Mass Spectrometry Image Creator (MSIC): Ion Mobility / Mass Spectrometry Imaging Workflow in Python

Mass spectrometry (MS) is a powerful characterization technique that enables identification of compounds in complex mixtures. Acquiring mass spectra in a spatially-resolved manner (i.e. over a grid), allows the data to be used to generate images that show the spatial distribution and relative intensities of every compound in a sample. These images can be used to monitor and identify biomarkers, explore the metabolism of compounds within tissues, and much more. However, the limitations of mass spectrometry can result in ambiguous compound identifications. Another characterization tool, ion mobility spectrometry (IM) can be integrated into existing MS routines to address this problem; measuring an ion mobility spectrum along with a mass spectrum over the grid results in more accurate compound identification in imaging experiments. While many software solutions exist for visualizing MS data, none of them support ion mobility. Thus, we have developed a novel program to incorporate this new dimension of data called Mass Spectrometry Image Creator (MSIC). Using existing software within a Python shell, MSIC creates images from raw IM-MS data through a semi-automated and batch-capable pipeline. Additionally, it includes several post-processing tools for further analysis and error correction

Molecular composition and photochemical lifetimes of brown carbon chromophores in biomass burning organic aerosol

To better understand the effects of wildfires on air quality and climate, it is important to assess the occurrence of chromophoric compounds in smoke and characterize their optical properties. This study explores the molecular composition of light-absorbing organic aerosol, or brown carbon (BrC), sampled at the Missoula Fire Sciences laboratory as a part of the FIREX Fall 2016 lab intensive. A total of 12 biomass fuels from different plant types were tested, including gymnosperm (coniferous) and angiosperm (flowering) plants and different ecosystem components such as duff, litter, and canopy. Emitted biomass burning organic aerosol (BBOA) particles were collected onto Teflon filters and analyzed offline using high-performance liquid chromatography coupled to a photodiode array spectrophotometer and a high-resolution mass spectrometer (HPLC-PDA-HRMS). Separated BrC chromophores were classified by their retention times, absorption spectra, integrated absorbance in the near-UV and visible spectral range (300-700 nm), and chemical formulas from the accurate m/z measurements. BrC chromophores were grouped into the following classes and subclasses: lignin-derived products, which include lignin pyrolysis products; distillation products, which include coumarins and flavonoids; nitroaromatics; and polycyclic aromatic hydrocarbons (PAHs). The observed classes and subclasses were common across most fuel types, although specific BrC chromophores varied based on plant type (gymnosperm or angiosperm) and ecosystem component(s) burned. To study the stability of the observed BrC compounds with respect to photodegradation, BBOA particle samples were irradiated directly on filters with near UV (300-400 nm) radiation, followed by extraction and HPLC-PDA-HRMS analysis. Lifetimes of individual BrC chromophores depended on the fuel type and the corresponding combustion condition. Lignin-derived and flavonoid classes of BrC generally had the longest lifetimes with respect to UV photodegradation. Moreover, lifetimes for the same type of BrC chromophores varied depending on biomass fuel and combustion conditions. While individual BrC chromophores disappeared on a timescale of several days, the overall light absorption by the sample persisted longer, presumably because the condensed-phase photochemical processes converted one set of chromophores into another without complete photobleaching or from undetected BrC chromophores that photobleached more slowly. To model the effect of BrC on climate, it is important to understand the change in the overall absorption coefficient with time. We measured the equivalent atmospheric lifetimes of the overall BrC absorption coefficient, which ranged from 10 to 41 d, with subalpine fir having the shortest lifetime and conifer canopies, i.e., juniper, having the longest lifetime. BrC emitted from biomass fuel loads encompassing multiple ecosystem components (litter, shrub, canopy) had absorption lifetimes on the lower end of the range. These results indicate that photobleaching of BBOA by condensed-phase photochemistry is relatively slow. Competing chemical aging mechanisms, such as heterogeneous oxidation by OH, may be more important for controlling the rate of BrC photobleaching in BBOA

Skeletal Muscle Undergoes Fiber Type Metabolic Switch Without Myosin Heavy Chain Switch in Response to Defective Fatty Acid Oxidation

OBJECTIVE: Skeletal muscle is a heterogeneous and dynamic tissue that adapts to functional demands and substrate availability by modulating muscle fiber size and type. The concept of muscle fiber type relates to its contractile (slow or fast) and metabolic (glycolytic or oxidative) properties. Here, we tested whether disruptions in muscle oxidative catabolism are sufficient to prompt parallel adaptations in energetics and contractile protein composition. METHODS: Mice with defective mitochondrial long-chain fatty acid oxidation (mLCFAO) in the skeletal muscle due to loss of carnitine palmitoyltransferase 2 (Cpt2(Sk−/−)) were used to model a shift in muscle macronutrient catabolism. Glycolytic and oxidative muscles of Cpt2(Sk−/−) mice and control littermates were compared for the expression of energy metabolism-related proteins, mitochondrial respiratory capacity, and myosin heavy chain isoform composition. RESULTS: Differences in bioenergetics and macronutrient utilization in response to energy demands between control muscles were intrinsic to the mitochondria, allowing for a clear distinction of muscle types. Loss of CPT2 ablated mLCFAO and resulted in mitochondrial biogenesis occurring most predominantly in oxidative muscle fibers. The metabolism-related proteomic signature of Cpt2(Sk−/−) oxidative muscle more closely resembled that of glycolytic muscle than of control oxidative muscle. Respectively, intrinsic substrate-supported mitochondrial respiration of CPT2 deficient oxidative muscles shifted to closely match that of glycolytic muscles. Despite this shift in mitochondrial metabolism, CPT2 deletion did not result in contractile-based fiber type switching according to myosin heavy chain composition analysis. CONCLUSION: The loss of mitochondrial long-chain fatty acid oxidation elicits an adaptive response involving conversion of oxidative muscle toward a metabolic profile that resembles a glycolytic muscle, but this is not accompanied by changes in myosin heavy chain isoforms. These data suggest that shifts in muscle catabolism are not sufficient to drive shifts in the contractile apparatus but are sufficient to drive adaptive changes in metabolic properties

