen sulfide (H(2)S) concentrations in biological and gaseous samples. The primary analytical drawback of the GC/MS methods for H(2)S measurement discussed in the literature was the absence of a specific H(2)S internal standard required to perform quantification. Although a deuterated hydrogen sulfide (D(2)S) standard is currently available, this standard is not often used because this standard is expensive and is only available in the gas phase. As an alternative approach, D(2)S can be generated in situ by reacting deuterated chloride with sodium sulfide; however, this technique can lead to low recovery yield and potential isotopic fractionation. Therefore, N(2)O was chosen for use as an internal standard. This method allows precise measurements of H(2)S concentrations in biological and gaseous samples. Therefore, a full validation using accuracy profile based on the β-expectation tolerance interval is presented. Finally, this method was applied to quantify H(2)S in an actual case of H(2)S fatal intoxication.

Construction and Quantitative Evaluation of a Dual Specific Promoter System for Monitoring the Expression Status of Stra8 and c-kit Genes.

Applications of genetic constructs with multiple promoters, which are fused with reporter genes and simultaneous monitoring of various events in cells, have gained special attention in recent years. Lentiviral vectors, with their distinctive characteristics, have been considered to monitor the developmental changes of cells in vitro. In this study, we constructed a novel lentiviral vector (FUM-M), containing two germ cell-specific promoters (Stra8 and c-kit), fused with ZsGreen and DsRed2 reporter genes, and evaluated its efficiency in different cells following treatments with retinoic acid and DMSO. Several cell lines (P19, GC-1 spg and HEK293T) were transduced with this vector, and functional capabilities of the promoters were verified by flow cytometry and quantitative RT-PCR. Our results indicate that FUM-M shows dynamic behavior in the presence and absence of extrinsic factors. A correlation was also observed between the function of promoters, present in the lentiviral construct and the endogenous level of the Stra8 and c-kit mRNAs in the cells. In conclusion, we recommend this strategy, which needs further optimization of the constructs, as a beneficial and practical way to screen chemical inducers involved in cellular differentiation toward germ-like cells.

Geoecological drivers of cerrado heterogeneity and 13C natural abundance in oxisols after land-use change

The 13C natural abundance technique was applied to study C dynamics after land-use change from native savanna to Brachiaria, Pinus, and Eucalyptus in differently textured Cerrado Oxisols. But due to differences in the d13C signatures of subsoils under native savanna and under introduced species, C substitution could only be calculated based on results of cultivated soils nearby. It was estimated that after 20 years, Pinus C had replaced only 5 % of the native C in the 0-1.2 m layer, in which substitution was restricted to the top 0.4 m. Conversely, after 12 years, Brachiaria had replaced 21 % of Cerrado C to a depth of 1.2 m, where substitution decreased only slightly throughout the entire profile. The high d13C values in the subsoils of the cultivated sites led to the hypothesis that the natural vegetation there had been grassland rather than Cerrado sensu stricto, in spite of the comparable soil and site characteristics and the proximity of the studied sites. The hypothesis was tested using aerial photographs of 1964, which showed that the cultivated sites were located on a desiccated runoff head. The vegetation shift to a grass-dominated savanna formation might therefore have occurred in response to waterlogging and reduced soil aeration. A simple model was developed thereof, which ascribes the different Cerrado formations mainly to the plant-available water content and soil aeration. Soil fertility is considered of minor significance only, since at the studied native savanna sites tree density was independent of soil texture or nutrient status.

1H-[13C] NMR spectroscopy of the rat brain during infusion of [2-13C] acetate at 14.1 T.

Full signal intensity (1)H-[(13)C] NMR spectroscopy, combining a preceding (13)C-editing block based on an inversion BISEP (B(1)-insensitive spectral editing pulse) with a spin-echo coherence-based localization, was developed and implemented at 14.1 T. (13)C editing of the proposed scheme was achieved by turning on and off the (13)C adiabatic full passage in the (13)C-editing block to prepare inverted and noninverted (13)C-coupled (1)H coherences along the longitudinal axis prior to localization. The novel (1)H-[(13)C] NMR approach was applied in vivo under infusion of the glia-specific substrate [2-(13)C] acetate. Besides a approximately 50% improvement in sensitivity, spectral dispersion was enhanced at 14.1 T, especially for J-coupled metabolites such as glutamate and glutamine. A more distinct spectral structure at 1.9-2.2 ppm(parts per million) was observed, e.g., glutamate C3 showed a doublet pattern in both simulated (1)H spectrum and in vivo (13)C-edited (1)H NMR spectra. Besides (13)C time courses of glutamate C4 and glutamine C4, the time courses of glutamate C3 and glutamine C3 obtained by (1)H-[(13)C] NMR spectroscopy were reported for the first time. Such capability should greatly improve the ability to study neuron-glial metabolism using (1)H-observed (13)C-edited NMR spectroscopy.

