Proteome signatures—how are they obtained and what do they teach us?

The dawn of a new Proteomics era, just over a decade ago, allowed for large-scale protein profiling studies that have been applied in the identification of distinctive molecular cell signatures. Proteomics provides a powerful approach for identifying and studying these multiple molecular markers in a vast array of biological systems, whether focusing on basic biological research, diagnosis, therapeutics, or systems biology. This is a continuously expanding field that relies on the combination of different methodologies and current advances, both technological and analytical, which have led to an explosion of protein signatures and biomarker candidates. But how are these biological markers obtained? And, most importantly, what can we learn from them? Herein, we briefly overview the currently available approaches for obtaining relevant information at the proteome level, while noting the current and future roles of both traditional and modern proteomics. Moreover, we provide some considerations on how the development of powerful and robust bioinformatics tools will greatly benefit high-throughput proteomics. Such strategies are of the utmost importance in the rapidly emerging field of immunoproteomics, which may play a key role in the identification of antigens with diagnostic and/or therapeutic potential and in the development of new vaccines. Finally, we consider the present limitations in the discovery of new signatures and biomarkers and speculate on how such hurdles may be overcome, while also offering a prospect for the next few years in what could be one of the most significant strategies in translational medicine research.     

Mechanosensitive channels: what can they do and how do they do it?

While mechanobiological processes employ diverse mechanisms, at their heart are force-induced perturbations in the structure and dynamics of molecules capable of triggering subsequent events. Among the best characterized force-sensing systems are bacterial mechanosensitive channels. These channels reflect an intimate coupling of protein conformation with the mechanics of the surrounding membrane; the membrane serves as an adaptable sensor that responds to an input of applied force and converts it into an output signal, interpreted for the cell by mechanosensitive channels. The cell can exploit this information in a number of ways: ensuring cellular viability in the presence of osmotic stress and perhaps also serving as a signal transducer for membrane tension or other functions. This review focuses on the bacterial mechanosensitive channels of large (MscL) and small (MscS) conductance and their eukaryotic homologs, with an emphasis on the outstanding issues surrounding the function and mechanism of this fascinating class of molecules.     

Autophagy and apoptosis: where do they meet?

Autophagy and apoptosis are two important cellular processes with complex and intersecting protein networks; as such, they have been the subjects of intense investigation. Recent advances have elucidated the key players and their molecular circuitry. For instance, the discovery of Beclin-1’s interacting partners has resulted in the identification of Bcl-2 as a central regulator of autophagy and apoptosis, which functions by interacting with both Beclin-1 and Bax/Bak respectively. When localized to the endoplasmic reticulum and mitochondria, Bcl-2 inhibits autophagy. Cellular stress causes the displacement of Bcl-2 from Beclin-1 and Bax, thereby triggering autophagy and apoptosis, respectively. The induction of autophagy or apoptosis results in disruption of complexes by BH3-only proteins and through post-translational modification. The mechanisms linking autophagy and apoptosis are not fully defined; however, recent discoveries have revealed that several apoptotic proteins (e.g., PUMA, Noxa, Nix, Bax, XIAP, and Bim) modulate autophagy. Moreover, autophagic proteins that control nucleation and elongation regulate intrinsic apoptosis through calpain- and caspase-mediated cleavage of autophagy-related proteins, which switches the cellular program from autophagy to apoptosis. Similarly, several autophagic proteins are implicated in extrinsic apoptosis. This highlights a dual cellular role for autophagy. On one hand, autophagy degrades damaged mitochondria and caspases, and on the other hand, it provides a membrane-based intracellular platform for caspase processing in the regulation of apoptosis. In this review, we highlight the crucial factors governing the crosstalk between autophagy and apoptosis and describe the mechanisms controlling cell survival and cell death.     

Safe and efficacious probiotics: what are they?

Each year, >20 billion doses of probiotics are used by healthy people and by those diagnosed with a range of medical conditions. Compared to many pharmaceutical agents, probiotics are well tolerated and extremely safe, and serious adverse effects rarely occur. Nevertheless, as many new researchers enter the field and companies launch "probiotic" products, it is essential that standards are set for naming a product "probiotic" to show that it meets an acceptable level of safety and efficacy, and to understand the strengths and limitations of its activity. In this Opinion article, recommendations are made based upon the current understanding of scientific, clinical and regulatory issues, with a special focus on safety.     

Cancer and diet: How are they related?

