Separating the wheat from the chaff: a prioritisation pipeline for the analysis of metabolomics datasets

Liquid Chromatography Mass Spectrometry (LC-MS) is a powerful and widely applied method for the study of biological systems, biomarker discovery and pharmacological interventions. LC-MS measurements are, however, significantly complicated by several technical challenges, including: (1) ionisation suppression/enhancement, disturbing the correct quantification of analytes, and (2) the detection of large amounts of separate derivative ions, increasing the complexity of the spectra, but not their information content. Here we introduce an experimental and analytical strategy that leads to robust metabolome profiles in the face of these challenges. Our method is based on rigorous filtering of the measured signals based on a series of sample dilutions. Such data sets have the additional characteristic that they allow a more robust assessment of detection signal quality for each metabolite. Using our method, almost 80% of the recorded signals can be discarded as uninformative, while important information is retained. As a consequence, we obtain a broader understanding of the information content of our analyses and a better assessment of the metabolites detected in the analyzed data sets. We illustrate the applicability of this method using standard mixtures, as well as cell extracts from bacterial samples. It is evident that this method can be applied in many types of LC-MS analyses and more specifically in untargeted metabolomics.

     

Are blue-green algae a suitable food for zooplankton? An overview

One of the reasons suggested to explain the dominance of blue-greens in eutrophic lakes is that they are not used as food by zooplankton; and even when ingested, they are poorly utilized.

An increase in herbivores might be the expected result of biomanipulation of the aquatic food chain. This attempt at controlling the algae population is, however, destined to fail if zooplankton do not also utilize blue-greens as food. In this respect, a series of in-lake experimental results indicates that after the food chain has been biomanipulated, there is a decrease in blue-green density in periods when there is an increase in herbivores. Is this only an accidental result or are the two facts interrelated; in other words, can the decrease in the density of blue-greens be attributed to the increased use of them by zooplankton herbivores?

The suitability of blue-greens as food for zooplankton has been widely investigated by many authors with contrasting and inconclusive results. Two main factors seem to play important role in determining their suitability as food: the biochemical properties of the different species, or even different strains of the same species; and the shape and size of the colonies.

In particular, biochemical properties can result in toxic effects on zooplankton, while size and shape may strongly interfere with filtering, thus reducing the possibility of gathering food.

     

Mass spectrometric techniques for characterisation of platinum–humic substance complexes in soil and street dust samples

Abstract

Increased platinum concentrations have been detected in environmental samples since the introduction of catalytic converters in Europe. It was previously believed that PGE are relatively inert and that the soluble fraction of automobile catalyst emitted PGE is only a few percent. However, new studies suggested that metallic Pt is oxidised in the soil and that the majority of the Pt species could be humic substance complexes.

The aim of the present paper is the characterisation of platinum-humic acid complexes in spiked soil and street dust samples. A number of different soft ionisation mass spectrometric techniques, such as ESI-Q-MS, ESI-ION TRAP-MS and MALDI-TOF-MS have been tested. The ESI mass spectra of the soil humic acids were characterised by high complexity and irreproducibility.

MALDI-TOF-MS was used for humic acid complexes characterisation in positive and negative modes. Positive ionisation was less effective and produced more simple and less informative spectra than negative ionisation. Two different MALDI matrices (CHCA, DHBA) were tested for use with humic substances. DHBA yielded better results, exhibiting superior ionisation efficiency, low spectral background and the matrix peaks were almost completely suppressed causing no interferences with identified analyte peaks. The application of MALDI-TOF-MS shows its suitability for humic substance characterisation. The comparison of the MALDI-spectra of humic acids, extracted from spiked and native soil proved that Pt undergoes transformation in the environment to humic acid complexes.     

