Application of proteomics to neutrophil biology

Polymorphonuclear leukocytes or neutrophils are a primary effector cell of the innate immune system and contribute to the development of adaptive immunity. Neutrophils participate in both the initiation and resolution of inflammatory responses through a series of highly coordinated molecular and phenotypic changes. To accomplish these changes, neutrophils express numerous receptors and use multiple overlapping and redundant signal transduction pathways. Dysregulation of the activation or resolution pathways plays a role in a number of human diseases. A comprehensive understanding of the regulation of neutrophil responses can be provided by high throughput proteomic technologies and sophisticated computational analysis. The first steps in the application of proteomics to understanding neutrophil biology have been taken. Here we review the application of expression, structural, and functional proteomic studies to neutrophils. Although defining the complex molecular events associated with neutrophil activation is in the early stages, the data generated to date suggest that proteomic technologies will dramatically enhance our understanding of neutrophil biology.     

Incorporating fundamental laws of biology and physics into population ecology: the metaphysiological approach

Models commonly used in population ecology have somewhat vague and often misleading connections with physical and biological processes connecting organisms with their environments. The metaphysiological modelling approach offers a conceptual framework that is consistent with basic laws and enables integration across levels of organization from cells to ecosystems. This perspective accommodates the intrinsically disequilibrial nature of biological systems in changing environments, as well as adaptive responses to these changes. More attention needs to be paid to factors governing mortality losses rather than the functional or intake response alone. Models need to be based more firmly on underlying biophysical processes in order to serve as reliable guides to conservation action in novel environments.     

Modification-specific proteomics in plant biology

Post-translational modifications (PTMs) are involved in the regulation of a wide range of biological processes, and affect e.g. protein structure, activity and stability. Several hundred PTMs have been described in the literature, but relatively few have been studied using mass spectrometry and proteomics. In general, methods for PTM characterization are developed to study yeast and mammalian biology and later adopted to investigate plants. Our point of view is that it is advantageous to enrich for PTMs on the peptide level as part of a quantitative proteomics strategy to not only identify the PTM, but also to determine the functional relevance in the context of regulation, response to abiotic stress etc. Protein phosphorylation is the only PTM that has been studied extensively at the proteome wide level in plants using mass spectrometry based methods.     

Population proteomics: an emerging discipline to study metapopulation ecology

Proteomics research has developed until recently in a relative isolation from other fast-moving disciplines such as ecology and evolution. This is unfortunate since applying proteomics to these disciplines has apparently the potential to open new perspectives. The huge majority of species indeed exhibit over their entire geographic range a metapopulation structure, occupying habitats that are fragmented and heterogeneous in space and/or through time. Traditionally, population genetics is the main tool used to studying metatopulations, as it describes the spatial structure of populations and the level of gene flow between them. In this Viewpoint, we present the reasons why we think that proteomics, because of the level of integration it promotes, has the potential to resolve interesting issues specific to metapopulation biology and adaptive processes.     

Introduction to proteomics: tools for the new biology

Towards revolutionary biomarkers, a considerable amount of research funds and time have been dedicated to proteomics. Although the discovery of novel biomarkers at the dawn of proteomics was a promising development, only a few identified biomarkers seemed to be beneficial for cancer patients. We may need to approach this issue differently, instead of only extending the conventional approaches that have been used historically. The study of biomarkers is essentially a study of diseases and the biochemistry relating to peptide, protein and post-translational modifications is only a tool. A problem-oriented approach should be needed in biomarker development. Clinician participation in the study of biomarkers will lead to realistic, practical and interesting biomarker candidates, which justify the time and expense involved in validation studies. Although discussion in this article is focused on cancer biomarkers, it can generally be applied to biomarker studies for other diseases.     

