SPUTNIK: an R package for filtering of spatially related peaks in mass spectrometry imaging data

Summary: SPUTNIK is an R package consisting of a series of tools to filter mass spectrometry imaging peaks characterized by a noisy or unlikely spatial distribution. SPUTNIK can produce mass spectrometry imaging datasets characterized by a smaller but more informative set of peaks, reduce the complexity of subsequent multi-variate analysis and increase the interpretability of the statistical results. Availability: SPUTNIK is freely available online from CRAN repository and at https://github.com/paoloinglese/SPUTNIK. The package is distributed under the GNU General Public License version 3 and is accompanied by example files and data. Supplementary information: Supplementary data are available at Bioinformatics online

How and why to study autophagy in Drosophila:It's more than just a garbage chute.

During the catabolic process of autophagy, cytoplasmic material is transported to the lysosome for degradation and recycling. This way, autophagy contributes to the homeodynamic turnover of proteins, lipids, nucleic acids, glycogen, and even whole organelles. Autophagic activity is increased by adverse conditions such as nutrient limitation, growth factor withdrawal and oxidative stress, and it generally protects cells and organisms to promote their survival. Misregulation of autophagy is likely involved in numerous human pathologies including aging, cancer, infections and neurodegeneration, so its biomedical relevance explains the still growing interest in this field. Here we discuss the different microscopy-based, biochemical and genetic methods currently available to study autophagy in various tissues of the popular model Drosophila. We show examples for results obtained in different assays, explain how to interpret these with regard to autophagic activity, and how to find out which step of autophagy a given gene product is involved in

Post-movement beta synchronization in Wilson's disease [Abstract]

Objective: To analyze the post-movement beta synchronization(PMBS) of the electroencephalogram (EEG) in Wilson’s disease. Background: Wilson’s disease is an autosomal recessive inherited disorder of copper metabolism. Its most common neurological symptoms (tremor, parkinsonism, dystonia, ataxia, chorea, dysarthria) are mainly related to dysfunction of the basal ganglia-thalamo-corticaland the cerebello-thalamo-cortical pathways. Post-movement beta synchronization is a transient power increase in the beta frequency band, which can be detected above the sensorimotor cortex 1-2 s after the termination of the movement. It is postulated that it reflects active inhibition and information processing. In essential tremor normal PMBS power but increased latency can be measured whereas in Parkinson’s disease PMBS latency is normal but its power is decreased. Methods: Ten patients with neurological manifestation of Wilson’s disease and ten controls performed self-paced movement with the dominant hand during EEG acquisition. Five electrodes located in the region of the sensorimotor cortical areas were selected for evaluation (C3, C1, Cz, C2, C4). The power and latency of post-movement beta synchronization were calculated after power spectral analysis with multi taper method. Results: PMBS power contralateral to the movement was significantly lower in patients with Wilson’s disease (1,9460,7%) than in controls (2,560,7%; p50,01). In all electrode position the latency of PMBS was significantly longer in the Wilson group (1,3460,45s) compared to controls (0,9360,44s; p50,005). The severity and type of neurological symptoms and the location and size of the MRI abnormalities were not correlated with the changes of PMBS. However, alterations of PMBS tended to be more pronounced in patients with more severe neurological symptoms. Conclusions: PMBS is affected in Wilson’s disease with neurological manifestation indicating altered information processing in the sensorimotor cortex. PMBS abnormalities are the combination of changes observed in Parkinson’s disease (decrease of power) and essential tremor (elongation of latencies). This may reflect the pathological changes in both the basal ganglia-thalamo-cortical circuit and cerebello-thalamo-cortical loop in Wilson’s disease

Near-infrared-shielding energy-saving borosilicate glass-ceramic window materials based on doping of defective tantalum tungsten oxide (Ta0.3W0.7O2.85) nanocrystals

NIR-shielding window materials were fabricated by direct embedding of Ta0.3W0.7O2.85 nanocrystals in bulk borosilicate glass-ceramics during a facile melt-quenching process. Optical and thermal performance of the prepared windows can be adjusted by varying the concentration of H2WO4 and Ta2O5 in the starting materials. The optimized window fabricated from raw materials containing 4.5 mol% H2WO4 and 0.3 mol% Ta2O5 exhibited high visible light transmittance 74.4% and strong NIR-shielding ability ΔT = 68.9%. Its thermal insulation performance is much better than soda lime glass or ITO glass, and its visible light transmission is higher than cesium-tungsten-bronze-based film coated glass. The distribution of Ta0.3W0.7O2.85 functional nanocrystals in the glass matrix was confirmed by sample characterization using XRD, Raman, XPS, HRTEM and EDS. The NIR-shielding property has been attributed to local surface plasmon resonance due to oxygen vacancies in the Ta0.3W0.7O2.85 nanocrystals. This study sheds a light on fabricating energy-saving windows with a tunable NIR-shielding performance

