Profiling the IgOme: Meeting the challenge

The entire repertoire of antibodies in our serum, the IgOme, is a historical record of our past experiences and a reflection of our immune status at any given moment. Understanding the dynamics of the IgOme and how the diversity and specificities of serum antibodies change in response to disease and maintenance of homeostasis can directly impact the ability to design and develop novel vaccines, diagnostics and therapeutics. Here we review both direct and indirect methodologies that are being developed to map the complexity and specificities of the antibodies in polyclonal serum – the IgOme.     

Steps towards sustainable harvest of Ophiocordyceps sinensis in Bhutan

The insect-pathogenic fungus Ophiocordyceps sinensis (better known as Cordyceps sinensis) is harvested over much of the Himalayan plateau as a highly prized remedy in traditional Oriental medicine. Over the past 10 years its financial value has increased dramatically, with collectors paid as much as US $12,500 kg⁻¹ for top-quality material. This is causing significant distortion to local economies, and there is widespread concern that the current rate of collection is unsustainable. This paper introduces the fungus and its insect hosts, documents some of the biological and social constraints to achieving sustainability, describes the socioeconomic climate within which harvest and sale occurs in Bhutan, and details the measures put in place by the Royal Government of Bhutan to promote wise management of this valuable natural resource.

Steps towards a mechanistic understanding of respiratory temperature responses

Temperature crucially affects the speed of metabolic processes in poikilotherm organisms, including plants. The instantaneous temperature responses of O(2)-reduction and CO(2)-release can be approximated by Arrhenius kinetics, even though respiratory gas exchange of plants is the net effect of many constituent biochemical processes. Nonetheless, the classical Arrhenius equation must be modified to account for a dynamic response to measurement temperatures. We show that this dynamic response is readily explained by combining Arrhenius and Michaelis-Menten kinetics, as part of a fresh appraisal of metabolic interpretations of instantaneous temperature responses. In combination with recent experimental findings, we argue that control of mitochondrial electron flow is shared among cytochrome oxidase and alternative oxidase under in vivo conditions, and is continuously coordinated. In this way, upstream carbohydrate metabolism and downstream electron transport appear to be optimized according to the demand of ATP, TCA-cycle intermediates and anabolic reducing power under differing metabolic states. We provide a link to the 'Growth and Maintenance Paradigm' of respiration and argue that respiratory temperature responses can be used as a tool to probe metabolic states of plant tissue, such that we can learn more about the mechanisms that govern longer-term acclimatization responses of plant metabolism.     

First Steps towards Underdominant Genetic Transformation of Insect Populations

The idea of introducing genetic modifications into wild populations of insects to stop them from spreading diseases is more than 40 years old. Synthetic disease refractory genes have been successfully generated for mosquito vectors of dengue fever and human malaria. Equally important is the development of population transformation systems to drive and maintain disease refractory genes at high frequency in populations. We demonstrate an underdominant population transformation system in Drosophila melanogaster that has the property of being both spatially self-limiting and reversible to the original genetic state. Both population transformation and its reversal can be largely achieved within as few as 5 generations. The described genetic construct {Ud} is composed of two genes; (1) a UAS-RpL14.dsRNA targeting RNAi to a haploinsufficient gene RpL14 and (2) an RNAi insensitive RpL14 rescue. In this proof-of-principle system the UAS-RpL14.dsRNA knock-down gene is placed under the control of an Actin5c-GAL4 driver located on a different chromosome to the {Ud} insert. This configuration would not be effective in wild populations without incorporating the Actin5c-GAL4 driver as part of the {Ud} construct (or replacing the UAS promoter with an appropriate direct promoter). It is however anticipated that the approach that underlies this underdominant system could potentially be applied to a number of species.     

Deep aspirations: towards a sustainable offshore Blue Economy

Reviews in Fish Biology and Fisheries - The ocean economy is experiencing rapid growth that will provide benefits but will also pose environmental and social risks. With limited space and degraded...     

Motifier: An IgOme Profiler Based on Peptide Motifs Using Machine Learning

Antibodies provide a comprehensive record of the encounters with threats and insults to the immune system. The ability to examine the repertoire of antibodies in serum and discover those that best represent “discriminating features” characteristic of various clinical situations, is potentially very useful. Recently, phage display technologies combined with Next-Generation Sequencing (NGS) produced a powerful experimental methodology, coined “Deep-Panning”, in which the spectrum of serum antibodies is probed. In order to extract meaningful biological insights from the tens of millions of affinity-selected peptides generated by Deep-Panning, advanced bioinformatics algorithms are a must. In this study, we describe Motifier, a computational pipeline comprised of a set of algorithms that systematically generates discriminatory peptide motifs based on the affinity-selected peptides identified by Deep-Panning. These motifs are shown to effectively characterize antibody binding activities and through the implementation of machine-learning protocols are shown to accurately classify complex antibody mixtures representing various biological conditions.     