Advances in ionisation techniques for mass spectrometry-based omics research

Omics analysis by mass spectrometry (MS) is a vast field, with proteomics, metabolomics and lipidomics dominating recent research by exploiting biological MS ionisation techniques. Traditional MS ionisation techniques such as electrospray ionisation have limitations in analyte-specific sensitivity, modes of sampling and throughput, leading to many researchers investigating new ionisation methods for omics research. In this review, we examine the current landscape of these new ionisation techniques, divided into the three groups of (electro)spray-based, laser-based and other miscellaneous ionisation techniques. Due to the wide range of new developments, this review can only provide a starting point for further reading on each ionisation technique, as each have unique benefits, often for specialised applications, which promise beneficial results for different areas in the omics world.     

Detection of hydroxyethylstarch (HES) in human urine by liquid chromatography-mass spectrometry

The objective of this study was to establish the possibility of using liquid chromatography coupled to mass spectrometry for the detection of hydroxyethylstarch (a corn starch derived product) in urine as an alternative to the current time consuming GC-MS methods. Analyses were performed using an ion trap instrument after acidic hydrolysis. Ionization was carried out using atmospheric pressure chemical ionisation (APCI) operated in negative ionization mode and detection was performed using MS(2). The results indicate that the developed method can successfully be applied as a fast and reliable method for the detection and identification of hydroxyethylstarch.     

Sensitivity of the IQM and MatriXX detectors in megavolt photon beams

AimThis study focused on evaluating the sensitivity of integral quality monitoring (IQM^®) system and MatriXX detectors. These two detectors are recommended for radiotherapy pre-treatment quality assurance (QA).BackgroundIQM is a large wedged-shaped ionisation chamber mounted to the linear accelerator (linac) head in practice. MatriXX consists of an array of ionisation chambers also attached to the linac head.Materials and methodsIn this study, the dosimetric performance and sensitivity of MatriXX and IQM detectors were evaluated using the following characteristics: reproducibility, linearity, error detection capability and three-dimensional conformal radiotherapy (3D-CRT) plans of the head and neck, thorax and pelvic regions.ResultsThis study indicates that the signal responses of the large ionisation chamber device (IQM) and the small pixel array of ionisation chambers device (MatriXX) are reproducible, linear and sensitive to MLC positional errors, backup jaw positional errors and dose errors. The local percentage differences for dose errors of 1%, 2%, and 3% were, respectively, within 0.35–8.23%, 0.78–16.21%, and 1.10–24.41% for the IQM device. While for the MatriXX detector, the ranges were between 0.24–3.19, 0.57–6.43 and 0.81–12.95, respectively. Since IQM is essentially a double wedge-shaped large ionisation chamber, its reproducibility and detection capability are competitive to that of MatriXX. In addition, the sensitivity of the two QA systems increases with an increase in escalation percentage, and the signal responses are patient plan specific.ConclusionsThe two detectors response signals have good correlations and they are accurate for pre-treatment QA. Statistically, (P < 0.05) there is a significant difference between the IQM and MatriXX response to dose errors.     

Designing hybrid life cycle assessment models based on uncertainty and complexity

Purpose

Despite the wide use of LCA for environmental profiling, the approach for determining the system boundary within LCA models continues to be subjective and lacking in mathematical rigor. As a result, life cycle models are often developed in an ad hoc manner, and are difficult to compare. Significant environmental impacts may be inadvertently left out. Overcoming this shortcoming can help elicit greater confidence in life cycle models and their use for decision making.

Methods

This paper describes a framework for hybrid life cycle model generation by selecting activities based on their importance, parametric uncertainty, and contribution to network complexity. The importance of activities is determined by structural path analysis—which then guides the construction of life cycle models based on uncertainty and complexity indicators. Information about uncertainty is from the available life cycle inventory; complexity is quantified by cost or granularity. The life cycle model is developed in a hierarchical manner by adding the most important activities until error requirements are satisfied or network complexity exceeds user-specified constraints.

Results and Discussion

The framework is applied to an illustrative example for building a hybrid LCA model. Since this is a constructed example, the results can be compared with the actual impact, to validate the approach. This application demonstrates how the algorithm sequentially develops a life cycle model of acceptable uncertainty and network complexity. Challenges in applying this framework to practical problems are discussed.

