- The Ways of Tails: the GET Pathway and more. [Review]
- PJProtein J 2019 Jun 15
- Due to their topology tail-anchored (TA) proteins must target to the membrane independently of the co-translational route defined by the signal sequence recognition particle (SRP), its receptor and t…
Due to their topology tail-anchored (TA) proteins must target to the membrane independently of the co-translational route defined by the signal sequence recognition particle (SRP), its receptor and the translocon Sec61. More than a decade of work has extensively characterized a highly conserved pathway, the yeast GET or mammalian TRC40 pathway, which is capable of countering the biogenetic challenge posed by the C-terminal TA anchor. In this review we briefly summarize current models of this targeting route and focus on emerging aspects such as the intricate interplay with the proteostatic network of cells and with other targeting pathways. Importantly, we consider the lessons provided by the in vivo analysis of the pathway in different model organisms and by the consideration of its full client spectrum in more recent studies. This analysis of the state of the field highlights directions in which the current models may be experimentally probed and conceptually extended.
- Geographical origin of Vitis vinifera cv. Cannonau established by the index of bioaccumulation and translocation coefficients. [Journal Article]
- EMEnviron Monit Assess 2019 Jun 15; 191(7):436
- Geochemical fingerprints in grape require an identification of major and trace elements that show correlations between concentrations in soil and in plant tissues: these correlations are relevant to …
Geochemical fingerprints in grape require an identification of major and trace elements that show correlations between concentrations in soil and in plant tissues: these correlations are relevant to discriminate grapes according to geographical origin. The Vitis vinifera cultivar Cannonau is used to produce the renowned Italian controlled designation of origin (DOC) wine "Cannonau" from Sardinia. Two Cannonau vineyards located in Sardinia Region were studied to establish the relationship between geochemical features of vineyard soil and chemical composition of leaves and grape berries. Major and trace elements were determined by X-ray fluorescence and inductively coupled plasma-mass spectrometry in soil, leaf, and grape berry samples. The index of bioaccumulation and the translocation coefficients were also calculated for all elements. Data from the two study areas were compared by a non-parametric test and multivariate statistics (principal component analysis). The results showed a specific assimilation of these elements in leaf and grape berry from vine in two different soils. Moreover, geochemical characterization and statistical analysis enabled to discriminate the cultivar "Cannonau" according to geographical origin. The results showed that the elements that could establish a reliable correlation between the soil vineyard and leaves and grape berries from the two study areas were B, Sr, and Zr. These elements may therefore be used as geochemical fingerprints to identify the geographic origin of V. vinifera cv. Cannonau in the two study areas.
- Metabolite signatures of grasspea suspension-cultured cells illustrate the complexity of dehydration response. [Journal Article]
- PPlanta 2019 Jun 15
- CONCLUSIONS: This represents the first report deciphering the dehydration response of suspension-cultured cells of a crop species, highlighting unique and shared pathways, and adaptive mechanisms via profiling of 330 metabolites. Grasspea, being a hardy legume, is an ideal model system to study stress tolerance mechanisms in plants. In this study, we investigated the dehydration-responsive metabolome in grasspea suspension-cultured cells (SCCs) to identify the unique and shared metabolites crucial in imparting dehydration tolerance. To reveal the dehydration-induced metabolite signatures, SCCs of grasspea were exposed to 10% PEG, followed by metabolomic profiling. Chromatographic separation by HPLC coupled with MRM-MS led to the identification of 330 metabolites, designated dehydration-responsive metabolites (DRMs), which belonged to 28 varied functional classes. The metabolome was found to be constituted by carboxylic acids (17%), amino acids (13.5%), flavonoids (10.9%) and plant growth regulators (10%), among others. Pathway enrichment analysis revealed predominance of metabolites involved in phytohormone biosynthesis, secondary metabolism and osmotic adjustment. Exogenous application of DRMs, arbutin and acetylcholine, displayed improved physiological status in stress-resilient grasspea as well as hypersensitive pea, while administration of lauric acid imparted detrimental effects. This represents the first report on stress-induced metabolomic landscape of a crop species via a suspension culture system, which would provide new insights into the molecular mechanism of stress responses and adaptation in crop species.