The biology and ecology of lotic Tardigrada

• 1 Tardigrades comprise a micrometazoan phylum that is a sister group of the arthropods.
• 2 They are components of the meiobenthos in lotic habitats, and ≈ 50–70 species have been reported in such habitats world‐wide. Approximately 800 species have been identified from all marine, freshwater, and terrestrial habitats.
• 3 Taxonomy is based primarily on the morphology of the claws, buccal‐pharyngeal apparatus, cuticle and eggs.
• 4 Reproductive modes include sexual reproduction (amphimixis) and parthenogenesis. The sexual condition of individuals may be either gonochorism, unisexuality, or hermaphroditism. Moulting occurs throughout the life of the tardigrade.
• 5 Latent states (cryptobiosis, including encystment, anoxybiosis, cryobiosis, osmobiosis and anhydrobiosis) enable tardigrades to withstand unfavourable environmental conditions.
• 6 Population densities, life histories, dissemination and biogeography of freshwater species are poorly known.

     

The biology and ecology of lotic microturbellarians

• 1 More than 200 known species of Microturbellaria occur in running waters world‐wide but discovery of many more is likely. Their population density varies greatly as a function of substratum, productivity, phenology and hydrology. The density may exceed 7 000 individuals m^‐2. The number of species in a single small sample may reach 20.
• 2 Many species appear to have microhabitat or stream section specialisation but community patterns are obscured to a certain extent by common and eurytopic species. The specialisation is particularly evident in the smaller, lower‐order streams.
• 3 Some of this habitat specialisation is attributable to the ecological origin of species that may include terrestrial, underground, marine and lentic species pools.
• 4 Feeding habits of Microturbellaria range from omnivory to specialised predation.
• 5 Quantitative field studies require extraction and examination of live specimens from samples. Such samples pose transportation and storage problems and must be processed within hours of collection.
• 6 Taxonomy is well resolved for the Northern Hemisphere but is likely to be a major challenge in other parts of the world. In any region, however, new species may demand caution while using current keys to their identification.

     

Mass spectrometry-based proteomics for systems biology

Mass spectrometry (MS)-based proteomics has significantly contributed to the development of systems biology, a new paradigm for the life sciences in which biological processes are addressed in terms of dynamic networks of interacting molecules. Because of its advanced analytical capabilities, MS-based proteomics has been used extensively to identify the components of biological systems, and it is the method of choice to consistently quantify the effects of network perturbation in time and space. Herein, we review recent contributions of MS to systems biology and discuss several examples that illustrate the importance of mass spectrometry to elucidate the components and interactions of molecular networks.     

The biology and ecology of lotic nematodes

• 1 Morphological structures for identifying freshwater nematodes, e.g. buccal cavity, sensory receptors, oesophagus, reproductive organs and tail are described.
• 2 Most freshwater nematodes belong to the Adenophorea and are characterised by the presence of setae, adhesive glands and conspicuous amphids.
• 3 Methods for collecting nematodes from the sediments of running water (e.g. corer, pumps), within plants and aufwuchs are listed. Methods for fixation, extracting and preparing nematodes for identification are described.
• 4 Life history parameters (e.g. generation time, eggs per female) are not available for lotic nematodes but are summarised for free‐living nematodes in soil, lakes and seas. Field studies indicate that, in contrast to laboratory experiments with nematode cultures, many species will have a generation time of several months.
• 5 Abundance and species diversity of nematodes of lotic habitats are provided; more than 100 nematode species inhabit lotic habitats and densities can reach 230 individuals per ml.
• 6 Links between meiobenthic nematodes and the micro‐ and macrobenthos are unclear at present. Evidence such as the increased bacterial activity due to nematode grazing suggests that such interactions may be significant.