Extensive research in the past decade has revealed cancer to be a multigenic disease caused by perturbation of multiple cell signalling pathways and dysregulation of numerous gene products, all of which have been linked to inflammation. It is also becoming evident that various lifestyle factors, such as tobacco and alcohol use, diet, environmental pollution, radiation and infections, can cause chronic inflammation and lead to tumourigenesis. Chronic diseases caused by ongoing inflammation therefore require chronic, not acute, treatment. Nutraceuticals, compounds derived from fruits, vegetables, spices and cereals, can be used chronically. This study discusses the molecular targets of some nutraceuticals that happen to be markers of chronic inflammation and how they can prevent or treat cancer. These naturally-occurring agents in the diet have great potential as anti-cancer drugs, thus proving Hippocrates, who proclaimed 25 centuries ago, 'Let food be thy medicine and medicine be thy food'.     

Disturbance–diversity models: what do they really predict and how are they tested?

The intermediate disturbance hypothesis (IDH) and the dynamic equilibrium model (DEM) are influential theories in ecology. The IDH predicts large species numbers at intermediate levels of disturbance and the DEM predicts that the effect of disturbance depends on the level of productivity. However, various indices of diversity are considered more commonly than the predicted number of species in tests of the hypotheses. This issue reaches beyond the scientific community as the predictions of the IDH and the DEM are used in the management of national parks and reserves. In order to compare responses with disturbance among measures of biodiversity, we used two different approaches of mathematical modelling and conducted an extensive meta-analysis. Two-thirds of the surveyed studies present different results for different diversity measures. Accordingly, the meta-analysis showed a narrow range of negative quadratic regression components for richness, but not evenness. Also, the two models support the IDH and the DEM, respectively, when biodiversity is measured as species richness, but predict evenness to increase with increasing disturbance, for all levels of productivity. Consequently, studies that use compound indices of diversity should present logical arguments, a priori, to why a specific index of diversity should peak in response to disturbance.     

Families Opisthorchiidae and Heterophyidae: are they distinct?

Superfamily Opisthorchioidea Looss, 1899 consists of three well-known families, Opisthorchiidae, Heterophyidae, and Cryptogonimidae, with basic similarities in morphology and life-cycles. Many species in the first two of these families are human pathogens, such as Opisthorchis viverrini, O. felineus, Clonorchis sinensis, Haplorchis spp. and Metagonimus spp. Recently, a molecular phylogenetic study on the classification of Digenea revealed a paraphyletic relationship between Opisthorchiidae and Heterophyidae. For our study, we gathered and analyzed all available data in GenBank, together with new data of nuclear 18S ribosomal DNA and ribosomal internal transcribed spacer 2 (ITS2) sequences of the families within the Opisthorchioidea. Maximum likelihood and Bayesian inference analyses suggested that families Opisthorchiidae and Heterophyidae are inseparable from each other, with the former nested within the latter. Groupings in molecular trees are generally consistent with morphological features used in taxonomy.     

Renal agenesis and dysgenesis: are they increasing?

Data from the Birth Defects Monitoring Program (BDMP) of the Centers for Disease Control (CDC) suggest that the birth prevalence of renal agenesis and dysgenesis combined is increasing. Medical records were reviewed for 1,404 of 1,669 (84%) infants in the BDMP with renal agenesis or dysgenesis noted on the newborn discharge summary to assess whether the observed trend reflects a true increase in one or both conditions or if it reflects changes in diagnostic, coding, or surveillance practices over time. For 1970-1982, the average rate per 100,000 live births and stillbirths was 3.5 for autopsy-confirmed bilateral renal agenesis and 1.7 for autopsy-confirmed bilateral renal dysgenesis. The birth prevalence of autopsy-confirmed bilateral renal agenesis fluctuated within this time period, peaking in 1975, while the rate of autopsy-confirmed bilateral renal dysgenesis increased steadily by 0.2 cases/100,000 births per year (P less than 0.001) with small peaks in 1976 and 1979. Unilateral renal agenesis or dysgenesis accounted for 17% of the confirmed cases, but most were detected by autopsy among infants who died shortly after birth rather than by diagnostic procedures such as ultrasound. Diagnostic information in the medical record suggested that the increase in the birth prevalence of renal agenesis and dysgenesis combined in the BDMF is due primary to the increasing prevalence of renal dysgenesis. Since medical records did not include sufficient information on risk factors, detailed analytic studies are needed to identify maternal risk factors that might account for the apparent increase in renal dysgenesis over time.     