Conclusion

The presented algorithm designs system boundaries between scales of hybrid LCA models, includes or omits activities from the system based on path analysis of environmental impact contribution at upstream network nodes, and provides model quality indicators that permit comparison between different LCA models.

     

Effect of Salts and Electron Transport on the Conformation of Isolated Chloroplasts. II. Electron Microscopy

Spinach chloroplasts isolated in media containing salts and the rare chloroplasts which are still within their envelopes alike retain grana similar to those seen in chloroplasts in situ.

Chloroplasts isolated in low-salt media lose their grana without losing any chlorophyll. These grana-free chloroplasts are considerably swollen and consist almost entirely of continuous sheets of paired-membrane structures. These double structures, the lamellae, are only loosely held together, primarily at the edges, by tenuous material which does not react with permanganate.

Addition of salts (methylamine hydrochloride, NaCl, MgCl₂) to the grana-free low-salt chloroplasts provide strong interlamellar attractions. These attractions result in a stacking of the lamellae which is sometimes almost random but sometimes results in regular structures indistinguishable from the original grana.

The phosphorylation-uncoupler atebrin causes further swelling of the chloroplasts in the absence of electron transport by increasing the space between the paired membranes of the lamellae.

The rapid electron transport (Hill reaction) made possible by atebrin-uncoupling is associated with a great decrease in chloroplast volume. This decrease results from a collapsing together of the widely separated lamellar membrane pairs. The pairs approach each other so closely that they usually appear as a single membrane when viewed with the electron microscope. The much slower electron transport which occurs in the absence of uncouplers is associated with a similar but smaller decrease in the space between the lamellar membrane pairs.

Chloroplasts swell during the rapid electron transport made possible by the phosphorylation-uncoupler methylamine. This swelling is accompanied by a degree of membrane distortion which precludes an interpretation of the mechanism. As with atebrin-faciliated electron transport, obviously paired membranes disappear but it is not yet clear whether this is by association or dissociation of the pairs.

     

A two way fully coupled fluid structure simulation of human ureter peristalsis

Abstract

Numerical simulations of ureter peristalsis have been carried out in the past to understand both the flow field and ureter wall mechanics. The main objective of the current investigations is to have a better understanding of the urine transport due to the peristalsis in the ureter, thus making the information helpful for a better treatment and diagnosis of ureteral complications like urine reflux. In the current study, a numerical simulation is performed using a finite-element-based solver with a two-way fully coupled fluid structure interaction approach between the ureter wall and urine. For the first time, the ureter wall is modeled as an anisotropic hyper-elastic material based on experiments performed in previous literature on the human ureter. Peristalsis in the ureter is modeled as a series of isolated boluses. By observing the flow field it is clear that the peristalsis mechanism has a natural tendency to create a backflow as the isolated bolus moves forward. As a result, the urine can flow back from the bladder to the ureter at the ureterovesical (ureter-bladder) junctions, if the one-way valve starts to malfunction.     

Blood and sputum protein biomarkers for chronic obstructive pulmonary disease (COPD)

ABSTRACT

Introduction: Chronic obstructive pulmonary disease (COPD) is a heterogeneous set of disorders, characterized by airflow limitation, and reduced lung function. Despite increasing knowledge regarding its pathophysiology, there has been limited advancement in therapeutics and the current treatment strategy is symptom management and prevention of exacerbations.

Areas covered: Biomarkers represent important tools for the implementation of precision medicine. As fundamental molecules of all living processes, proteins could provide crucial information about how genes interact with the environment. Proteomics studies could act as important tools in identifying reliable biomarkers to enable a more precise therapeutic approach. In this review, we will explore the most promising blood and sputum protein biomarkers in COPD that have been consistently reported in the literature.

Expert commentary: Given the complexity of COPD, no single protein biomarker has been able to improve the outcomes of COPD patients. According to preliminary studies, precision medicine in COPD will likely require a combination of different proteins in a biomarker panel for clinical translation. With advancements in current mass spectrometry techniques, an enhancement in the identification of new biomarkers will be observed, and improvements in sequence database search can fill in potential gaps between biomarker discovery and patient care.     