- Bioactivation of the tobacco carcinogens 4-aminobiphenyl (4-ABP) and 2-amino-9H-pyrido[2,3-b]indole (AαC) in human bladder RT4 cells. [Journal Article]
- ATArch Toxicol 2019 Jun 15
- Occupational and tobacco exposure to aromatic amines (AAs) including 4-aminobiphenyl (4-ABP) and 2-naphthylamine (2-NA) are associated with bladder cancer (BC) risk. Several epidemiological studies h…
Occupational and tobacco exposure to aromatic amines (AAs) including 4-aminobiphenyl (4-ABP) and 2-naphthylamine (2-NA) are associated with bladder cancer (BC) risk. Several epidemiological studies have also reported a possible role for structurally related heterocyclic aromatic amines (HAAs) formed in tobacco smoke or cooked meats with BC risk. We had screened for DNA adducts of 4-ABP, 2-NA, and several prominent HAAs formed in tobacco smoke or grilled meats including 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP), 2-amino-3,8-dimethylmidazo[4,5-f]quinoxaline (MeIQx), and 2-amino-9H-pyrido[2,3-b]indole (AαC) in the bladder DNA of BC patients, using liquid chromatography/mass spectrometry. We detected DNA adducts of 4-ABP, but not adducts of the other carcinogens. In this study, we have examined the capacity of RT4 cells, an epithelial human bladder cell line, to bioactivate AAs and HAAs to DNA damaging agents, which may contribute to BC. 4-ABP and AαC formed DNA adducts, but DNA adducts of 2-NA, PhIP, and MeIQx were not detected. 4-ABP DNA adducts were formed at tenfold higher levels than AαC adducts. Pretreatment of RT4 cells with α-naphthoflavone (1-10 µM), a specific cytochrome P450 1 (CYP1) inhibitor, decreased AαC adduct formation by 50% but did not affect the level of 4-ABP adducts. However, cell pretreatment with 8-methoxypsoralen (0.1-1 µM), a potent inhibitor of CYP2A, resulted in a 90% decrease of 4-ABP DNA adducts levels. These data signify that CYP2A and CYP1A isoforms expressed in the target urothelium bioactivate 4-ABP and AαC, respectively, and may be a critical feature of aromatic amine-induced urinary bladder carcinogenesis. The bioactivation of other tobacco and environmental AAs by bladder CYPs and their ensuing bladder DNA damage warrants further study.
- Tensor decomposition of hyperspectral images to study autofluorescence in age-related macular degeneration. [Journal Article]
- MIMed Image Anal 2019 May 31; 56:96-109
- Autofluorescence is the emission of light by naturally occurring tissue components on the absorption of incident light. Autofluorescence within the eye is associated with several disorders, such as A…
Autofluorescence is the emission of light by naturally occurring tissue components on the absorption of incident light. Autofluorescence within the eye is associated with several disorders, such as Age-related Macular Degeneration (AMD) which is a leading cause of central vision loss. Its pathogenesis is incompletely understood, but endogenous fluorophores in retinal tissue might play a role. Hyperspectral fluorescence microscopy of ex-vivo retinal tissue can be used to determine the fluorescence emission spectra of these fluorophores. Comparisons of spectra in healthy and diseased tissues can provide important insights into the pathogenesis of AMD. However, the spectrum from each pixel of the hyperspectral image is a superposition of spectra from multiple overlapping tissue components. As spectra cannot be negative, there is a need for a non-negative blind source separation model to isolate individual spectra. We propose a tensor formulation by leveraging multiple excitation wavelengths to excite the tissue sample. Arranging images from different excitation wavelengths as a tensor, a non-negative tensor decomposition can be performed to recover a provably unique low-rank model with factors representing emission and excitation spectra of these materials and corresponding abundance maps of autofluorescent substances in the tissue sample. We iteratively impute missing values common in fluorescence measurements using Expectation-Maximization and use L2 regularization to reduce ill-posedness. Further, we present a framework for performing group hypothesis testing on hyperspectral images, finding significant differences in spectra between AMD and control groups in the peripheral macula. In the absence of ground truth, i.e. molecular identification of fluorophores, we provide a rigorous validation of chosen methods on both synthetic and real images where fluorescence spectra are known. These methodologies can be applied to the study of other pathologies presenting autofluorescence that can be captured by hyperspectral imaging.