     

外来种入侵的生物学与生态学基础的若干问题

外来物种的入侵及其所造成的危害已越来越为人们所认识。一个外来物种入侵一个新的生境无疑要具备一定的条件 ,尽管目前对这种条件的研究还只是初步的。首先从其自身来说 ,需要有足够的入侵性 ,这可以认为是入侵种的生物学基础 ,可能表现为具有多倍性、一定的遗传变异、杂合性或表型可塑性 ,以及不同的交配系统等 ;其次一个物种的入侵成功还取决于入侵生境的可入侵性 ,这可以认为是入侵种的生态学基础 ,而新的种间关系的形成 ,尤其是入侵种与其他种类的互惠共生关系的建成是关键。本文主要介绍了有关入侵种的生物学和生态学基础中的一些最新进展 ,希望有助于我国学者对相关研究内容的开展以及对有害外来种入侵的防治     

The biology and ecology of lotic microcrustaceans

• 1 Copepoda, Ostracoda and ‘Cladocera’ are important meiobenthic Crustacea which can be both numerically abundant and species rich in running waters. Harpacticoids and ostracods are well adapted to benthic life because they are typical crawlers, walkers, and burrowers. Many cladocerans are substratum dwellers, but most benthic species among these can also swim. Cyclopoids which are generally good swimmers are nevertheless often bottom frequenters and actively colonise sediment interstices (the hyporheic zone).
  • 2 The subclass Copepoda includes 10 orders. With 53 families, the order Harpacticoida dominates the benthos. Only five of these families are represented in fresh waters (ca. 1 000 species and subspecies). The order Cyclopoida includes 12 families of which the Cyclopidae is well represented in freshwater habitats with 900 species and subspecies. Freshwater Ostracods belong to the order Podocopida (5 000 species) with three superfamilies occurring in running fresh waters. The group ‘Cladocera’ contains four orders, 12 families, more than 80 genera, and 450–600 freshwater species. Most of the benthic species are found in the families Chydoridae (39 genera), Macrothricidae, Ilyocryptidae and Sididae.
• 3 For each of the three major taxa, morphological characteristics are presented, specimen collection and preparation are described and references to available taxonomical keys are provided.
• 4 Biological characteristics are extremely diverse among and within the three taxa, resulting in a great variety of strategies in meiobenthic crustaceans. Characteristics of reproduction, sexual dimorphism, cyclomorphosis and population parameters (i.e. clutch size, lifespan, growth, moulting) are provided for some of the most common species.
• 5 Important differences between the three main taxa were found at the species level. Ecological requirements such as hydraulic microhabitats and geomorphologic features of the streambed are the major determinants of species diversity and abundance for benthic microcrustacea of lotic habitats. Many studies on the ecology of these communities are limited by a lack of knowledge of the life history characterisitics of lotic (especially interstitial) crustacean populations.

     

Schistosome biology and proteomics: progress and challenges

The recent availability of schistosomal genome-sequence information allows protein identification in schistosome-derived samples by mass spectrometry (proteomics). Over the last few years, several proteome studies have been performed that addressed important questions in schistosome biology. This review summarizes the applied experimental approaches that have been used so far, it provides an overview of the most important conclusions that can be drawn from the performed studies and finally discusses future challenges in this research area.     

Frontiers in population ecology of microtine rodents: A pluralistic approach to the study of population ecology

Current challenges for the study of population ecology of microtine rodents are reviewed. Comparisons with other taxonomic groups (other mammals, birds and insects) are given throughout. A major challenge is to link patterns and processes (i.e. mechanisms) better than is the case today. Other major challenges include the furthering of our understanding of the interaction between deterministic and stochastic processes, and as part thereof, the interaction between density-dependent and density-independent processes. The applicability of comparative studies on populations exhibiting different temporal dynamical patterns is, in this connection, emphasized. Understanding spatiotemporal dynamical patterns is another major challenge, not the least from a methodological point of view. Long-term and large-scale ecological data on population dynamics (in space and time) are critical for this purpose. Looking for consistency between hypothesized mechanisms and observed patterns is emphasized as a good platform for further empirical and theoretical work. The intellectual feedback process between different approaches to the study of microtine population ecology (observational studies, experimental manipulative studies, statistical modeling and mathematical modeling) are discussed. We recommend a pluralistic approach (involving both observational and experimental as well as theoretical studies) to the study of small rodent ecology.