Rapid protein domain assignment from amino acid sequence using predicted secondary structure

The elucidation of the domain content of a given protein sequence in the absence of determined structure or significant sequence homology to known domains is an important problem in structural biology. Here we address how successfully the delineation of continuous domains can be accomplished in the absence of sequence homology using simple baseline methods, an existing prediction algorithm (Domain Guess by Size), and a newly developed method (DomSSEA). The study was undertaken with a view to measuring the usefulness of these prediction methods in terms of their application to fully automatic domain assignment. Thus, the sensitivity of each domain assignment method was measured by calculating the number of correctly assigned top scoring predictions. We have implemented a new continuous domain identification method using the alignment of predicted secondary structures of target sequences against observed secondary structures of chains with known domain boundaries as assigned by Class Architecture Topology Homology (CATH). Taking top predictions only, the success rate of the method in correctly assigning domain number to the representative chain set is 73.3%. The top prediction for domain number and location of domain boundaries was correct for 24% of the multidomain set (±20 residues). These results have been put into context in relation to the results obtained from the other prediction methods assessed

The anti-epileptic drug Valproic Acid (VPA) inhibits steroidogenesis in bovine theca and granulosa cells in vitro

Valproic acid (VPA) is used widely to treat epilepsy and bipolar disorder. Women undergoing VPA treatment reportedly have an increased incidence of polycystic ovarian syndrome (PCOS)-like symptoms including hyperandrogenism and oligo- or amenorrhoea. To investigate potential direct effects of VPA on ovarian steroidogenesis we used primary bovine theca (TC) and granulosa (GC) cells maintained under conditions that preserve their 'follicular' phenotype. Effects of VPA (7.8-500 µg/ml) on TC were tested with/without LH. Effects of VPA on GC were tested with/without FSH or IGF analogue. VPA reduced (P<0.0001) both basal (70% suppression; IC(50) 67±10 µg/ml) and LH-induced (93% suppression; IC(50) 58±10 µg/ml) androstenedione secretion by TC. VPA reduced CYP17A1 mRNA abundance (>99% decrease; P<0.0001) with lesser effects on LHR, STAR, CYP11A1 and HSD3B1 mRNA (<90% decrease; P<0.05). VPA only reduced TC progesterone secretion induced by the highest (luteinizing) LH dose tested; TC number was unaffected by VPA. At higher concentrations (125-500 µg/ml) VPA inhibited basal, FSH- and IGF-stimulated estradiol secretion (P<0.0001) by GC without affecting progesterone secretion or cell number. VPA reversed FSH-induced upregulation of CYP19A1 and HSD17B1 mRNA abundance (P<0.001). The potent histone deacetylase (HDAC) inhibitors trichostatin A and scriptaid also suppressed TC androstenedione secretion and granulosal cell oestrogen secretion suggesting that the action of VPA reflects its HDAC inhibitory properties. In conclusion, these findings refute the hypothesis that VPA has a direct stimulatory action on TC androgen output. On the contrary, VPA inhibits both LH-dependent androgen production and FSH/IGF-dependent estradiol production in this in vitro bovine model, likely by inhibition of HDAC.

Identification of polycyclic aromatic hydrocarbons in sugar cane soot by gas chromatography mass spectrometry

Fly soot samples collected in the sugar cane fields after the process of burning were extracted in a Soxhlet apparatus (methylene chloride:methanol 4:1). The extracts were fractionated on silica gel Sep-Pak cartridges into three fractions. A gas chromatographic-mass spectrometric study of the fly soot extracts allowed the identification of the PAH with mutagenic and carcinogenic properties. Large amounts of aliphatic hydrocarbons, fatty acid esters and some PAHs were identified by GCMS in full scan mode. GC-MS in the selective ion monitoring mode (SIM) was suitable for the determination of many PAHs, which are often present in the burnt biomass. 31 PAHs and 7 thiophens derivatives were identified. The presence of these compounds should be regarded as a caution to workers and the general population to avoid exposure to the fly soot.

Distribution of acid phosphatases in the hypopharyngeal glands from workers, queens and males of a Brazilian stingless bee Scaptotrigona postica Latreille: An ultrastructural cytochemical study

The present study reports the localization of acid phosphatase in the hypopharyngeal gland cells from workers (newly-emerged, nurse and forager), queens (newly-emerged and laying) and males (newly-emerged and mature for mating) of the Brazilian stingless bee, Scaptotrigona postica. The phosphatase activity varied in intensity and localization depending on the individual class, physiological age and the substrate used. In newly-emerged workers, the phosphatase-positive sites suggest the involvement of the enzyme with cellular differentiation that occurs in the presecretory phase, in nurse workers with protein synthesis and in forager workers with changes in cellular activity or glandular regression. In males mature for mating and laying queens, the positive sites are related to secretory activity, showing that the gland maintains some activity in spite of the regressive aspect. Of the substrates used, β-glycerophosphate gave the least specific localization.

Identification of ellagic acid derivatives in methanolic extracts from Qualea species

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Detecção in silico e caracterização estrutural dos constituintes micromoleculares majoritários presentes no fungo endofitico Phomopsis stipata isolado de folhas de Styrax camporum Pohl (Styracaceae) usando CLAE-DAD/EMAR e CG-MS

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Supplementation of conjugated linoleic acid in dairy cows reduces endogenous glucose production during early lactation.

