Do bridge construction activities influence birds using the River Mersey,in northwest England?

Capsule: Bridge construction works over a major river did not adversely impact the overall wintering and breeding bird assemblage, although contrasting species-specific trends in breeding number were noted.

Aims: To determine whether the wintering water-bird and breeding bird assemblage using the River Mersey, in northwest England, was influenced by bridge construction works.

Methods: Common bird census and wintering bird surveys were carried out before and during construction of the Mersey Gateway bridge. The species abundance and richness of wintering water-birds, assigned to a group (‘Waterfowl’, ‘Wader’, ‘Wetland species’ and ‘Gull’) and breeding birds, assigned to a group (‘Salt marsh species’, ‘Waterfowl species’, ‘Wader species’, ‘Warbler species’ and ‘Other passerine species’), were separately compared before and during the works.

Results: We found little evidence that the bridge construction displaced wintering water-birds and instead found that for most bird groups, their assemblages were higher during the construction works, compared to before. Similarly, we found no evidence that the bridge construction reduced breeding density of any bird group. Contrasting species-specific trends were, however, noted, with some species only recorded breeding during the construction works, and other species recorded in higher breeding densities before the works.

Conclusion: The inadvertent increase in the mud-flats around the bridge structure since the works resulted in more mud-flat being exposed for a greater amount of time, and thus increased the foraging opportunities for many birds. This may at least partly explain why overall wintering bird abundance and richness increased since the works began. Although most breeding birds either increased or remained stable, in number since the works, a small number reduced. This may have been a consequence of the removal of suitable nesting habitat. This study provides a preliminary assessment of the influence of bridge construction on birds.     

The diversity and community dynamics of hazelwood lichens and bryophytes along a major gradient of human impact

Background: Oceanic hazelwoods in western Scotland are hypothesised to be unmanaged post-glacial relicts, representing an unusual type of old-growth forest habitat in Europe. They are characterised by an exceptionally high epiphytic diversity, including their status as ‘hotspots’ for indicators of woodland ecological continuity.

Aims: The aim of this study was to evaluate the effects of climate, pollution and management on the occurrence of epiphytic lichens and bryophytes on Corylus avellana.

Methods: Thirteen hazelwood study sites were systematically sampled along a climate, pollution and management gradient in Britain. Epiphyte composition and richness were examined in a strict hierarchical framework, and compared against site-, stool- and stem-scale environmental predictors.

Results: The study showed that along the gradient from ‘clean-air’ relict sites to ‘polluted’ coppiced sites: (i) epiphytic local stem-scale diversity declined, (ii) there was a loss of late-successional species including foliose cyano- and tripartite lichens and bryophytes and (iii) stem sizes were reduced, providing a further limit to the accumulation of species richness within a site.

Conclusions: Relict hazelwoods in western Scotland are confirmed as an example of the most intact epiphyte communities. In particular, we show that the transition to coppicing can be clearly linked to ecological processes causing species loss.     

Insights into apoptotic proteins in chemotherapy: quantification techniques and informing therapy choice

Introduction: Cancer is one of the leading causes of morbidity and mortality worldwide. A hallmark of cancer is evasion of apoptosis leading to tumor progression and drug resistance. Biomarker research has become a sign of the times, and proteins involved in apoptosis may be used for clinical diagnostic or prognostic purposes in cancer treatment. The recent progress in proteomic technology has triggered an emerging number of researchers to study the molecular mechanisms that regulate the apoptotic signal transduction pathways in cancer.

Areas covered: A PubMed search for ‘Proteomics’ and ‘cancer’ and ‘chemotherapy’ and ‘apoptosis’ has been conducted for literature until December 2017.

Results: The study of apoptotic protein signatures in cancer provides valuable information for more effective prognosis, response to therapy and the identification of novel drug targets. A huge number of bioinformatic tools are available to interpret raw data. For quantification, mass spectrometry is the most reliable technique.