MassSieve: Panning MS/MS peptide data for proteins

We present MassSieve, a Java‐based platform for visualization and parsimony analysis of single and comparative LC‐MS/MS database search engine results. The success of mass spectrometric peptide sequence assignment algorithms has led to the need for a tool to merge and evaluate the increasing data set sizes that result from LC‐MS/MS‐based shotgun proteomic experiments. MassSieve supports reports from multiple search engines with differing search characteristics, which can increase peptide sequence coverage and/or identify conflicting or ambiguous spectral assignments.     

Steps towards a repertoire of comprehensive maps of human protein interaction networks: the Human Proteotheque Initiative (HuPI).

Defining human protein interaction networks has become essential to develop an overall, systems-based understanding of the molecular events that sustain cell growth in normal and disease conditions. To characterize protein interaction networks from human cells, we have undertaken the development of a systematic, unbiased technology pipeline that couples experimental and computational approaches. This discovery engine is central to the Human Proteotheque Initiative (HuPI), a multidisciplinary project aimed at building a repertoire of comprehensive maps of human protein interaction networks, the Human Proteotheque. The information contained in the Proteotheque is made publicly available through an interactive web site that can be consulted to visualize some of the fundamental molecular connections formed in human cells and to determine putative functions of previously uncharacterized proteins based on guilt by association. The process governing the evolution of HuPI towards becoming a repository of accurate and complete protein interaction maps is described.     

Steps towards a miniaturized, robust and autonomous measurement device for the long-term monitoring of patient activity: ActiBelt.

We describe the first steps in the development of a wearable measurement device for measuring a subject's three-dimensional acceleration. The ultimate aim is a standard measurement instrument integrated in a belt buckle that allows objective evaluation of treatment and rehabilitation measures in patients, in particular for disabling chronic diseases such as multiple sclerosis. In a first step we combined standard hardware elements to record test data from healthy volunteers. We then developed algorithms to automatically distinguish between different stages of activity, such as jogging, walking, lying, standing and sitting, and to detect and count steps. Distinction between standing and sitting is the most difficult to accomplish. As a first validation, we calculated the distance traveled from data of 17 experiments and a total of 4.5 h, for which one proband was walking and running for a known distance, and compared the results with two commercially available pedometers. We could show that the relative error for the ActiBelt is only half of that for the two pedometers. Apart from developing much smaller, robust and integrated hardware, we describe ideas on how to develop algorithms that allow extraction of a "baseline step pattern" in analogy to baseline ECG to define and detect clinically relevant deviations.     

Steps towards flexible docking: modeling of three-dimensional structures of the nuclear receptors bound with peptide ligands mimicking co-activators' sequences

We developed a fully flexible docking method that uses a reduced lattice representation of protein molecules, adapted for modeling peptide–protein complexes. The CABS model (Carbon Alpha, Carbon Beta, Side Group) employed here, incorporates three pseudo-atoms per residue—C, Cβ and the center of the side group instead of full-atomic protein representation. Force field used by CABS was derived from statistical analysis of non-redundant database of protein structures. Application of our method included modeling of the complexes between various nuclear receptors (NRs) and peptide co-activators, for which three-dimensional structures are known. We tried to rebuild the native state of the complexes, starting from separated components. Accuracy of the best obtained models, calculated as coordinate root-mean-square deviation (cRMSD) between the target and the modeled structures, was under 1 Å, which is competitive with experimental methods, such as crystallography or NMR. Forthcoming modeling study should lead to better understanding of mechanisms of macromolecular assembly and will explain co-activators’ effects on receptors activity, especially on vitamin D receptor and other nuclear receptors.     

