Quantitative analysis of tetrahydrofolate metabolites from <Emphasis Type="Italic">clostridium autoethanogenum</Emphasis>

Introduction

Quantification of tetrahydrofolates (THFs), important metabolites in the Wood–Ljungdahl pathway (WLP) of acetogens, is challenging given their sensitivity to oxygen.

Objective

To develop a simple anaerobic protocol to enable reliable THFs quantification from bioreactors.

Methods

Anaerobic cultures were mixed with anaerobic acetonitrile for extraction. Targeted LC–MS/MS was used for quantification.

Results

Tetrahydrofolates can only be quantified if sampled anaerobically. THF levels showed a strong correlation to acetyl-CoA, the end product of the WLP.

Conclusion

Our method is useful for relative quantification of THFs across different growth conditions. Absolute quantification of THFs requires the use of labelled standards.

     

Extraction of natural products from bark of <Emphasis Type="Italic">Betula pendula</Emphasis> using ionic liquids

Introduction

Aqueous–methanol mixtures have successfully been applied to extract a broad range of metabolites from plant tissue. However, a certain amount of material remains insoluble.

Objectives

To enlarge the metabolic compendium, two ionic liquids were selected to extract the methanol insoluble part of trunk from Betula pendula.

Methods

The extracted compounds were analyzed by LC/MS and GC/MS.

Results

The results show that 1-butyl-3-methylimidazolium acetate (IL-Ac) predominantly resulted in fatty acids, whereas 1-ethyl-3-methylimidazolium tosylate (IL-Tos) mostly yielded phenolic structures. Interestingly, bark yielded more ionic liquid soluble metabolites compared to interior wood.

Conclusion

From this one can conclude that the application of ionic liquids may expand the metabolic snapshot.

     

The importance of using life cycle assessment in policy support to determine the sustainability of fishing fleets: a case study for the small-scale <Emphasis Type="Italic">xeito</Emphasis> fishery in Galicia,Spain

Purpose

Drift net fishing activities have undergone a thorough revision at a European Union level, since authorities argue that several loopholes still exist in the legislation that allow small-scale fisheries to use these gears. High incidental catches, or the lack of selectivity, are some of the primary scientific criteria behind this discussion. This new framework is of particular interest in the region of Galicia (NW Spain) due to the social importance of small-scale fishing vessels using drift nets. In fact, over 400 vessels have a licence to capture European pilchard (Sardina pilchardus) with a fishing gear called xeito, which is a small-scale drift net.

Methods

The main goal of this article is to provide stakeholders in the fishing sector with environmentally relevant results regarding the life cycle impacts linked to fishing practices performed by small-scale vessels using the xeito gear to target European pilchard. We hypothesize that environmental impacts computed with LCA will provide additional insights to the sustainability of the pilchard small-scale fishery in NW Spain, adding a series of criteria that may be useful for policy-makers to determine the consequences of forbidding this type of drift netting in the future.

Results and discussion

Results show that environmental impacts across impact categories and operational activities do not differ much from that of other similar fishing fleets examined in recent years, with fuel for propulsion being the main environmental burden in most impact categories. When conducting a statistical analysis, no significant difference in energy use was identified between this small-scale fleet and purse seiners targeting pilchard in Galicia. Moreover, the results obtained demonstrate, in line with previous studies, that European pilchard is still an energy-efficient source of animal protein option as compared to demersal fish alternatives, crustaceans, or livestock.

Conclusions

The results do not indicate that European pilchard landed with small-scale drift nets generates higher environmental life cycle impacts than pilchard landed by purse seiners in NW Spain. However, longer time frames for the analysis should be performed to attain results with lower uncertainty.

     

rDolphin: a GUI R package for proficient automatic profiling of 1D <Superscript>1</Superscript>H-NMR spectra of study datasets

Introduction

Adoption of automatic profiling tools for ¹H-NMR-based metabolomic studies still lags behind other approaches in the absence of the flexibility and interactivity necessary to adapt to the properties of study data sets of complex matrices.