Roe and fallow deer: are they compatible neighbours?

The analysis of the relationships between population density and habitat features is important to evaluate the ecological needs of a species, its potential impact on ecosystems and its interspecific interactions. We analysed the spatial variation of roe deer Capreolus capreolus and fallow deer Dama dama densities in a Mediterranean area in summer 2007 and winter 2007/2008. Previous research has shown that fallow deer can actively displace and exclude roe deer from natural feeding sites. Here we show that both species have the greatest densities in ecotone habitats between wood and open fields (abandoned olive groves and pastures), but with contrasting geographic patterns. The fallow deer showed the greatest densities in the central northern part of the study area near to local historical release sites. The densities of roe deer were great where fallow deer were rare and low where fallow deer were abundant. Spatial overlap was great at the habitat scale, indicating a high potential for competition, but was low at the plot scale, suggesting that partitioning of space occurred at a fine scale. Supporting great numbers of deer, the ecotone areas are crucial for the management of ecosystems. We suggest that roe deer avoid areas with great densities of fallow deer and that interspecific interference from the latter affects the density and distribution of the former both at a fine and at a large scale.     

Serine hydroxymethyltransferase and threonine aldolase: are they identical?

Serine hydroxymethyltransferase, a pyridoxal phosphate-dependent enzyme, catalyses the interconversion of serine and glycine, both of which are major sources of one-carbon units necessary for the synthesis of purine, thymidylate, methionine, and so on. Threonine aldolase catalyzes the pyridoxal phosphate-dependent, reversible reaction between threonine and acetaldehyde plus glycine. No extensive studies have been carried out on threonine aldolase in animal tissues, and it has long been believed that serine hydroxymethyltransferase and threonine aldolase are the same, i.e. one entity. This is based on the finding that rabbit liver serine hydroxymethyltransferase possesses some threonine aldolase activity. Recently, however, many kinds of threonine aldolase and corresponding genes were isolated from micro-organisms, and these enzymes were shown to be distinct from serine hydroxymethyltransferase. The experiments with isolated hepatocytes and cell-free extracts from various animals revealed that threonine is degraded mainly through the pathway initiated by threonine 3-dehydrogenase, and there is little or no contribution by threonine aldolase. Thus, although serine hydroxymethyltransferase from some mammalian livers exhibits a low threonine aldolase activity, the two enzymes are distinct from each other and mammals lack the "genuine" threonine aldolase.     

Why do men marry and why do they stray?

Humans are quite unusual compared to other great apes in that reproduction typically takes place within long-term, iteroparous pairings--social arrangements that have been culturally reified as the institution of marriage. With respect to male behaviour, explanations of marriage fall into two major schools of thought. One holds that marriage facilitates a sexual division of labour and paternal investment, both important to the rearing of offspring that are born helpless and remain dependent for remarkably long periods (provisioning model). And the other suggests that the main benefits which men receive from entering into marriage derive from monopolizing access to women's fertility (mating effort model). In this paper, we explore extramarital sexual relationships and the conditions under which they occur as a means of testing predictions derived from these two models. Using data on men's extramarital sexual relationships among Tsimane forager-horticulturists in lowland Bolivia, we tested whether infidelity was more common when men had less of an opportunity to invest in their children or when they risked losing less fertility. We found that Tsimane men appear to be biasing the timing of their affairs to when they are younger and have fewer children, supporting the provisioning model.     

Electrical signaling and photosynthesis: Can they co-exist together?