Expert commentary: This field of research is, however, still in its infancy and more intensive research is warranted to explore the full potential of biomarkers for clinical use. Progress in this field is influenced by the detection limit of current quantification methods as well as patient and cancer inter-individual profiles.     

Fuel load,fuel deposition rate and stopover duration of the Common Sandpiper Actitis hypoleucos during the autumn migration

Capsule: Common sandpipers stopping over in a tidal marsh in northern Iberia during the autumn migration period showed a moderate mean fuel load and low fuel deposition rate, but relatively long stopover periods, suggesting a ‘hopping’ strategy of migration.

Aims: The main objectives of this paper were to analyse the stopover ecology of migrant Common Sandpipers at Txingudi coastal marshes, northern Iberia, in autumn.

Methods: Common sandpipers were captured during the autumn migration of 2007–2013 at the Txingudi marshlands (province of Gipuzkoa, northern Iberia). Data were obtained from a constant effort ringing station working on a daily basis.

Results: We observed a moderate fuel load and fuel deposition rate and long stopovers.

Conclusion: Our results suggest overall a ‘hopping’ migration strategy. When moving along the coast of northern Iberia, Common Sandpipers may not use key wetlands to gain much fuel, as found in other waders or in some wetlands of inland Iberia, but all coastal marshes seem to be potentially used in the same way.     

Effects of floral diversity and pollinator behaviour on the persistence of hybrid zones between plants sharing pollinators

Background: Plant hybrid zones often display a large diversity in floral traits due to segregation and recombination occurring in the second and later hybrid generations. Such diversity can have important effects on pollinator behaviour.

Aims: We hypothesised that the number of floral types and their relative densities may influence pollinator preferences and level of flower constancy.

Methods: To test the influence of floral diversity on the number of visits to inflorescences of the most common type and on the level of flower constancy, we monitored bumblebees’ behaviour in experimental arrays of artificial inflorescences with a common (‘parental’) floral type mixed with either one or three uncommon (‘hybrid’) floral types.

Results: We found that pollinators preferentially visited the most common flower colour and showed slightly greater constancy when the number of uncommon floral types was increased.

Conclusions: We conclude that diversity in flower colour could promote moderate pollinator constancy in some types of hybrid zones. Segregation of floral phenotypes due to hybridisation may result in small levels of pollinator-mediated assortative mating and contribute, to a small extent, and most probably in combination with other factors, to the persistence of some hybrid zones.     

Major depressive disorder: insight into candidate cerebrospinal fluid protein biomarkers from proteomics studies

Introduction: Major Depressive Disorder (MDD) is the leading cause of global disability, and an increasing body of literature suggests different cerebrospinal fluid (CSF) proteins as biomarkers of MDD. The aim of this review is to summarize the suggested CSF biomarkers and to analyze the MDD proteomics studies of CSF and brain tissues for promising biomarker candidates.

Areas covered: The review includes the human studies found by a PubMed search using the following terms: ‘depression cerebrospinal fluid biomarker’, ‘major depression biomarker CSF’, ‘depression CSF biomarker’, ‘proteomics depression’, ‘proteomics biomarkers in depression’, ‘proteomics CSF biomarker in depression’, and ‘major depressive disorder CSF’. The literature analysis highlights promising biomarker candidates and demonstrates conflicting results on others. It reveals 42 differentially regulated proteins in MDD that were identified in more than one proteomics study. It discusses the diagnostic potential of the biomarker candidates and their association with the suggested pathologies.

Expert commentary: One ultimate goal of finding biomarkers for MDD is to improve the diagnostic accuracy to achieve better treatment outcomes; due to the heterogeneous nature of MDD, using bio-signatures could be a good strategy to differentiate MDD from other neuropsychiatric disorders. Notably, further validation studies of the suggested biomarkers are still needed.     

Mass spectrometry imaging: How will it affect clinical research in the future?