EMSL Science Theme Advisory Panel Workshop - Atmospheric Aerosol Chemistry, Climate Change, and Air Quality

This report contains the workshop scope and recommendations from the workshop attendees in identifying scientific gaps in new particle formation, growth and properties of particles and reactions in and on particles as well as the laboratory-focused capabilities, field-deployable capabilities and modeling/theory tools along with linking of models to fundamental data

2020 American College of Rheumatology Guideline for the Management of Reproductive Health in Rheumatic and Musculoskeletal Diseases

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/154675/1/art41191.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/154675/2/art41191_am.pd

Molecular Characterization of Organosulfates in Organic Aerosols from Shanghai and Los Angeles Urban Areas by Nanospray-Desorption Electrospray Ionization High-Resolution Mass Spectrometry

Fine aerosol particles in the urban areas of Shanghai and Los Angeles were collected on days that were characterized by their stagnant air and high organic aerosol concentrations. They were analyzed by nanospray-desorption electrospray ionization mass spectrometry with high mass resolution (m/Δm = 100,000). Solvent mixtures of acetonitrile and water and acetonitrile and toluene were used to extract and ionize polar and nonpolar compounds, respectively. A diverse mixture of oxygenated hydrocarbons, organosulfates, organonitrates, and organics with reduced nitrogen were detected in the Los Angeles sample. A majority of the organics in the Shanghai sample were detected as organosulfates. The dominant organosulfates that were detected at two locations have distinctly different molecular characteristics. Specifically, the organosulfates in the Los Angeles sample were dominated by biogenic products, while the organosulfates of a yet unknown origin found in the Shanghai sample had distinctive characteristics of long aliphatic carbon chains and low degrees of oxidation and unsaturation. The use of the acetonitrile and toluene solvent facilitated the observation of this type of organosulfates, which suggests that they could have been missed in previous studies that relied on sample extraction using common polar solvents. The high molecular weight and low degree of unsaturation and oxidization of the uncommon organosulfates suggest that they may act as surfactants and plausibly affect the surface tension and hygroscopicity of atmospheric particles. We propose that direct esterification of carbonyl or hydroxyl compounds by sulfates or sulfuric acid in the liquid phase could be the formation pathway of these special organosulfates. Long-chain alkanes from vehicle emissions might be their precursors

The human body at cellular resolution: the NIH Human Biomolecular Atlas Program

Abstract: Transformative technologies are enabling the construction of three-dimensional maps of tissues with unprecedented spatial and molecular resolution. Over the next seven years, the NIH Common Fund Human Biomolecular Atlas Program (HuBMAP) intends to develop a widely accessible framework for comprehensively mapping the human body at single-cell resolution by supporting technology development, data acquisition, and detailed spatial mapping. HuBMAP will integrate its efforts with other funding agencies, programs, consortia, and the biomedical research community at large towards the shared vision of a comprehensive, accessible three-dimensional molecular and cellular atlas of the human body, in health and under various disease conditions

EMSL and Institute for Integrated Catalysis (IIC) Catalysis Workshop

Within the context of significantly accelerating scientific progress in research areas that address important societal problems, a workshop was held in November 2010 at EMSL to identify specific and topically important areas of research and capability needs in catalysis-related science

Integrating precision cancer medicine into healthcare—policy, practice, and research challenges

Abstract Precision medicine (PM) can be defined as a predictive, preventive, personalized, and participatory healthcare service delivery model. Recent developments in molecular biology and information technology make PM a reality today through the use of massive amounts of genetic, ‘omics’, clinical, environmental, and lifestyle data. With cancer being one of the most prominent public health threats in developed countries, both the research community and governments have been investing significant time, money, and efforts in precision cancer medicine (PCM). Although PCM research is extremely promising, a number of hurdles still remain on the road to an optimal integration of standardized and evidence-based use of PCM in healthcare systems. Indeed, PCM raises a number of technical, organizational, ethical, legal, social, and economic challenges that have to be taken into account in the development of an appropriate health policy framework. Here, we highlight some of the more salient issues regarding the standards needed for integration of PCM into healthcare systems, and we identify fields where more research is needed before policy can be implemented. Key challenges include, but are not limited to, the creation of new standards for the collection, analysis, and sharing of samples and data from cancer patients, and the creation of new clinical trial designs with renewed endpoints. We believe that these issues need to be addressed as a matter of priority by public health policymakers in the coming years for a better integration of PCM into healthcare