Biopolymer nanoparticle production for controlled release of biopharmaceuticals

Abstract

For drug applications, nanoparticles, used as drug carriers, offer the advantage of controlled release, therapeutic impact and targeted delivery. In drug delivery applications, biodegradable polymers can be extracted from natural sources or prepared synthetically by polymerization. Natural polymers typically have varying compositions and physiochemical properties. As a result, methods which utilize natural polymers to encapsulate drugs are more varied and polymer dependent. The following polymers are discussed in this review article: alginate, chitosan, gelatin, albumin, gliadin, pullulan, and dextran. Specialized encapsulation nanotechnologies will be discussed such as ionotropic gelation, complexation, the reverse microemulsion technique, cross-linking methods, emulsion-dependent methods, desolvation methods and self-assembly methods. For each biopolymer an overview of the structure is presented with the corresponding encapsulation techniques. Understanding the structure of the biopolymer is important as to not only understand the rational for current encapsulation techniques but to continue to develop new encapsulation techniques in pursuit of the ideal drug carrier for application in therapeutic treatments.     

Arsenic removal from the aqueous system using plant biomass: a bioremedial approach

Metal species released into the environment by technological activities tend to persist indefinitely, circulating and eventually accumulating throughout the food chain, thus becoming a serious threat to the environment. Environment pollution by toxic metals occurs globally through military, industrial, and agricultural processes and waste disposal. Bioremediation processes are the target of recent research and are considered low-cost, ecofriendly methods to alleviate the current problems of water decontamination, particularly for remote and rural areas. The present piece of work reports the unexploited sorption properties of the powdered seed of the plant Moringa oleifera (SMOS) for the removal of Arsenic [As(III) and As(V)] from aqueous solutions. Sorption studies, using standard practices, result in the standardization of optimum conditions such as biomass dosages (2.0 g), metal concentrations (25 ppm), contact time (60 min) and volume of the test solutions (200 ml) at pH 7.5, for As(III) and pH 2.5 for As(V). Maximum sorption for As(III) and As(V) species is 60.21 and 85.6%, respectively. Protein/Amino acid–Arsenic interactions are found to play an important role in the biosorption process using plant biomass SMOS.

     

REPRODUCTION SEXUÉE D'UNE ASTÉRIE FISSIPARE,SCLERASTERIAS RICHARDI (PERRIER, 1882) / SEXUAL REPRODUCTION IN A FISSIPAROUS ASTEROID,SCLERASTERIAS RICHARDI (PERRIER, 1882)

Sclerasterias richardi, a relatively deep sea asteroid (140–200 m) from the border of the Mediterranean continental shelf, is characterized by an asexual reproduction by fissiparity concomitant with a functional sexuality.

A monthly sampling of a population from Calvi (Corsica) has allowed a study of the complete sexual cycle from 354 histologically-treated specimens.

The 218 sexually defined animals (62% males, 38% females) show strict gonochorism. In males, spermatogenesis is cyclic and sexual maturity seems to be reached before that of the females. In females, the different stages of oogenesis are well marked: oogonia and parietal oocytes disappear only at maturity. Oligolecithic oocytes (120–150 μn) show a synchronous growth.

The annual reproductive cycle is well defined in both sexes with one spawning period from mid-September to mid-October.

After spawning, a resting period (from mid-October to mid-January) occurs during which unspawned oocytes are phagocytized by more or less isolated accessory cells. These phagocytic cells have never been found in male specimens.

Each month the presence of specimens without gonads or unsexable individuals is one of the characteristics of this cycle. Their high proportion during the organization stage and after spawning can be easily explained. In March they are frequent too, owing to the infestation of gonads by Ciliates.

As shown by our samples, the bottom water temperature is nearly the same during the whole year and cannot be directly involved as the dominant exogenous variable stimulating spawning.

As a consequence of fissiparity which affects the main part of the population there is a great inter- and intra-individual variability.