Introduction: Mass spectrometry imaging (MSI) is a label free, multiplex imaging technology able to simultaneously record the distributions of 100’s to 1000’s of species, and which may be configured to study metabolites, lipids, glycans, peptides, and proteins simply by changing the tissue preparation protocol.

Areas covered: The capability of MSI to complement established histopathological practice through the identification of biomarkers for differential diagnosis, patient prognosis, and response to therapy; the capability of MSI to annotate tissues on the basis of each pixel’s mass spectral signature; the development of reproducible MSI through multicenter studies.

Expert commentary: We discuss how MSI can be combined with microsampling/microdissection technologies in order to investigate, with more depth of coverage, the molecular changes uncovered by MSI.     

Proteomic studies in the discovery of cerebrospinal fluid biomarkers for amyotrophic lateral sclerosis

Introduction: Amyotrophic lateral sclerosis (ALS) is a progressive degenerative motor neuron disease, which usually leads to death within a few years. The diagnosis is mainly based on clinical symptoms and there is a need for ALS-specific biomarkers to make an early and precise diagnosis, for development of disease-modifying drugs and to gain new insights into pathophysiology.

Areas covered: In the present review, we summarize studies using mass spectrometric (MS) approaches to identify protein alterations in the cerebrospinal fluid (CSF) of ALS patients. In total, we identified 11 studies fulfilling our criteria by searching in the PubMed database using the keywords ‘ALS’ and ‘CSF’ combined with ‘proteome’, ‘proteomic’, ‘mass spectrometry’ or ‘protein biomarker’. Ten proteins were differently regulated in ALS CSF compared to controls in at least 2 studies. We will discuss the relevance of the identified proteins regarding the frequency of identification, extent of alteration and brain-specificity.

Expert commentary: Most of the identified CSF biomarker candidates are irreproducible or mainly blood-derived. We assign the missing success of CSF proteomic studies in biomarker discovery to a lack of sensitivity, unsuitable normalization, low quality assurance and variations originating from sample preparation. These issues must be improved in future proteomic studies in CSF.     

Little evidence for local adaptation to soils or microclimate in the post-fire recruitment of three Californian shrubs

Background: Seedling recruitment following fire is an infrequent yet critical demographic transition for woody plants in Mediterranean ecosystems.

Aims: Here we examine whether post-fire seedling recruitment of three widespread Californian chaparral shrubs is affected by local adaptation within an edaphically and topographically complex landscape.

Methods: We reciprocally transplanted 6-month-old seedlings of Adenostema fasciculatum, Ceanothus cuneatus and Eriodictyon californicum to serpentine and sandstone soils, and cool northerly and warm southerly slopes.

Results: At the age of 2 years, none of the species manifested higher survival or growth on ‘home’ compared with ‘away’ soils or slopes, indicating an absence of local adaptation with respect to seedling recruitment in these environments. Seedlings of all species manifested lower survival and relative growth on serpentine soils regardless of seedling source, as well as a variety of other destination and source effects.

Conclusions: The ability of these three species to recruit in new environments, such as in restoration settings or in response to shifting climates, is unlikely to be impeded by a need for seeds from sources that closely match their edaphic or topographic destination.     

Deciphering the MHC-associated peptidome: a review of naturally processed ligand data

Introduction: The availability of big data sets (‘OMICS’) has greatly impacted fundamental and translational science. High-throughput analysis of HLA class I and II associated peptidomes by mass spectrometry (MS) has generated large datasets, with the last decade witnessing tremendous growth in the breadth and number of studies.

Areas covered: For this, we first analyzed naturally processed peptide (NP) data captured within the IEDB to survey and characterize the current state of NP data. We next asked to what extent the NP data overlap with existing T cell epitope and MHC binding data.