Objectives

To provide an open source tool that fully integrates these needs and enables the reproducibility of the profiling process.

Methods

rDolphin incorporates novel techniques to optimize exploratory analysis, metabolite identification, and validation of profiling output quality.

Results

The information and quality achieved in two public datasets of complex matrices are maximized.

Conclusion

rDolphin is an open-source R package (http://github.com/danielcanueto/rDolphin) able to provide the best balance between accuracy, reproducibility and ease of use.

     

Estimating the global warming emissions of the LCAXVII conference: connecting flights matter

Purpose

Conferences are an important element of scientific activity but can also be a major cause of environmental burden. With this in mind, we analysed the global warming emissions of the 2017 annual conference of the American Center for Life Cycle Assessment (ACLCA), in order to estimate the carbon footprint and identify potential ways to reduce it.

Methods

We used survey data from participants as well as literature sources to complete an attributional assessment of the greenhouse gas emissions per participant. A method to calculate the ‘ideal’ location is proposed, which can be used to identify ‘unreasonably’ distant conference locations.

Results and discussion

The average emissions per participant were found to be 952 kg CO_2eq, but with a large variability due to differences in travelled distance. Connecting flights were found to increase emissions up to 32% compared to direct flights, due to the increased number of take-offs and landings.

Conclusions

Results indicate that future studies should use distance-dependent flight emissions to increase the accuracy of the assessment. Some measures, such as meat-free menus, had a relatively minor contribution to emission reductions, but could be important as scientists advocating for the reduction of environmental burden should lead by example.

     

Iridoid and phenylethanoid/phenylpropanoid metabolite profiles of <Emphasis Type="Italic">Scrophularia</Emphasis> and <Emphasis Type="Italic">Verbascum</Emphasis> species used medicinally in North America

Introduction

Botanicals containing iridoid and phenylethanoid/phenylpropanoid glycosides are used worldwide for the treatment of inflammatory musculoskeletal conditions that are primary causes of human years lived with disability, such as arthritis and lower back pain.

Objectives

We report the analysis of candidate anti-inflammatory metabolites of several endemic Scrophularia species and Verbascum thapsus used medicinally by peoples of North America.

Methods

Leaves, stems, and roots were analyzed by ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) and partial least squares-discriminant analysis (PLS-DA) was performed in MetaboAnalyst 3.0 after processing the datasets in Progenesis QI.

Results

Comparison of the datasets revealed significant and differential accumulation of iridoid and phenylethanoid/phenylpropanoid glycosides in the tissues of the endemic Scrophularia species and Verbascum thapsus.

Conclusions

Our investigation identified several species of pharmacological interest as good sources for harpagoside and other important anti-inflammatory metabolites.

     

Metabolic response of porcine colon explants to in vitro infection by <Emphasis Type="Italic">Brachyspira hyodysenteriae</Emphasis>: a leap into disease pathophysiology

Introduction

Swine dysentery caused by Brachyspira hyodysenteriae is a production limiting disease in pig farming. Currently antimicrobial therapy is the only treatment and control method available.

Objective

The aim of this study was to characterize the metabolic response of porcine colon explants to infection by B. hyodysenteriae.

Methods

Porcine colon explants exposed to B. hyodysenteriae were analyzed for histopathological, metabolic and pro-inflammatory gene expression changes.

Results

Significant epithelial necrosis, increased levels of l-citrulline and IL-1α were observed on explants infected with B. hyodysenteriae.

Conclusions

The spirochete induces necrosis in vitro likely through an inflammatory process mediated by IL-1α and NO.

     

Opportunities and challenges of implementing life cycle assessment in seafood certification: a case study for Spain

Purpose

Eco-labelling has become part of the business strategy of companies thanks to numerous advantages in terms of engaging with consumers and gaining market quota. The aim of this article is to present a critical discussion on the development and implementation of a new eco-label named pescaenverde, registered in Spain, as the first type III eco-label in the Spanish fishing sector that is based on life cycle approaches for seafood products.