Carbono total e δ13C em agregados do solo sob vegetação nativa e pastagem no bioma cerrado

Diferentes sistemas de uso e manejo alteram o teor de carbono no solo (C), porém diminuições no C do solo têm sido reportadas quando áreas de Cerrado nativo são convertidas em pastagem. Disso resulta a necessidade da realização de pesquisas em diferentes sistemas e condições edafoclimáticas, a fim de elucidar as tendências encontradas. O objetivo deste trabalho foi avaliar a agregação, os teores de C e a abundância natural de δ13C do solo em uma área cultivada há nove anos sob lavoura seguida de 20 anos sob pastagem, a qual atualmente apresenta sinais de degradação (PA), comparando-a a uma vegetação nativa no bioma Cerrado (CE) que ocorre em área adjacente. As áreas de estudo estão localizadas no município de Rio Verde (GO), em solo classificado como Latossolo Vermelho distrófico, de textura argilosa. Em amostras de solo coletadas nas camadas de 0-5, 5-10 e 10-20 cm de profundidade, foram determinados a distribuição de agregados estáveis em água (micro, meso e macroagregados), o diâmetro médio aritmético (DMA) e geométrico (DMG), os teores de C total e de δ13C, o tempo de residência média do C (TRM) e a fração da matéria orgânica leve livre (FLL). Os resultados indicaram que o uso sob lavoura seguido de pastagem reduziu em 21 % o estoque de C original, possivelmente devido ao menor aporte de material na FLL. O solo apresentou elevada agregação e não houve diferenças significativas entre as áreas avaliadas. No entanto, os teores de C nos macroagregados foram menores na PA em relação ao CE, enquanto nos microagregados não houve diferença entre os sistemas de uso, sugerindo, respectivamente, maior e menor sensibilidade ao manejo e menor e maior proteção do C por essas classes de agregados. Os valores de TRM e as análises isotópicas reforçaram esses resultados, mostrando, ainda, substituição de 83 % do C original durante os 29 anos de cultivo. O constante aporte de resíduos vegetais, assim como a manutenção do C no interior dos macro e mesoagregados, são importantes fatores para que ocorra o acúmulo de C nesse tipo de solo.

Carbono, nitrogênio e abundância natural de δ13c e δ15n em uma cronossequência de agricultura sob plantio direto no cerrado goiano

A conversão do cerrado nativo em sistemas agropecuários pode alterar com o passar dos anos de cultivo os teores de C e N, bem como o sinal isotópico do δ13C e δ15N do solo. Desta forma, o objetivo deste trabalho foi avaliar os teores de C, N e abundância natural de δ13C e δ15N no perfil do solo em uma cronossequência de agricultura sob sistema plantio direto (SPD) no cerrado goiano. Para isso, em Montividiu, GO, foram selecionadas áreas sob SPD com diferentes tempos de implantação: SPD com três anos de implantação (SPD3), SPD com 15 anos de implantação (SPD15) e SPD com 20 anos de implantação (SPD20), as quais foram comparadas com áreas de cerrado nativo (CE) e pastagem (PA). Foram coletadas amostras de solo nas profundidades de 0,00-0,05; 0,05-0,10; 0,10-0,20; 0,20-0,30; 0,30-0,40; 0,40-0,50; 0,50-0,60; 0,60-0,80; e 0,80-1,00 m. O solo das áreas de estudo foi classificado como Latossolo Vermelho distroférrico. O manejo do solo sob SPD após 20 anos aumentou os teores de C e N na camada superficial do solo (0,00-0,05 m), em relação às outras áreas avaliadas. Nas demais profundidades avaliadas, observou-se que está ocorrendo aumento nos teores C e N com o passar dos anos de adoção do SPD (três para 15 anos); no entanto, tais áreas ainda não foram capazes de recuperar os teores desses elementos em relação à vegetação nativa de CE. Por meio dos resultados de δ13C, pôde-se constatar que a origem da MOS nas áreas de SPD é referente à plantas do ciclo fotossintético C4. Verificou-se que até os 0,30 m do perfil do solo os resultados de δ13C estão reduzindo com o passar dos anos de adoção do SPD. Os menores e maiores valores de δ15N foram encontrados nas áreas de CE e PA, SPD3, enquanto SPD15 e SPD20 apresentaram valores intermediários de δ15N, em relação às demais áreas avaliadas.