Expert commentary: The current collection of NP data represents a large and diverse set of class I/II peptides mostly derived from self-antigens. These data overlap only marginally with existing immunogenicity and binding data and it is thus difficult to ascertain the correspondence between the different assay methodologies. This highlights a need for unbiased studies benchmarking in model antigen systems how well MHC binding and NP data predicts immunogenicity. Going forward, efforts at generating an integrated process for capturing all NP, curating associated metadata and accessing NP data from an immunological viewpoint will be important for development of novel methods for identifying optimal target antigens and for class I and II epitope prediction.     

Bacterial pili,with emphasis on Mycobacterium tuberculosis curli pili: potential biomarkers for point-of care tests and therapeutics

Context: Novel biomarkers are essential for developing rapid diagnostics and therapeutic interventions

Objective: This review aimed to highlight biomarker characterisation and assessment of unique bacterial pili.

Methods: A PubMed search for bacterial pili, diagnostics, vaccine and therapeutics was performed, with emphasis on the well characterised pili.

Results: In total, 46 papers were identified and reviewed.

Conclusion: Extensive analyses of pili enabled by advanced nanotechnology and whole genome sequencing provide evidence that they are strong biomarker candidates. Mycobacterium tuberculosis curli pili are emphasised as important epitopes for the development of much needed point-of-care diagnostics and therapeutics.     

Proteomics approach to identify biomarkers for upper gastrointestinal cancer

Introduction: The prognosis for patients with upper gastrointestinal cancers remains dismal despite the development of multimodality therapies that incorporate surgery, chemotherapy, and radiotherapy. Early diagnosis and personalized treatment should lead to better prognosis. Given the advances in proteomic technologies over the past decades, proteomics promises to be the most effective technique to identify novel diagnostics and therapeutic targets.

Areas covered: For this review, keywords were searched in combination with ‘proteomics’ and ‘gastric cancer’ or ‘esophageal cancer’ in PubMed. Studies that evaluated proteomics associated with upper gastrointestinal cancer were identified through reading, with several studies quoted at second hand. We summarize the proteomics involved in upper gastrointestinal cancer and discuss potential biomarkers and therapeutic targets.

Expert commentary: In particular, the development of mass spectrometry has enabled detection of multiple proteins and peptides in more biological samples over a shorter time period and at lower cost than was previously possible. In addition, more sophisticated protein databases have allowed a wider variety of proteins in samples to be quantified. Novel biomarkers that have been identified by new proteomic technologies should be applied in a clinical setting.     

‘Draw your pelvis’ test for assessing pelvic schema in people with Parkinsonʼs disease: a validity and reliability study

Aim: Body schema (i.e., the mental representation of the body and its parts) is important for cognitive and motor functions, with the pelvis constituting a core element in such schema. Although people with Parkinson?s disease exhibit misperceptions and deficits in body schema, there are currently no published tools available for assessing pelvic schema in this population. This study aimed to develop and establish feasibility, reliability, and validity of a novel drawing test ? ‘Draw Your Pelvis’ ? for assessing pelvic schema in people with Parkinson?s disease.

Materials and methods: Twenty people with idiopathic Parkinson?s disease (Hoehn &Yahr stages I–III; M age: 65.75?±?10.13) volunteered and were asked to manually draw a picture of their pelvis. Drawings were assessed and scored by 13 blinded raters over two sessions. Intra- and inter-rater reliability and content and criterion validity were investigated.

Results: The ‘Draw Your Pelvis’ test is shown to be feasible and quick to administer, with excellent inter-rater reliability for consistency (0.954–0.968) and absolute agreement (0.946–0.961). It also demonstrates good-excellent (0.614–0.950) intra-rater reliability, and is content valid.

Conclusions: The ‘Draw Your Pelvis’ test holds potential for clinicians and researchers in assessing pelvic schema and its deficits in people with Parkinson?s disease. In addition, this test could be used for investigating the effect of therapeutic interventions on body schema in this population. Future studies should explore this test in additional populations.     