Methods

More specifically, it aims to complement ecosystem-based eco-labels with the computation of the carbon footprint and the energy return on investment (EROI) of seafood products. Furthermore, it proposes to discuss the ecological criteria, certification process or the opportunities and challenges of the market implementation of this eco-label in detail. Finally, the authors argue that life cycle eco-labels should be considered important complements for more specific sector- or ecosystem-oriented labels already in use, rather than direct competitors.

Results and discussion

There has been much criticism towards the eco-labelling sector as regards the transparency and scientific rigour of its standards. The fishing and seafood sector, which has experienced a boom in eco-labelling in recent years, due mainly to the strength of the Marine Stewardship Council certification scheme, is not alien to this controversy, since critics advocate expanding the concept of sustainable fisheries beyond an ecosystem approach in order to account for global environmental concerns such as greenhouse gas (GHG) emissions or energy use. Not surprisingly, the European Union and other authorities currently encourage eco-labels to base their ecological criteria on life cycle approaches. Therefore, the current study discusses the ecological criteria, certification process or the opportunities and challenges of the market implementation of this eco-label in detail.

Conclusions

The specificity of the life cycle inventory scheme used in pescaenverde delivers an accurate computation of environmental impacts for the specific case of Spanish fisheries. However, the geographical expansion of this scheme to other nations or regions will be conditioned by an important software adaptation to the particular inventory characteristics of the new fisheries, fleets and products.

Recommendations

Adapting ecological criteria to other situations would also need substantial discussion, since the use of this certification scheme is not intended to contrast or compare seafood products against each other but to provide consumers with an easily identifiable label through which they can detect environmentally sustainable practices in terms of GHG emissions and energy use in the fishing fleets supporting the seafood products purchased.

     

<Emphasis Type="Italic">massPix</Emphasis>: an R package for annotation and interpretation of mass spectrometry imaging data for lipidomics

Introduction

Mass spectrometry imaging (MSI) experiments result in complex multi-dimensional datasets, which require specialist data analysis tools.

Objectives

We have developed massPix—an R package for analysing and interpreting data from MSI of lipids in tissue.

Methods

massPix produces single ion images, performs multivariate statistics and provides putative lipid annotations based on accurate mass matching against generated lipid libraries.

Results

Classification of tissue regions with high spectral similarly can be carried out by principal components analysis (PCA) or k-means clustering.

Conclusion

massPix is an open-source tool for the analysis and statistical interpretation of MSI data, and is particularly useful for lipidomics applications.

     

Synthesis and physicochemical characterization of the one-carbon carrier 10-formyltetrahydrofolate; a reference standard for metabolomics

Introduction

Metabolomics analysis depends on the identification and validation of specific metabolites. This task is significantly hampered by the absence of well-characterized reference standards. The one-carbon carrier 10-formyltetrahydrofolate acts as a donor of formyl groups in anabolism, where it is a substrate in formyltransferase reactions in purine biosynthesis. It has been reported as an unstable substance and is currently unavailable as a reference standard for metabolomics analysis.

Objectives

The current study was undertaken to provide the metabolomics community thoroughly characterized 10-formyltetrahydrofolate along with analytical methodology and guidelines for its storage and handling.

Methods

Anaerobic base treatment of 5,10-methenyltetrahydrofolate chloride in the presence of antioxidant was utilized to prepare 10-formyltetrahydrofolate.

Results

Pure 10-formyltetrahydrofolate has been prepared and physicochemically characterized. Conditions toward maintaining the stability of a solution of the dipotassium salt of 10-formyltetrahydrofolate have been determined.

Conclusion

This study describes the facile preparation of pure (>90%) 10-formyltetrahydrofolate, its qualitative physicochemical characterization, as well as conditions to enable its use as a reference standard in physiologic samples.