Combining protein identification and quantification: C-terminal isotope-coded tagging using sulfanilic acid.

Two methods of differential isotopic coding of carboxylic groups have been developed to date. The first approach uses d0- or d3-methanol to convert carboxyl groups into the corresponding methyl esters. The second relies on the incorporation of two 18O atoms into the C-terminal carboxylic group during tryptic digestion of proteins in H(2)18O. However, both methods have limitations such as chromatographic separation of 1H and 2H derivatives or overlap of isotopic distributions of light and heavy forms due to small mass shifts. Here we present a new tagging approach based on the specific incorporation of sulfanilic acid into carboxylic groups. The reagent was synthesized in a heavy form (13C phenyl ring), showing no chromatographic shift and an optimal isotopic separation with a 6 Da mass shift. Moreover, sulfanilic acid allows for simplified fragmentation in matrix-assisted laser desorption/ionization (MALDI) due the charge fixation of the sulfonate group at the C-terminus of the peptide. The derivatization is simple, specific and minimizes the number of sample treatment steps that can strongly alter the sample composition. The quantification is reproducible within an order of magnitude and can be analyzed either by electrospray ionization (ESI) or MALDI. Finally, the method is able to specifically identify the C-terminal peptide of a protein by using GluC as the proteolytic enzyme.

A comparison of in vivo 13C MR brain glycogen quantification at 9.4 and 14.1 T.

The high molecular weight and low concentration of brain glycogen render its noninvasive quantification challenging. Therefore, the precision increase of the quantification by localized (13) C MR at 9.4 to 14.1 T was investigated. Signal-to-noise ratio increased by 66%, slightly offset by a T(1) increase of 332 ± 15 to 521 ± 34 ms. Isotopic enrichment after long-term (13) C administration was comparable (≈ 40%) as was the nominal linewidth of glycogen C1 (≈ 50 Hz). Among the factors that contributed to the 66% observed increase in signal-to-noise ratio, the T(1) relaxation time impacted the effective signal-to-noise ratio by only 10% at a repetition time = 1 s. The signal-to-noise ratio increase together with the larger spectral dispersion at 14.1 T resulted in a better defined baseline, which allowed for more accurate fitting. Quantified glycogen concentrations were 5.8 ± 0.9 mM at 9.4 T and 6.0 ± 0.4 mM at 14.1 T; the decreased standard deviation demonstrates the compounded effect of increased magnetization and improved baseline on the precision of glycogen quantification.

Glutamatergic and GABAergic energy metabolism measured in the rat brain by (13) C NMR spectroscopy at 14.1 T.

Energy metabolism supports both inhibitory and excitatory neurotransmission processes. This study investigated the specific contribution of astrocytic metabolism to γ-aminobutyric acid (GABA) synthesis and inhibitory GABAergic neurotransmission that remained to be ilucidated in vivo. Therefore, we measured (13) C incorporation into brain metabolites by dynamic (13) C nuclear magnetic resonance spectroscopy at 14.1 T in rats under α-chloralose anaesthesia during infusion of [1,6-(13) C]glucose. The enhanced sensitivity at 14.1 T allowed to quantify incorporation of (13) C into the three aliphatic carbons of GABA non-invasively. Metabolic fluxes were determined with a mathematical model of brain metabolism comprising glial, glutamatergic and GABAergic compartments. GABA synthesis rate was 0.11 ± 0.01 μmol/g/min. GABA-glutamine cycle was 0.053 ± 0.003 μmol/g/min and accounted for 22 ± 1% of total neurotransmitter cycling between neurons and glia. Cerebral glucose oxidation was 0.47 ± 0.02 μmol/g/min, of which 35 ± 1% and 7 ± 1% was diverted to the glutamatergic and GABAergic tricarboxylic acid cycles, respectively. The remaining fraction of glucose oxidation was in glia, where 12 ± 1% of the TCA cycle flux was dedicated to oxidation of GABA. 16 ± 2% of glutamine synthesis was provided to GABAergic neurons. We conclude that substantial metabolic activity occurs in GABAergic neurons and that glial metabolism supports both glutamatergic and GABAergic neurons in the living rat brain. We performed (13) C NMR spectroscopy in vivo at high magnetic field (14.1 T) upon administration of [1,6-(13) C]glucose. This allowed to measure (13) C incorporation into the three aliphatic carbons of GABA in the rat brain, in addition to those of glutamate, glutamine and aspartate. These data were then modelled to determine fluxes of energy metabolism in GABAergic and glutamatergic neurons and glial cells.