Mechanical irritation of trigger hairs and subsequent generation of action potentials have significant impact on photosynthesis and respiration in carnivorous Venus flytrap (Dionaea muscipula). Action potential-mediated inhibition of photosynthesis and stimulation of respiration is confined only to the trap and was not recorded in adjacent photosynthetic lamina. We showed that the main primary target of electrical signals on assimilation is in the dark enzymatic reaction of photosynthesis. Without doubt, the electrical signaling is costly, and the possible co-existence of such type of signals and photosynthesis in plant cell is discussed.Key words: action potential, carnivorous plant, Dionaea muscipula, electrical signaling, photosynthesis, respiration, Venus flytrapTrap closure of the Venus flytrap (Dionaea muscipula) is one of the fastest movements in plant kingdom. Mechanical irritation of trigger hairs protruding from upper leaf epidermis results in generation of action potential. At room temperature, two touches generate two action potentials and activate the trap snap shut in a fraction of second.¹ After the rapid movement secures the prey, struggling results in generation of further action potentials which cease to occur when the prey stops moving.² We documented that trigger hair irritation and subsequent generation of action potentials have significant effect on photosynthesis and respiration. Action potentials propagate in the trap and were not recorded in adjacent lamina (Fig. 1). This is in accordance with the observation that no changes of photosynthetic and respiration rate as well as effective quantum yield of photosystem II photochemistry were recorded in lamina. Detailed analysis of chlorophyll fluorescence kinetics revealed that the main primary target of action potentials is in the dark enzymatic reaction of photosynthesis and changes in quantum yield of primary photochemistry are just a consequence of decreased CO₂ fixation. However, electrical signals have probably also small effect on excitation energy trapping, charge stabilization and recombination reaction in photosystem II as measurements of fast chlorophyll a fluorescence transient indicates. This effect may be explained by repulsion of charges in reaction center of photosystem II.^3,4 The changes of photosynthesis upon impact of electrical signals probably have no benefit for plant and are only a negative consequences caused by the changes of the ionic environment.Open in a separate windowFigure 1Dionaea muscipula with entrapped wasp of the genus Polistes. Action potentials and rate of net assimilation at irradiance 80 µmol m⁻²s⁻ PAR (A_n) in response to 15 s mechanical trigger hair irritation (between 160–175 s) in trap (upper row) and photosynthetic lamina (lower row).These findings may have more consequences for plants in general. The electrical activity of plant cell was for the first time described by Burdon-Sanderson in 1873.⁵ Hence electrical signals do not belong exclusively to animal kingdom however they never develop the same degree of complexity as in animal nerves. Electrical signals are capable of transmitting signals more quickly over long distances when compared with chemical signals (e.g., hormones).^6,7 They are not confined only to the sensitive plants (e.g., Mimosa, Dionaea), but play also an important role in every non-sensitive plants and in both groups have significant effect on photosynthesis and respiration.^8–14 It is not surprising, that if electrical signals are costly in term of consumption of ATP and increased respiration with concurrent inhibition of photosynthesis, the same degree of complexity as in animals could not be developed. If plant growth depends on photosynthesis, this raises the question whether electrical signals and photosynthesis may co-exist together. The continuous electrical activity would inhibit the main source of energy for plants—photosynthetic assimilation. This may also explain why the plants are sessile organisms. For rapid coordinated movements, electrical activity plays an important role in animals. Unlike animals, plants usually rely on slow movements in which the role of plant hormones is indispensable. In this concept, it is not surprising that the more complex electrical activity was recorded in root transition zone—the heterotrophic part of plant body.^15,16 And this may also explain why the more evident electrical activity in the plant world has evolved in the traps of carnivorous plants like Dionaea, Aldrovanda or Drosera.^17–19 In general the traps of carnivorous plants are considered to be less efficient in photosynthesis.²⁰ Any of the action potentials produced by Drosera tentacles or Dionaea trap do not spread to photosynthetic active lamina, thus the main side of CO₂ fixation is protected.²¹ It is possible that such temporal carbon costs associated with insect trapping and retention may be outweighed by the benefits gained later from the prey—increased nitrogen concentration in the leaves stimulates photosynthetic assimilation.²² The possible ecophysiological impact of electrical signals on daily carbon gain in sensitive plants remains to be elucidated. We still do not completely understand the electrical signals in plants, and further research in this area is necessary to understand the full meaning of electrical activity in plants.     

Genetic instability and rapid speciation: are they coupled?

Models of rapid speciation by fixation of underdominant chromosomal rearrangements are constrained by multiple conditions on population structure and chromosomal performance. Realistic population conditions impose long periods of time to fixation or reproductive isolation, even under a model of accumulation of successive advantageous slightly underdominant rearrangements. However, when increased mutation rates are considered, fixation time is significantly reduced. Evidence is presented of high rates of chromosomal rearrangement production under genomic stress, such as in inbred and interspecific crosses. These episodes of high instability are most probably the result of mobile element transpositions, since transposition is also increased under genomic stress. Nonetheless, the evolutionary value of mobile elements to speed up speciation will be only significant if their mutagenic potential is activated in concert with population scenarios favorable to speciation events. Although this coupling needs to be demonstrated, many models of rapid speciation are carried out under population conditions favoring inbreeding and/or hybridization.     