The reproductive potentiality is low: as a female emits approximatly 400–500 ova whose development produces planktotrophic larvae with a long pelagic life, it is clear that sexual reproduction is accessory in comparison with asexual reproduction by fission.     

‘I'm American,not Japanese!’: the struggle for racial citizenship among later-generation Japanese Americans

Abstract

As one of the oldest Asian American groups in the USA, most Japanese Americans are of the third and fourth generations and have become well integrated in mainstream American society. However, they are still racialized as foreigners simply because of their Asian appearance. Their Asian phenotype continues to have a foreigner connotation because of large-scale immigration from Asia and an American national identity that is racially defined as white. This paper analyses how later-generation Japanese Americans are racialized as outsiders in their daily interaction with mainstream Americans, which is often accompanied by essentialized assumptions that they are also culturally foreign. In response, they engage in everyday struggles for racial citizenship by demanding inclusion in the national community as Americans despite their racial differences. It is uncertain whether such attempts to contest their racialization will cause current mono-racial notions of American identity to be reconsidered in more inclusive and multiracial ways.     

Degrees of honesty: cleaning by the redlip cleaner wrasse Labroides rubrolabiatus

Cleaning symbioses among coral reef fishes are highly variable. Cleanerfishes vary in how much they cooperate with (i.e. remove only ectoparasites) or cheat (i.e. bite healthy tissue, scales or mucus) on their fish clients. As a result, clients use various strategies to enforce cooperation by cleaners (e.g. punishment or partner choice), and cleaners use tactile stimulation to manipulate cheated client behaviour. We provide the first detailed observations of cleaning behaviour of the redlip cleaner wrasse Labroides rubrolabiatus and ask where interactions with this cleanerfish lie on the continuum of cleanerfish honesty, client control, and cleanerfish manipulation. Ninety per cent of redlip cleaner wrasses took jolt-inducing cheating bites from their clients, but they did so at a very low rate (~ 2 jolts per 100 s inspection). Retaliatory chases by clients were uncommon. Three-quarters (30 of 40) of cleaner wrasses used tactile stimulation on their clients, but rarely did so to reconcile with cheated clients. Instead, the majority (70%) of tactile stimulation events targeted a passing client that then stopped for inspection. The relationship between redlip cleaner wrasses and their clients appears to be less conflictual than those documented in other Labroides cleanerfishes. Future studies should test whether this low level of conflict is consistent across space and time and is underpinned by a preference for ectoparasites over other client-gleaned items. As an active cleaner that appears to take few cheating bites from their clients, L. rubrolabiatus has the potential to be as important a driver of fish health and community structure on coral reefs as its better-known relatives.

     

New Building Blocks for the Preparation of Branched Oligonucleotides

Abstract

New building blocks 2 and 3 were prepared and successfully employed for the synthesis of branched oligonucleotides 5 and 6. The structure of oligomers obtained was confirmed by electrospray ionisation mass spectrometry.     

Synthesis of Novel Plant Growth Inhibitors Structurally Related to Abscisic Acid

When paraffin wax is dispersed in medium as emulsion, some kinds of bacteria and yeasts readily grow on it. This paper presents a study on microbial cell production from solid paraffin. In this study a paraffin wax which contains 91% of normal paraffins ranging from C₂₅ to C₃₇ with the melting point of 62.5°C was used as a substate, but no solvent was used for the dispersion of the wax.

As a result of this study, the following have been found out. (1) Many strains of liquid normal paraffin assimilating bacteria and yeasts can assimilate paraffin wax. (2) Dried cell yields on added hydrocarbons of Corynebacterium hydrocarboclastus S-12-B2 and Candida tropicalis S-315-Y1 are 70% and 56% respectively, when they are cultured by wax emulsion of 0.6% concentration. (3) When nonion surface-active agent (Plysurf A210G) was added as an emulsifing agent, highly concentrated wax emulsion was obtained, but the growth of microorganisms on it was slower. Further investigation is needed to obtain better strains of bacteria and yeasts and also to find out optimum culture conditions.