Measurements of glial metabolic fluxes with C-11-acetate using positron emission and an adapted NMR-based metabolic modeling approach

Objectives: Acetate brain metabolism has the particularity to occur specifically in glial cells. Labeling studies, using acetate labeled either with 13C (NMR) or 11C (PET), are governed by the same biochemical reactions and thus follow the same mathematical principles. In this study, the objective was to adapt an NMR acetate brain metabolism model to analyse [1-11C]acetate infusion in rats. Methods: Brain acetate infusion experiments were modeled using a two-compartment model approach used in NMR.1-3 The [1-11C]acetate labeling study was done using a beta scintillator.4 The measured radioactive signal represents the time evolution of the sum of all labeled metabolites in the brain. Using a coincidence counter in parallel, an arterial input curve was measured. The 11C at position C-1 of acetate is metabolized in the first turn of the TCA cycle to the position 5 of glutamate (Figure 1A). Through the neurotransmission process, it is further transported to the position 5 of glutamine and the position 5 of neuronal glutamate. After the second turn of the TCA cycle, tracer from [1-11C]acetate (and also a part from glial [5-11C]glutamate) is transferred to glial [1-11C]glutamate and further to [1-11C]glutamine and neuronal glutamate through the neurotransmission cycle. Brain poster session: oxidative mechanisms S460 Journal of Cerebral Blood Flow & Metabolism (2009) 29, S455-S466 Results: The standard acetate two-pool PET model describes the system by a plasma pool and a tissue pool linked by rate constants. Experimental data are not fully described with only one tissue compartment (Figure 1B). The modified NMR model was fitted successfully to tissue time-activity curves from 6 single animals, by varying the glial mitochondrial fluxes and the neurotransmission flux Vnt. A glial composite rate constant Kgtg=Vgtg/[Ace]plasma was extracted. Considering an average acetate concentration in plasma of 1 mmol/g5 and the negligible additional amount injected, we found an average Vgtg = 0.08±0.02 (n = 6), in agreement with previous NMR measurements.1 The tissue time-activity curve is dominated by glial glutamate and later by glutamine (Figure 1B). Labeling of neuronal pools has a low influence, at least for the 20 mins of beta-probe acquisition. Based on the high diffusivity of CO2 across the blood-brain barrier; 11CO2 is not predominant in the total tissue curve, even if the brain CO2 pool is big compared with other metabolites, due to its strong dilution through unlabeled CO2 from neuronal metabolism and diffusion from plasma. Conclusion: The two-compartment model presented here is also able to fit data of positron emission experiments and to extract specific glial metabolic fluxes. 11C-labeled acetate presents an alternative for faster measurements of glial oxidative metabolism compared to NMR, potentially applicable to human PET imaging. However, to quantify the relative value of the TCA cycle flux compared to the transmitochondrial flux, the chemical sensitivity of NMR is required. PET and NMR are thus complementary.

Effects of high-intensity exercises on 13C-nandrolone excretion in trained athletes.

OBJECTIVE: Nandrolone is an anabolic steroid widely used in several sports. The numerous nandrolone positive cases in the recent years (International Olympic Committee statistics) led to several studies in the antidoping field. Nevertheless, essential questions pertaining to nandrolone endogenous production, the effects of physical exercise on the excretion of nandrolone metabolites, and contamination from nutritional supplements must still be addressed. The purpose of this study was to evaluate the influence of exhaustive exercises on 19-norandrosterone (19-NA) and 19-noretiocholanolone (19-NE) urinary excretion rates after administration of labeled nandrolone. SETTING AND PARTICIPANTS: A total of 34 healthy male Caucasian volunteers from the Institute of Sports Sciences and Physical Education (University of Lausanne) applied to participate in the study. All subjects were free from any physical drug addiction and were instructed strictly to avoid any nutritional supplement or steroid before and during the study. The participants were randomly dispatched in 2 groups in a double-blind way: a placebo group and a group treated with C-labeled nandrolone. MAIN OUTCOME MEASUREMENTS: The urinary concentrations of the 2 main nandrolone metabolites, 19-NA and 19-NE, were measured using gas chromatography coupled with mass spectrometry. In addition, clinical parameters such as creatinine, total protein, and beta2-microglobuline levels were determined using immunologic assays. RESULTS: After an oral ingestion of a 25 mg 3,4-C2-nandrolone dose, followed by a second identical dose 24 hours later, 19-NA and 19-NE could be detected in the urine for a period of 6 days after the initial intake. Despite several interesting observations, the measurements were very scattered and did not appear to be significantly influenced by exercise sessions in the athlete population. CONCLUSIONS: The results of this study suggest that physical exercise cannot be considered as a reliable parameter that systematically affects nandrolone metabolite concentrations in the urine.