Industrial-scale proteomics: from liters of plasma to chemically synthesized proteins

Human blood plasma is a useful source of proteins associated with both health and disease. Analysis of human blood plasma is a challenge due to the large number of peptides and proteins present and the very wide range of concentrations. In order to identify as many proteins as possible for subsequent comparative studies, we developed an industrial-scale (2.5 liter) approach involving sample pooling for the analysis of smaller proteins (M(r) generally < ca. 40 000 and some fragments of very large proteins). Plasma from healthy males was depleted of abundant proteins (albumin and IgG), then smaller proteins and polypeptides were separated into 12 960 fractions by chromatographic techniques. Analysis of proteins and polypeptides was performed by mass spectrometry prior to and after enzymatic digestion. Thousands of peptide identifications were made, permitting the identification of 502 different proteins and polypeptides from a single pool, 405 of which are listed here. The numbers refer to chromatographically separable polypeptide entities present prior to digestion. Combining results from studies with other plasma pools we have identified over 700 different proteins and polypeptides in plasma. Relatively low abundance proteins such as leptin and ghrelin and peptides such as bradykinin, all invisible to two-dimensional gel technology, were clearly identified. Proteins of interest were synthesized by chemical methods for bioassays. We believe that this is the first time that the small proteins in human blood plasma have been separated and analyzed so extensively.     

In vitro and in silico processes to identify differentially expressed proteins

We present an integrated proteomics platform designed for performing differential analyses. Since reproducible results are essential for comparative studies, we explain how we improved reproducibility at every step of our laboratory processes, e.g. by taking advantage of the powerful laboratory information management system we developed. The differential capacity of our platform is validated by detecting known markers in a real sample and by a spiking experiment. We introduce an innovative two-dimensional (2-D) plot for displaying identification results combined with chromatographic data. This 2-D plot is very convenient for detecting differential proteins. We also adapt standard multivariate statistical techniques to show that peptide identification scores can be used for reliable and sensitive differential studies. The interest of the protein separation approach we generally apply is justified by numerous statistics, complemented by a comparison with a simple shotgun analysis performed on a small volume sample. By introducing an automatic integration step after mass spectrometry data identification, we are able to search numerous databases systematically, including the human genome and expressed sequence tags. Finally, we explain how rigorous data processing can be combined with the work of human experts to set high quality standards, and hence obtain reliable (false positive < 0.35%) and nonredundant protein identifications.     

Alpha-Synuclein Levels in Blood Plasma Decline with Healthy Aging

There is unequivocal evidence that alpha-synuclein plays a pivotal pathophysiological role in neurodegenerative diseases, and in particular in synucleinopathies. These disorders present with a variable extent of cognitive impairment and alpha-synuclein is being explored as a biomarker in CSF, blood serum and plasma. Considering key events of aging that include proteostasis, alpha-synuclein may not only be useful as a marker for differential diagnosis but also for aging per se. To explore this hypothesis, we developed a highly specific ELISA to measure alpha-synuclein. In healthy males plasma alpha-synuclein levels correlated strongly with age, revealing much lower concentrations in older (avg. 58.1 years) compared to younger (avg. 27.6 years) individuals. This difference between the age groups was enhanced after acidification of the plasmas (p<0.0001), possibly reflecting a decrease of alpha-synuclein-antibody complexes or chaperone activity in older individuals. Our results support the concept that alpha-synuclein homeostasis may be impaired early on, possibly due to disturbance of the proteostasis network, a key component of healthy aging. Thus, alpha-synuclein may be a novel biomarker of aging, a factor that should be considered when analyzing its presence in biological specimens.     

The absence of fire can cause a lag phase: The invasion dynamics of Banksia ericifolia (Proteaceae)

The transition from a species introduction to an invasion often spans many decades (a lag phase). However, few studies have determined the mechanisms underlying lag phases. Such a mechanistic understanding is vital if the potential ecosystem‐level impacts are to be predicted and the invasion risks to be managed proactively. Here we examine Banksia ericifolia, introduced for floriculture to South Africa, as a case study. We found 18 sites where the species has been planted, with self‐sustaining (naturalized) populations at four sites, and an invasive population at one site. The invasion originated from around 100 individuals planted 35 years ago; after several fires this population has grown to approximately 10 000 plants covering about 127 ha. The current invasion of B. ericifolia already has ecosystem‐level impacts, for example the nectar available to bird pollinators has more than doubled, potentially disrupting native pollination networks. If fires occurred at the other naturalized sites we anticipate populations would rapidly spread and densify with invaded areas ultimately become banksia‐dominated woodlands. Indeed the only site other than the invasive site where fire has occurred regularly is already showing signs of rapid population growth and spread. However, recruitment is mainly immediately post fire and no seed bank accumulates in the soil, mechanical control of adult plants is cheap and effective, and immature plants are easily detected. This study is a first in illustrating the importance of fire in driving lag phases and provides a valuable example for why it is essential to determine the mechanisms that mediate lag phases in introduced plant species. Serotinous species that have been introduced to areas where fire is suppressed could easily be misinterpreted as low risk species whilst they remain in a lag phase, but they can represent a major invasion risk.     