Analysis of sulfates on low molecular weight heparin using mass spectrometry: structural characterization of enoxaparin

Introduction: Structural characterization of low molecular weight heparin (LMWH) is critical to meet biosimilarity standards. In this context, the review focuses on structural analysis of labile sulfates attached to the side-groups of LMWH using mass spectrometry. A comprehensive review of this topic will help readers to identify key strategies for tackling the problem related to sulfate loss. At the same time, various mass spectrometry techniques are presented to facilitate compositional analysis of LMWH, mainly enoxaparin.

Areas covered: This review summarizes findings on mass spectrometry application for LMWH, including modulation of sulfates, using enzymology and sample preparation approaches. Furthermore, popular open-source software packages for automated spectral data interpretation are also discussed. Successful use of LC/MS can decipher structural composition for LMWH and help evaluate their sameness or biosimilarity with the innovator molecule. Overall, the literature has been searched using PubMed by typing various search queries such as ‘enoxaparin’, ‘mass spectrometry’, ‘low molecular weight heparin’, ‘structural characterization’, etc.

Expert commentary: This section highlights clinically relevant areas that need improvement to achieve satisfactory commercialization of LMWHs. It also primarily emphasizes the advancements in instrumentation related to mass spectrometry, and discusses building automated software for data interpretation and analysis.     

Detection and analysis of endogenous polar volatile organic compounds (PVOCs) in urine for human exposome research

Background: The human exposome, defined as ‘…everything that is not the genome’, comprises all chemicals in the body interacting with life processes. The exposome drives genes x environment (GxE) interactions that can cause long-term latency and chronic diseases. The exposome constantly changes in response to external exposures and internal metabolism. Different types of compounds are found in different biological media.

Objective: Measure polar volatile organic compounds (PVOCs) excreted in urine to document endogenous metabolites and exogenous compounds from environmental exposures.

Methods: Use headspace collection and sorbent tube thermal desorption coupled with bench-top gas chromatography-mass spectrometry (GC-MS) for targeted and non-targeted approaches. Identify and categorize PVOCs that may distinguish among healthy and affected individuals.

Results: Method is successfully demonstrated to tabulate a series of 28 PVOCs detected in human urine across 120 samples from 28 human subjects. Median concentrations range from below detect to 165?ng/mL. Certain PVOCs have potential health implications.

Conclusions: Headspace collection with sorbent tubes is an effective method for documenting PVOCs in urine that are otherwise difficult to measure. This methodology can provide probative information regarding biochemical processes and adverse outcome pathways (AOPs) for toxicity testing.     

Proteomic approaches for cancer epigenetics research

Introduction: Epigenetic dysregulation drives or supports numerous human cancers. The chromatin landscape in cancer cells is often marked by abnormal histone post-translational modification (PTM) patterns and by aberrant assembly and recruitment of protein complexes to specific genomic loci. Mass spectrometry-based proteomic analyses can support the discovery and characterization of both phenomena.

Areas covered: We broadly divide this literature into two parts: ‘modification-centric’ analyses that link histone PTMs to cancer biology; and ‘complex-centric’ analyses that examine protein–protein interactions that occur de novo as a result of oncogenic mutations. We also discuss proteomic studies of oncohistones. We highlight relevant examples, discuss limitations, and speculate about forthcoming innovations regarding each application.

Expert commentary: ‘Modification-centric’ analyses have been used to further understanding of cancer’s histone code and to identify associated therapeutic vulnerabilities. ‘Complex-centric’ analyses have likewise revealed insights into mechanisms of oncogenesis and suggested potential therapeutic targets, particularly in MLL-associated leukemia. Proteomic experiments have also supported some of the pioneering studies of oncohistone-mediated tumorigenesis. Additional applications of proteomics that may benefit cancer epigenetics research include middle-down and top-down histone PTM analysis, chromatin reader profiling, and genomic locus-specific protein identification. In the coming years, proteomic approaches will remain powerful ways to interrogate the biology of cancer.     