     

Optimization of fecal sample preparation for untargeted LC-HRMS based metabolomics

Introduction

Collecting feces is easy. It offers direct outcome to endogenous and microbial metabolites.

Objectives

In a context of lack of consensus about fecal sample preparation, especially in animal species, we developed a robust protocol allowing untargeted LC-HRMS fingerprinting.

Methods

The conditions of extraction (quantity, preparation, solvents, dilutions) were investigated in bovine feces.

Results

A rapid and simple protocol involving feces extraction with methanol (1/3, M/V) followed by centrifugation and a step filtration (10 kDa) was developed.

Conclusion

The workflow generated repeatable and informative fingerprints for robust metabolome characterization.

     

Crystal structure of <Emphasis Type="Italic">Escherichia coli</Emphasis> protein ybgI,a toroidal structure with a dinuclear metal site

Background

The protein encoded by the gene ybgI was chosen as a target for a structural genomics project emphasizing the relation of protein structure to function.

Results

The structure of the ybgI protein is a toroid composed of six polypeptide chains forming a trimer of dimers. Each polypeptide chain binds two metal ions on the inside of the toroid.

Conclusion

The toroidal structure is comparable to that of some proteins that are involved in DNA metabolism. The di-nuclear metal site could imply that the specific function of this protein is as a hydrolase-oxidase enzyme.

     

Characterization of ankylosing spondylitis and rheumatoid arthritis using <Superscript>1</Superscript>H NMR-based metabolomics of human fecal extracts

Introduction

The differences in fecal metabolome between ankylosing spondylitis (AS)/rheumatoid arthritis (RA) patients and healthy individuals could be the reason for an autoimmune disorder.

Objectives

The study explored the fecal metabolome difference between AS/RA patients and healthy controls to clarify human immune disturbance.

Methods

Fecal samples from 109 individuals (healthy controls 34, AS 40, and RA 35) were analyzed by ¹H NMR spectroscopy. Data were analyzed with principal component analysis (PCA) and orthogonal projection to latent structure discriminant (OPLS-DA) analysis.

Results

Significant differences in the fecal metabolic profiles could distinguish AS/RA patients from healthy controls but could not distinguish between AS and RA patients. The significantly decreased metabolites in AS/RA patients were butyrate, propionate, methionine, and hypoxanthine. Significantly increased metabolites in AS/RA patients were taurine, methanol, fumarate, and tryptophan.

Conclusion

The metabolome variations in feces indicated AS and RA were two homologous diseases that could not be distinguished by ¹H NMR metabolomics.

     

Accumulation of Fascin<Superscript>+</Superscript> cells during experimental autoimmune neuritis

Background

Experimental autoimmune neuritis (EAN) is a well-known animal model of human demyelinating polyneuropathies and is characterized by inflammation and demyelination in the peripheral nervous system. Fascin is an evolutionarily highly conserved cytoskeletal protein of 55 kDa containing two actin binding domains that cross-link filamentous actin to hexagonal bundles.

Methods

Here we have studied by immunohistochemistry the spatiotemporal accumulation of Fascin?+?cells in sciatic nerves of EAN rats.

Results

A robust accumulation of Fascin?+?cell was observed in the peripheral nervous system of EAN which was correlated with the severity of neurological signs in EAN.

Conclusion

Our results suggest a pathological role of Fascin in EAN.

Virtual slides

The virtual slides for this article can be found here: http://www.diagnosticphatology.diagnomx.eu/vs/6734593451114811

     

A lost opportunity for science: journals promote data sharing in metabolomics but do not enforce it

Introduction

Data sharing is being increasingly required by journals and has been heralded as a solution to the ‘replication crisis’.

Objectives

(i) Review data sharing policies of journals publishing the most metabolomics papers associated with open data and (ii) compare these journals’ policies to those that publish the most metabolomics papers.