Differential Sensitivity of Wheat Embryos against Extracts Containing Toxins of Septoria nodorum: First Steps towards in vitro Selection

As a first step towards the development of an in vitro -selection system for septoria nodorum blotch resistance, wheat embryo culture on media containing extracts from Septoria nodorum was established. Extracts prepared from inoculated wheat grains had a toxic activity. Control extracts from uninoculated grains showed at least a 10-fold lower toxic activity. Two wheat breeding lines susceptible to Septoria nodorum showed reduced growth in the presence of the fungal extract whencompared to a breeding line known to have good resistance in the field. A test with seven additional wheat lines showed a good agreement between field resistance of the ear and embryo resistance. Mellein is one of the toxins produced by Septoria nodorum and was used in pure form for in vitro -selection. It showed toxic effects at 50 μg/ml, a concentration which is about 200-fold higher than the mellein concentration in the diluted extract with embryotoxic activity. This indicates the importance of additional toxic compounds in the crude extract. Mellein acted non-selectively on embryos of the different cultivars.     

Comprehensive In Vitro Toxicity Testing of a Panel of Representative Oxide Nanomaterials: First Steps towards an Intelligent Testing Strategy

Nanomaterials (NMs) display many unique and useful physico-chemical properties. However, reliable approaches are needed for risk assessment of NMs. The present study was performed in the FP7-MARINA project, with the objective to identify and evaluate in vitro test methods for toxicity assessment in order to facilitate the development of an intelligent testing strategy (ITS). Six representative oxide NMs provided by the EC-JRC Nanomaterials Repository were tested in nine laboratories. The in vitro toxicity of NMs was evaluated in 12 cellular models representing 6 different target organs/systems (immune system, respiratory system, gastrointestinal system, reproductive organs, kidney and embryonic tissues). The toxicity assessment was conducted using 10 different assays for cytotoxicity, embryotoxicity, epithelial integrity, cytokine secretion and oxidative stress. Thorough physico-chemical characterization was performed for all tested NMs. Commercially relevant NMs with different physico-chemical properties were selected: two TiO₂ NMs with different surface chemistry – hydrophilic (NM-103) and hydrophobic (NM-104), two forms of ZnO – uncoated (NM-110) and coated with triethoxycapryl silane (NM-111) and two SiO₂ NMs produced by two different manufacturing techniques – precipitated (NM-200) and pyrogenic (NM-203). Cell specific toxicity effects of all NMs were observed; macrophages were the most sensitive cell type after short-term exposures (24-72h) (ZnO>SiO₂>TiO₂). Longer term exposure (7 to 21 days) significantly affected the cell barrier integrity in the presence of ZnO, but not TiO₂ and SiO₂, while the embryonic stem cell test (EST) classified the TiO₂ NMs as potentially ‘weak-embryotoxic’ and ZnO and SiO₂ NMs as ‘non-embryotoxic’. A hazard ranking could be established for the representative NMs tested (ZnO NM-110 > ZnO NM-111 > SiO₂ NM-203 > SiO₂ NM-200 > TiO₂ NM-104 > TiO₂ NM-103). This ranking was different in the case of embryonic tissues, for which TiO₂ displayed higher toxicity compared with ZnO and SiO₂. Importantly, the in vitro methodology applied could identify cell- and NM-specific responses, with a low variability observed between different test assays. Overall, this testing approach, based on a battery of cellular systems and test assays, complemented by an exhaustive physico-chemical characterization of NMs, could be deployed for the development of an ITS suitable for risk assessment of NMs. This study also provides a rich source of data for modeling of NM effects.     

Probing cytokines, chemokines and matrix metalloproteinases towards better immunotherapies of multiple sclerosis

Multiple sclerosis (MS) is an autoimmune disease with a spectrum of clinical evolutions. We here summarize recent insights into the neuroinflammatory processes of demyelination, vascular cuffing, destruction of the blood brain barrier (BBB), neuronal toxicity and the ensuing (re)activation of autoreactive lymphocytes. Translation of these processes in molecular terms indicates that cytokines, including interferons, ligands of the tumor necrosis factor receptor family and interleukins, and also chemokines and matrix metalloproteinases play pivotal roles in MS. This not only helps to understand disease mechanisms in the central nervous system of affected patients, but also forms a solid scientific basis to improve present therapies. Treatment of MS with parenterally administered anti-inflammatory agents may be improved, based on present knowledge and new insights obtained with animal models. Such innovations include better use of knowledge about the formulation, administration, turnover and glycosylation of interferon-β (IFN-β), combinations of IFN-β with inhibitors of IFN-β-degrading proteinases in MS, and new ways to diminish vascular cuffs and the transmigration of leukocytes across the two basement membranes of the BBB. Novel molecules interfering with matrix metalloproteinases and chemokines, such as EMMPRIN, COAM and monoclonal antibodies are currently being investigated, demonstrating continued efforts to find new drugs for MS treatment.