Patterns of seed dispersal syndromes on serpentine soils: examining the roles of habitat patchiness,soil infertility and correlated functional traits

Background: It is critical to understand the ecological factors shaping seed dispersal in plant communities in order to predict their fate in the face of global change. Communities restricted to patchy habitats may contain more species with ‘directed’ dispersal syndromes that facilitate successful seed dispersal to other patches; however, habitat quality may constrain the presence of and efficiency of dispersal syndromes found within those habitats.

Aims: The aim of this study was to hypothesise that if habitat patchiness is an important filter on dispersal syndromes, ‘directed’ vertebrate dispersal should be more prevalent in serpentine habitats because of their patchiness. Alternatively, if habitat quality is more important, wind dispersal should be more prevalent in serpentine habitats because of their low fertility.

Methods: Using three datasets representing grassland, chaparral and forest vegetation types, we analysed differences in the composition of dispersal syndromes (vertebrate, wind, passive, water and ant) between communities on patchy infertile serpentine soils and on continuous, fertile non-serpentine soils. Our analyses also accounted for correlated functional traits and phylogenetic relatedness.

Results: Across and within all three vegetation types, serpentine communities had significantly higher proportions of wind dispersed and lower proportions of vertebrate-dispersed species. These patterns were not independent of functional traits. Proportions of the other dispersal syndromes did not differ.

Conclusions: Our results suggest that on low-fertility soils, habitat quality may outweigh habitat patchiness as a filter on the availability of dispersal syndromes, potentially adding to the vulnerability of such communities to stochastic extinctions and global change.     

Soluble CD40 ligand in haemodialysis patients: survival impact and cardiovascular prognostic role

Context: Soluble CD40 ligand (sCD40l) can predict cardiovascular events (CVE) and mortality in haemodialysis (HD) patients (short-, medium-term follow-up studies).

Objective: To evaluate the relationship between sCD40l and survival, CVE and mortality in HD patients on long-term follow-up.

Methods: We registered 46?HD patients’ baseline characteristics, mortality and CVE for 108 months.

Results: SCD40l correlated positively with C-reactive protein, was higher in survivors, but had no impact on survival and was not predictive for CVE or CV mortality.

Conclusion: The levels of sCD40l have no influence on survival or CVE and mortality in HD patients in a long-term follow-up.     

A model of lipid rearrangements during pore formation in the DPPC lipid bilayer

Context: The molecular bases of pore formation in the lipid bilayer remain unclear, as do the exact characteristics of their sizes and distributions. To understand this process, numerous studies have been performed on model lipid membranes including cell-sized giant unilamellar vesicles (GUV). The effect of an electric field on DPPC GUV depends on the lipid membrane state: in the liquid crystalline phase the created pores have a cylinder-like shape, whereas in the gel phase a crack has been observed.

Objective: The aim of the study was to investigate the geometry of pores created in a lipid bilayer in gel and liquid crystalline phases in reference to literature experimental data.

Methods: A mathematical model of the pore in a DPPC lipid bilayer developed based on the law of conservation of mass and the assumption of constant volume of lipid molecules, independent of their conformation, allows for analysis of pore shape and accompanying molecular rearrangements.

Results: The membrane area occupied by the pore of a cylinder-like shape is greater than the membrane area occupied by lipid molecules creating the pore structure (before pore appearance). Creation of such pores requires more space, which can be achieved by conformational changes of lipid chains toward a more compact state. This process is impossible for a membrane in the most compact, gel phase.

Discussion and conclusions: We show that the geometry of the pores formed in the lipid bilayer in the gel phase must be different from the cylinder shape formed in the lipid bilayer in a liquid crystalline state, confirming experimental studies. Furthermore, we characterize the occurrence of the ‘buffer’ zone surrounding pores in the liquid crystalline phase as a mechanism of separation of neighbouring pores.