De novo lipogenesis alters the phospholipidome of esophageal adenocarcinoma

The incidence of esophageal adenocarcinoma is rising, survival remains poor, and new tools to improve early diagnosis and precise treatment are needed. Cancer phospholipidomes quantified with mass spectrometry imaging can support objective diagnosis in minutes using a routine frozen tissue section. However, whether mass spectrometry imaging can objectively identify primary esophageal adenocarcinoma is currently unknown and represents a significant challenge, as this microenvironment is complex with phenotypically similar tissue-types. Here we used desorption electrospray ionisation mass spectrometry imaging (DESI-MSI) and bespoke chemometrics to assess the phospholipidomes of esophageal adenocarcinoma and relevant control tissues. Multivariable models derived from phospholipid profiles of 117 patients were highly discriminant for esophageal adenocarcinoma both in discovery (area-under-curve = 0.97) and validation cohorts (AUC = 1). Among many other changes, esophageal adenocarcinoma samples were markedly enriched for polyunsaturated phosphatidylglycerols with longer acyl chains, with stepwise enrichment in pre-malignant tissues. Expression of fatty acid and glycerophospholipid synthesis genes was significantly upregulated, and characteristics of fatty acid acyls matched glycerophospholipid acyls. Mechanistically, silencing the carbon switch ACLY in esophageal adenocarcinoma cells shortened GPL chains, linking de novo lipogenesis to the phospholipidome. Thus, DESI-MSI can objectively identify invasive esophageal adenocarcinoma from a number of pre-malignant tissues and unveils mechanisms of phospholipidomic reprogramming. These results call for accelerated diagnosis studies using DESI-MSI in the upper gastrointestinal endoscopy suite as well as functional studies to determine how polyunsaturated phosphatidylglycerols contribute to esophageal carcinogenesis

Type IIb Supernova SN 2011dh: Spectra and Photometry from the Ultraviolet to the Near-Infrared

We report spectroscopic and photometric observations of the Type IIb SN 2011dh obtained between 4 and 34 days after the estimated date of explosion (May 31.5 UT). The data cover a wide wavelength range from 2,000 Angstroms in the UV to 2.4 microns in the NIR. Optical spectra provide line profiles and velocity measurements of HI, HeI, CaII and FeII that trace the composition and kinematics of the SN. NIR spectra show that helium is present in the atmosphere as early as 11 days after the explosion. A UV spectrum obtained with the STIS reveals that the UV flux for SN 2011dh is low compared to other SN IIb. The HI and HeI velocities in SN 2011dh are separated by about 4,000 km/s at all phases. We estimate that the H-shell of SN 2011dh is about 8 times less massive than the shell of SN 1993J and about 3 times more massive than the shell of SN 2008ax. Light curves (LC) for twelve passbands are presented. The maximum bolometric luminosity of $1.8 \pm 0.2 \times 10^{42}$ erg s$^{-1}$ occurred about 22 days after the explosion. NIR emission provides more than 30% of the total bolometric flux at the beginning of our observations and increases to nearly 50% of the total by day 34. The UV produces 16% of the total flux on day 4, 5% on day 9 and 1% on day 34. We compare the bolometric light curves of SN 2011dh, SN 2008ax and SN 1993J. The LC are very different for the first twelve days after the explosions but all three SN IIb display similar peak luminosities, times of peak, decline rates and colors after maximum. This suggests that the progenitors of these SN IIb may have had similar compositions and masses but they exploded inside hydrogen shells that that have a wide range of masses. The detailed observations presented here will help evaluate theoretical models for this supernova and lead to a better understanding of SN IIb.Comment: 23 pages, 14 figures, 9 tables, accepted by Ap

Evaluation of formalin-fixed and FFPE tissues for spatially resolved metabolomics and drug distribution studies

Fixation of samples is broadly used prior to the histological evaluation of tissue samples. Though recent reports demonstrated the ability to use fixed tissues for mass spectrometry imaging (MSI) based proteomics, glycomics and tumor classification studies, to date comprehensive evaluation of fixation-related effects for spatially resolved metabolomics and drug disposition studies is still missing. In this study we used matrix assisted laser desorption/ionization (MALDI) and desorption electrospray ionization (DESI) MSI to investigate the effect of formalin-fixation and formalin-fixation combined with paraffin embedding on the detectable metabolome including xenobiotics. Formalin fixation was found to cause significant washout of polar molecular species, including inorganic salts, amino acids, organic acids and carnitine species, oxidation of endogenous lipids and formation of reaction products between lipids and fixative ingredients. The slow fixation kinetics under ambient conditions resulted in increased lipid hydrolysis in the tissue core, correlating with the time-dependent progression of the fixation. Paraffin embedding resulted in subsequent partial removal of structural lipids resulting in the distortion of the elucidated biodistributions