- Synthesis of amino-functionalized magnetic aerobic granular sludge-biochar for Pb(II) removal: Adsorption performance and mechanism studies. [Journal Article]
- STSci Total Environ 2019 Jun 01; 685:681-689
- In the present study, a novel amino-functionalized magnetic aerobic granular sludge-biochar (NH2-M-AGS) was successfully fabricated through magnetization and functional modification and applied for P…
In the present study, a novel amino-functionalized magnetic aerobic granular sludge-biochar (NH2-M-AGS) was successfully fabricated through magnetization and functional modification and applied for Pb(II) sorption. The composite was characterized by using scanning electron microscopy (SEM), energy dispersive spectrum (EDS), Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), Zeta potential analysis, vibrating sample magnetometer (VSM) and X-ray photoelectron spectroscopy (XPS). The effects of adsorbent dosage, pH value, contact time and initial metal concentration on the adsorption of Pb(II) were investigated by using batch equilibrium experiments. It was concluded that the pseudo-second-order model was better to describe adsorption kinetic of Pb(II) onto NH2-M-AGS. The Langmuir model was more accorded with the experimental data, and the maximum adsorption capacity of Pb(II) was 127.0 mg/g. A possible adsorption mechanism could be mainly caused by surface complexation, electrostatic attraction and precipitation. In five adsorption-desorption cycles, the desorption efficiency of Pb(II) exhibited a slight decline and still reached at 88.14%. Furthermore, the good reproducibility indicated that NH2-M-AGS could be used a desirable, economic and recyclable adsorbent in practical metal-contaminated wastewater treatment.
- Study of BDE-47 induced Parkinson's disease-like metabolic changes in C57BL/6 mice by integrated metabolomic, lipidomic and proteomic analysis. [Journal Article]
- JHJ Hazard Mater 2019 Jun 06; 378:120738
- As the predominant congener of polybrominated diphenyl ethers (PBDEs) detected in human serum, 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) has been reported to induce neurotoxicity. However, the poss…
As the predominant congener of polybrominated diphenyl ethers (PBDEs) detected in human serum, 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) has been reported to induce neurotoxicity. However, the possible linkage between BDE-47 and typical neurodegenerative diseases such as Parkinson's disease (PD) is still unclear. Here we carried out omics studies using liquid chromatography-orbitrap mass spectrometry (LC-orbitrap MS) to depict the BDE-47 induced metabolic changes in C57BJ/L mice to explore the possible contribution of BDE-47 exposure to PD pathology. BDE-47 dissolved in corn oil was orally administered to mice for 30 consecutive days. Results of metabolomics and lipidomics studies of PD-related brain regions revealed significant metabolite changes in pathways involved in oxidative stress and neurotransmitter production. Moreover, isobaric tags for relative and absolute quantitation (iTRAQ) proteomics study of the striatum, which is the part of brain that is most intensively studied in PD pathogenesis, revealed that BDE-47 could induce neurotransmitter system disturbance, abnormal phosphorylation, mitochondrial dysfunction and oxidative stress. Overall, this study depicts the possible contribution of BDE-47 exposure to PD pathology and highlights the powerfulness of omics platforms to deepen the mechanistic understanding of environmental pollutant-caused toxicity.
- Determination of gold leaf thickness using X-ray fluorescence spectrometry: Accuracy comparison using analytical methodology and Monte Carlo simulations. [Journal Article]
- ARAppl Radiat Isot 2019 Jun 12; 152:6-10
- In this work, we compared the accuracy of gold leaves thickness determination using X-ray Fluorescence (XRF) setups for different X-ray excitation sources. The sources used consisted on: a) direct Br…
In this work, we compared the accuracy of gold leaves thickness determination using X-ray Fluorescence (XRF) setups for different X-ray excitation sources. The sources used consisted on: a) direct Bremsstrahlung from an Amptek Mini-X X-ray tube with Rh target, b) partially monochromatized radiation of the same X-ray tube using combination of Al and Ag filters and, c) monochromatic radiation using secondary target, in a portable setup with triaxial geometry. The performance of the used setups was compared using model samples made with gold foil standard reference materials of known thicknesses (1, 2 and 2.5 μm). Thickness determination was based on the selective attenuation that the different energies of a given element of an under-layer undergo in the gilded layer. Ideally, as it can be expected from physics fundamentals, monochromatic radiation is needed for improved accuracy. However, considering the difficulties in using monochromatic radiation in portable instrumentation applicable in Cultural Heritage studies, filtered radiation can also be used for reliable results. Moreover, Monte Carlo simulations of the portable setup with conventional planar geometry were performed for comparison and for future application in more complex samples.