Trans-10,cis-12 conjugated linoleic acid (CLA) supplementation causes milk fat depression in dairy cows, but CLA effects on glucose metabolism are not clear. The objective of the study was to investigate glucose metabolism, especially endogenous glucose production (eGP) and glucose oxidation (GOx), as well as hepatic genes involved in endogenous glucose production in Holstein cows supplemented either with 50 g of rumen-protected CLA (9% trans-10,cis-12 and 10% cis-9,trans-11; CLA; n=10) or 50 g of control fat (24% C18:2; Ctrl; n=10) from wk 2 before parturition to wk 9 of lactation. Animal performance data were recorded and blood metabolites and hormones were taken weekly from 2 wk before to 12 wk after parturition. During wk 3 and 9 after parturition, glucose tolerance tests were performed and eGP and GOx were measured by [U-(13)C] glucose infusion. Liver biopsies were taken at the same time to measure total fat and glycogen concentrations and gene expression of pyruvate carboxylase, cytosolic phosphoenolpyruvate carboxykinase, glucose-6-phosphatase, and carnitine palmitoyl-transferase 1. Conjugated linoleic acid feeding reduced milk fat, but increased milk lactose output; milk yield was higher starting 5 wk after parturition in CLA-fed cows than in Ctrl-fed cows. Energy balance was more negative during CLA supplementation, and plasma concentrations of glucose were higher immediately after calving in CLA-fed cows. Conjugated linoleic acid supplementation did not affect insulin release during glucose tolerance tests, but reduced eGP in wk 3, and eGP and GOx increased with time after parturition. Hepatic gene expression of cytosolic phosphoenolpyruvate carboxykinase tended to be lower in CLA-fed cows than in Ctrl-fed cows. In spite of lower eGP in CLA-fed cows, lactose output and plasma glucose concentrations were greater in CLA-fed cows than in Ctrl-fed cows. This suggests a CLA-related glucose sparing effect most likely due to lower glucose utilization for milk fat synthesis and probably because of a more efficient whole-body energy utilization in CLA-fed cows.

Chlorine isotope composition in chlorofluorocarbons CFC-11, CFC-12 and CFC-113 in firn, stratospheric and tropospheric air

The stratospheric degradation of chlorofluorocarbons (CFCs) releases chlorine, which is a major contributor to the destruction of stratospheric ozone (O3). A recent study reported strong chlorine isotope fractionation during the breakdown of the most abundant CFC (CFC-12, CCl2F2, Laube et al., 2010a), similar to effects seen in nitrous oxide (N2O). Using air archives to obtain a long-term record of chlorine isotope ratios in CFCs could help to identify and quantify their sources and sinks. We analyse the three most abundant CFCs and show that CFC-11 (CCl3F) and CFC-113 (CClF2CCl2F) exhibit significant stratospheric chlorine isotope fractionation, in common with CFC-12. The apparent isotope fractionation (ϵapp) for mid- and high-latitude stratospheric samples are respectively −2.4 (0.5) and −2.3 (0.4) ‰ for CFC-11, −12.2 (1.6) and −6.8 (0.8) ‰ for CFC-12 and −3.5 (1.5) and −3.3 (1.2) ‰ for CFC-113, where the number in parentheses is the numerical value of the standard uncertainty expressed in per mil. Assuming a constant isotope composition of emissions, we calculate the expected trends in the tropospheric isotope signature of these gases based on their stratospheric 37Cl enrichment and stratosphere–troposphere exchange. We compare these projections to the long-term δ (37Cl) trends of all three CFCs, measured on background tropospheric samples from the Cape Grim air archive (Tasmania, 1978–2010) and tropospheric firn air samples from Greenland (North Greenland Eemian Ice Drilling (NEEM) site) and Antarctica (Fletcher Promontory site). From 1970 to the present day, projected trends agree with tropospheric measurements, suggesting that within analytical uncertainties, a constant average emission isotope delta (δ) is a compatible scenario. The measurement uncertainty is too high to determine whether the average emission isotope δ has been affected by changes in CFC manufacturing processes or not. Our study increases the suite of trace gases amenable to direct isotope ratio measurements in small air volumes (approximately 200 mL), using a single-detector gas chromatography–mass spectrometry (GC–MS) system.

Fatty acids and intact polar lipids of laminated microbial sediments from St. Peter Ording, German Wadden Sea

Hidden for the untrained eye through a thin layer of sand, laminated microbial sediments occur in supratidal beaches along the North Sea coast. The inhabiting microbial communities organize themselves in response to vertical gradients of light, oxygen or sulfur compounds. We performed a fine-scale investigation on the vertical zonation of the microbial communities using a lipid biomarker approach, and assessed the biogeochemical processes using a combination of microsensor measurements and a 13C-labeling experiment. Lipid biomarker fingerprinting showed the overarching importance of cyanobacteria and diatoms in these systems, and heterocyst glycolipids revealed the presence of diazotrophic cyanobacteria even in 9 to 20 mm depth. High abundance of ornithine lipids (OL) throughout the system may derive from sulfate reducing bacteria, while a characteristic OL profile between 5 and 8 mm may indicate presence of purple non-sulfur bacteria. The fate of 13C-labeled bicarbonate was followed by experimentally investigating the uptake into microbial lipids, revealing an overarching importance of cyanobacteria for carbon fixation. However, in deeper layers, uptake into purple sulfur bacteria was evident, and a close microbial coupling could be shown by uptake of label into lipids of sulfate reducing bacteria in the deepest layer. Microsensor measurements in sediment cores collected at a later time point revealed the same general pattern as the biomarker analysis and the labeling experiments. Oxygen and pH-microsensor profiles showed active photosynthesis in the top layer. The sulfide that diffuses from deeper down and decreases just below the layer of active oxygenic photosynthesis indicates the presence of sulfur bacteria, like anoxygenic phototrophs that use sulfide instead of water for photosynthesis.