Methods

A PubMed search was used to identify metabolomics papers. Metabolomics data repositories were manually searched for linked publications.

Results

Journals that support data sharing are not necessarily those with the most papers associated to open metabolomics data.

Conclusion

Further efforts are required to improve data sharing in metabolomics.

     

Atorvastatin prevents <Emphasis Type="Italic">Plasmodium falciparum</Emphasis> cytoadherence and endothelial damage

Background

The adhesion of Plasmodium falciparum parasitized red blood cell (PRBC) to human endothelial cells (EC) induces inflammatory processes, coagulation cascades, oxidative stress and apoptosis. These pathological processes are suspected to be responsible for the blood-brain-barrier and other organs' endothelial dysfunctions observed in fatal cases of malaria. Atorvastatin, a drug that belongs to the lowering cholesterol molecule family of statins, has been shown to ameliorate endothelial functions and is widely used in patients with cardiovascular disorders.

Methods

The effect of this compound on PRBC induced endothelial impairments was assessed using endothelial co-culture models.

Results

Atorvastatin pre-treatment of EC was found to reduce the expression of adhesion molecules and P. falciparum cytoadherence, to protect cells against PRBC-induced apoptosis and to enhance endothelial monolayer integrity during co-incubation with parasites.

Conclusions

These results might suggest a potential interest use of atorvastatin as a protective treatment to interfere with the pathophysiological cascades leading to severe malaria.

     

Assessing broad life cycle impacts of daily onboard decision-making,annual strategic planning,and fisheries management in a northeast Atlantic trawl fishery

Purpose

Capture fisheries are the only industrial-scale harvesting of a wild resource for food. Temporal variability in environmental performance of fisheries has only recently begun to be explored, but only between years, not within a year. Our aim was to better understand the causes of temporal variability within and between years and to identify improvement options through management at a company level and in fisheries management.

Methods

We analyzed the variability in broad environmental impacts of a demersal freeze trawler targeting cod, haddock, saithe, and shrimp, mainly in the Norwegian Sea and in the Barents Sea. The analysis was based on daily data for fishing activities between 2011 and 2014 and the functional unit was a kilo of landing from one fishing trip. We used biological indicators in a novel hierarchic approach, depending on data availability, to quantify biotic impacts. Landings were categorized as target (having defined target reference points) or bycatch species (classified as threatened or as data-limited). Indicators for target and bycatch impacts were quantified for each fishing trip, as was the seafloor area swept.

Results and discussion

No significant difference in fuel use was found between years, but variability was considerable within a year, i.e., between fishing trips. Trips targeting shrimp were more fuel intensive than those targeting fish, due to a lower catch rate. Steaming to and from port was less important for fuel efficiency than steaming between fishing locations. A tradeoff was identified between biotic and abiotic impacts. Landings classified as main target species generally followed the maximum sustainable yield (MSY) framework, and proportions of threatened species were low, while proportions of data-limited bycatch were larger. This improved considerably when reference points were defined for saithe in 2014.

Conclusions

The variability between fishing trips shows that there is room for improvement through management. Fuel use per landing was strongly influenced by target species, fishing pattern, and fisheries management. Increased awareness about the importance of onboard decision-making can lead to improved performance. This approach could serve to document performance over time helping fishing companies to better understand the effect of their daily and more long-term decision-making on the environmental performance of their products.

Recommendations

Fishing companies should document their resource use and production on a detailed level. Fuel use should be monitored as part of the management system. Managing authorities should ensure that sufficient data is available to evaluate the sustainability of exploitation levels of all harvested species.