Four‐dimensional imaging of murine subpleural alveoli using high‐speed optical coherence tomography

The investigation of lung dynamics on alveolar scale is crucial for the understanding and treatment of lung diseases, such as acute lung injury and ventilator induced lung injury, and to promote the development of protective ventilation strategies. One approach to this is the establishment of numerical simulations of lung tissue mechanics where detailed knowledge about three‐dimensional alveolar structure changes during the ventilation cycle is required. We suggest four‐dimensional optical coherence tomography (OCT) imaging as a promising modality for visualizing the structural dynamics of single alveoli in subpleural lung tissue with high temporal resolution using a mouse model. A high‐speed OCT setup based on Fourier domain mode locked laser technology facilitated the acquisition of alveolar structures without noticeable motion artifacts at a rate of 17 three‐dimensional stacks per ventilation cycle. The four‐dimensional information, acquired in one single ventilation cycle, allowed calculating the volume‐pressure curve and the alveolar compliance for single alveoli. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

High-resolution analysis of salmonellae from turtles within a headwater spring ecosystem

Sediments and water from the pristine headwaters of the San Marcos River, Texas, USA, as well as swabs from biofilms on the carapace and from the cloacae of 17 musk turtles (Sternotherus odoratus) and one snapping turtle (Chelydra serpentina serpentina) caught at the same site, were analysed for salmonellae by culture and molecular techniques. Whereas enrichment cultures from sediment and water samples were negative for salmonellae in PCR- and in situ hybridization-based analyses, both techniques detected salmonellae after enrichments from both carapace and cloacae of nine (i.e. of 53%) musk turtles. Further characterization of 10 isolates obtained from the enrichment cultures of four selected individuals and confirmed as salmonellae by PCR analysis was achieved by fingerprinting techniques (rep-PCR). The results show differences between individuals and, in one case, variation among isolates from a single individual. All isolates from two individuals displayed identical profiles. These profiles were different from those obtained from the isolates of the third individual, which were, themselves, also identical for all isolates. Salmonellae were much more diverse in samples from the carapace of the last individual with five different rep-PCR profiles retrieved. Serotyping of seven isolates representative for each rep-PCR profile identified all isolates as representing Salmonella enterica subspecies enterica serotype Rubislaw, which demonstrates the presence of different strains of potentially human pathogenic salmonellae naturally occurring on turtles even within pristine environments. The frequent detection of these organisms in biofilms on the carapace opens the door for speculations on the role of this habitat as a reservoir for salmonellae, and on potential implications for turtles acting as a dispersal vector.     

Role of the N- and C-lobes of calmodulin in the activation of Ca(2+)/calmodulin-dependent protein kinase II

Understanding the principles of calmodulin (CaM) activation of target enzymes will help delineate how this seemingly simple molecule can play such a complex role in transducing Ca (2+)-signals to a variety of downstream pathways. In the work reported here, we use biochemical and biophysical tools and a panel of CaM constructs to examine the lobe specific interactions between CaM and CaMKII necessary for the activation and autophosphorylation of the enzyme. Interestingly, the N-terminal lobe of CaM by itself was able to partially activate and allow autophosphorylation of CaMKII while the C-terminal lobe was inactive. When used together, CaMN and CaMC produced maximal CaMKII activation and autophosphorylation. Moreover, CaMNN and CaMCC (chimeras of the two N- or C-terminal lobes) both activated the kinase but with greater K act than for wtCaM. Isothermal titration calorimetry experiments showed the same rank order of affinities of wtCaM > CaMNN > CaMCC as those determined in the activity assay and that the CaM to CaMKII subunit binding ratio was 1:1. Together, our results lead to a proposed sequential mechanism to describe the activation pathway of CaMKII led by binding of the N-lobe followed by the C-lobe. This mechanism contrasts the typical sequential binding mode of CaM with other CaM-dependent enzymes, where the C-lobe of CaM binds first. The consequence of such lobe specific binding mechanisms is discussed in relation to the differential rates of Ca (2+)-binding to each lobe of CaM during intracellular Ca (2+) oscillations.     

Managing invasive species in cities: a decision support framework applied to Cape Town

It has been suggested that existing frameworks for guiding management of invasive species in rural areas and protected areas are inadequate for dealing with invasions in urban settings. A framework for selecting appropriate goals for managing invasive species in urban areas was developed by Gaertner et al. (Landsc Urban Plan 151:1–9, 2016). This framework groups species into three management approaches (control priority, active engagement, and tolerance) depending on their real or perceived benefits and their potential to generate negative impacts. This study tests the practical application of the framework using the example of Cape Town. We assess the suitability of the framework to support decision-making for managing invasive species in urban ecosystems using a questionnaire-based survey of members of the public, and an e-mail-based survey and a workshop with invasion biology researchers and managers. Specifically, we (1) determine the differences in perceptions regarding the benefits and impacts of invasive species between the public, managers and researchers; (2) investigate how consistently managers and researchers group invasive species into the three management categories; and (3) identify, with the help of managers and researchers, issues linked to the framework and give suggestions to overcome the identified issues. We found no clear pattern in the perceptions of the public, managers and researchers regarding perceived benefits and negative impacts of invasive species. Instead, the answers were widely scattered among all groups for most of the species that were considered. However, using the framework leads to a higher consistency among managers in placing the species into management categories, compared to invasive species grouping without guidance of the framework. We conclude that decision-support frameworks can assist managers in placing invasive species into management categories. However, even more specific guidelines on the use of invasive species management frameworks in urban areas are needed.