- Stage-dependent changes in oviductal phospholipid profiles throughout the estrous cycle in cattle. [Journal Article]
- TTheriogenology 2019 Jun 06; 135:65-72
- Sperm capacitation, fertilization and embryo development take place in the oviduct during the periovulatory period of the estrous cycle. Phospholipids are crucial metabolites for sperm capacitation a…
Sperm capacitation, fertilization and embryo development take place in the oviduct during the periovulatory period of the estrous cycle. Phospholipids are crucial metabolites for sperm capacitation and early embryo development. The aim of this study was to monitor the abundance of phospholipids in the bovine oviductal fluid (OF) according to the stage of the estrous cycle and the side relative to ovulation. Pairs of bovine oviducts were collected in a slaughterhouse and classified into four stages of the estrous cycle: post-ovulatory (Post-ov), mid-luteal (Mid-lut), late-luteal (Late-lut) and pre-ovulatory (Pre-ov) phases (n = 17 cows/stage). Cell-free OF from oviducts ipsilateral and contralateral to the site of ovulation were analyzed using MALDI-TOF mass spectrometry. Lipid identification was achieved by high resolution mass spectrometry. A total of 274 lipid masses were detected in the mass range of 400-1000 Da, corresponding mostly to phosphatidylcholines (PC), lysoPC, phosphatidylethanolamine (PE), lysoPE and sphingomyelins (SM). Ipsilateral and contralateral OF did not differ in their lipid profiles at any stage of the cycle. However, 127 and 96 masses were differentially abundant between stages in ipsilateral and contralateral OF, respectively. Highest differences in lipid profiles were observed in the Pre-ov vs. Mid-lut and Pre-ov vs. Late-lut comparisons in both sides relative to ovulation. Differential abundance of specific molecules of PC, PE, SM and l-carnitine were observed at Pre-ov and Post-ov compared with the luteal phase. This work proposes new candidates potentially able to regulate sperm capacitation and early embryo development.
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- Mechanism of oxytetracycline removal by aerobic granular sludge in SBR. [Journal Article]
- WRWater Res 2019 Jun 06; 161:308-318
- In this study, oxytetracycline (OTC) as a target pollutant in swine wastewater was removed by aerobic granular sludge (AGS). The removal rate of 300 μg/L OTC in aerobic granular sludge sequencing bat…
In this study, oxytetracycline (OTC) as a target pollutant in swine wastewater was removed by aerobic granular sludge (AGS). The removal rate of 300 μg/L OTC in aerobic granular sludge sequencing batch reactor (AGSBR) increased to 88.00% in 33 days and maintained stable. The chemical oxygen demand (COD), ammonium nitrogen (NH4+-N) and total phosphorus (TP) in wastewater were also efficiently removed. The removal of OTC mainly depended on the adsorption and biodegradation of AGS, and the biodegradation was increased obviously after AGS adaptation to OTC. The degradation products of OTC were analyzed by mass spectrometry. The analysis of metagenome sequencing revealed that the enzymes, such as glycosyl transferases (GTs), polysaccharide lyases (PLs) and auxiliary activities (AAs), may play an important role in the removal of OTC. The Lefse analysis showed that the Flavobacteriia, Flavobacteriales, Cryomorphaceae and Fluviicola were four kinds of microbes with significant difference in OTC feed reactor, which are considered to be drug-resistant bacteria in AGSBR. Furthermore, the dynamics of microbial community changed significantly at three levels, including the enrichment of drug-resistant microorganisms and the microorganisms that gradually reduced or even disappeared under the pressure of OTC.