     

A life cycle comparison of disposal and beneficial use of coal combustion products in Florida

Background, Goal, and Scope

Currently, only 40%, or 44.5 million metric tons, of coal combustion products (CCPs) generated in the United States each year by electric utilities are diverted from disposal in landfills or surface impoundments and recycled. Despite promising economic and environmental savings, there has been scant attention devoted to assessing life cycle impacts of CCP disposal and beneficial use. The objective of this paper is to present a life cycle inventory considering two cases of CCP management, including the stages of coal mining and preparation, coal combustion, CCP disposal, and CCP beneficial use. Six beneficial uses were considered: concrete production, structural fills, soil amendments, road construction, blasting grit and roofing granules, and wallboard.

Methods

Primary data for raw material inputs and emissions of all stages considered were obtained from surveys and site visits of coal-burning utilities in Florida conducted in 2002, and secondary data were obtained from various published sources and from databases available in SimaPro 5.1 (PRé Consultants, Amersfoort, The Netherlands).

Results

Results revealed that 50 percent of all CCPs produced, or 108 kg per 1,000 kg of coal combusted, are diverted for application in a beneficial use; however, the relative amounts sold by each utility is dependent on the process operating parameters, air emission control devices, and resulting quality of CCP. Diversion of 50% of all CCPs to beneficial use applications yields a decrease in the total raw materials requirements (with the exception of gravel and iron) and most emissions to air, water, and land, as compared to 100% disposal.

Discussion

The greatest reduction of raw materials was attributed to replacing Portland cement with fly ash, using bottom ash as an aggregate in concrete production and road construction in place of natural materials, and substituting FGD gypsum for natural gypsum in wallboard. The use of fly ash as cementitious material in concrete also promised significant reductions in emissions, particularly the carbon dioxide that would be generated from Portland cement production. Beneficial uses of fly ash and gypsum showed reductions of emissions to water (particularly total dissolved solids) and emissions of metals to land, although these reductions were small compared to simply diverting 50% of all CCPs from landfills or surface impoundments.

Conclusions

This life cycle inventory (LCI) provides the foundation for assessing the impacts of CCP disposal and beneficial use. Beneficial use of CCPs is shown here to yield reductions in raw material requirements and various emissions to all environmental compartments, with potential tangible savings to human health and the environment.

Recommendations and Perspectives

Extension of this life cycle inventory to include impact assessment and sensitivity analysis will enable a determination of whether the savings in emissions reported here actually result in significant improvements in environmental and human health impacts.

     

Pseudo current density maps of electrophysiological heart,nerve or brain function and their physical basis

Background

In recent years the visualization of biomagnetic measurement data by so-called pseudo current density maps or Hosaka-Cohen (HC) transformations became popular.

Methods

The physical basis of these intuitive maps is clarified by means of analytically solvable problems.

Results

Examples in magnetocardiography, magnetoencephalography and magnetoneurography demonstrate the usefulness of this method.

Conclusion

Hardware realizations of the HC-transformation and some similar transformations are discussed which could advantageously support cross-platform comparability of biomagnetic measurements.

     

Atripla<Superscript>R</Superscript>/anti-TB combination in TB/HIV patients. Drug in focus

Background

Co-administration of anti-tuberculosis and antiretroviral therapy is often inevitable in high-burden countries where tuberculosis is the most common opportunistic infection associated with HIV/AIDS. Concurrent use of rifampicin and several antiretroviral drugs is complicated by pharmacokinetic drug-drug interaction.

Method

Pubmed and Google search following the key words tuberculosis, HIV, emtricitabine, tenofovir efavirenz, interaction were used to find relevant information on each drug of the fixed dose combination Atripla^R

Results

Information on generic name, trade name, pharmacokinetic parameter, metabolism and the pharmacokinetic interaction with Anti-TB drugs of emtricitabine, tenofovir, and efavirenz was obtained.

Conclusion

Fixed dose combination of emtricitabine/tenofovir/efavirenz (ATRIPLA^R) which has been approved by Food and Drug Administration shows promising results as far as safety and efficacy is concerned in TB/HIV co-infection patients, hence can be considered effective and safe antiretroviral drug in TB/HIV management for adult and children above 3 years of age.