Inbreeding and relatedness coefficients: what do they measure?

This paper reviews and discusses what is known about the relationship between identity in state, allele frequency, inbreeding coefficients, and identity by descent in various uses of these terms. Generic definitions of inbreeding coefficients are given, as ratios of differences of probabilities of identity in state. Then some of their properties are derived from an assumption in terms of differences between distributions of coalescence times of different genes. These inbreeding coefficients give an approximate measurement of how much higher the probability of recent coalescence is for some pair of genes relative to another pair. Such a measure is in general not equivalent to identity by descent; rather, it approximates a ratio of differences of probabilities of identity by descent. These results are contrasted with some other formulas relating identity, allele frequency, and inbreeding coefficients. Additional assumptions are necessary to obtain most of them, and some of these assumptions are not always correct, for example when there is localized dispersal. Therefore, definitions based on such formulas are not always well-formulated. By contrast, the generic definitions are both well-formulated and more broadly applicable.     

Nectar and pollination drops: how different are they?

Background

Pollination drops and nectars (floral nectars) are secretions related to plant reproduction. The pollination drop is the landing site for the majority of gymnosperm pollen, whereas nectar of angiosperm flowers represents a common nutritional resource for a large variety of pollinators. Extrafloral nectars also are known from all vascular plants, although among the gymnosperms they are restricted to the Gnetales. Extrafloral nectars are not generally involved in reproduction but serve as ‘reward’ for ants defending plants against herbivores (indirect defence).

Scope

Although very different in their task, nectars and pollination drops share some features, e.g. basic chemical composition and eventual consumption by animals. This has led some authors to call these secretions collectively nectar. Modern techniques that permit chemical analysis and protein characterization have very recently added important information about these sugary secretions that appear to be much more than a ‘reward’ for pollinating (floral nectar) and defending animals (extrafloral nectar) or a landing site for pollen (pollination drop).

Conclusions

Nectar and pollination drops contain sugars as the main components, but the total concentration and the relative proportions are different. They also contain amino acids, of which proline is frequently the most abundant. Proteomic studies have revealed the presence of common functional classes of proteins such as invertases and defence-related proteins in nectar (floral and extrafloral) and pollination drops. Invertases allow for dynamic rearrangement of sugar composition following secretion. Defence-related proteins provide protection from invasion by fungi and bacteria. Currently, only few species have been studied in any depth. The chemical composition of the pollination drop must be investigated in a larger number of species if eventual phylogenetic relationships are to be revealed. Much more information can be provided from further proteomic studies of both nectar and pollination drop that will contribute to the study of plant reproduction and evolution.Key words: Nectar, pollination drop, ovular secretion, plant reproduction, proteins, sugars, gymnosperms, angiosperms, plant–animal interaction     

Inflammation,Depression and Dementia: Are they Connected?

Chronic inflammation is now considered to be central to the pathogenesis not only of such medical disorders as cardiovascular disease, multiple sclerosis, diabetes and cancer but also of major depression. If chronic inflammatory changes are a common feature of depression, this could predispose depressed patients to neurodegenerative changes in later life. Indeed there is now clinical evidence that depression is a common antecedent of Alzheimer’s disease and may be an early manifestation of dementia before the cognitive declines becomes apparent. This review summarises the evidence that links chronic low grade inflammation with changes in brain structure that could precipitate neurodegenerative changes associated with Alzheimer’s disease and other dementias. For example, neuronal loss is a common feature of major depression and dementia. It is hypothesised that the progress from depression to dementia could result from the activation of macrophages in the blood, and microglia in the brain, that release pro-inflammatory cytokines. Such cytokines stimulate a cascade of inflammatory changes (such as an increase in prostaglandin E2, nitric oxide in addition to more pro-inflammatory cytokines) and a hypersecretion of cortisol. The latter steroid inhibits protein synthesis thereby reducing the synthesis of neurotrophic factors and preventing reairto damages neuronal networks. In addition, neurotoxic end products of the tryptophan-kynurenine pathway, such as quinolinic acid, accumulate in astrocytes and neurons in both depression and dementia. Thus increased neurodegeneration, reduced neuroprotection and neuronal repair are common pathological features of major depression and dementia. Such changes may help to explain why major depression is a frequent prelude to dementia in later life. Special issue dedicated to Dr. Moussa Youdim.     

Biomarkers in outpatient heart failure management; Are they correlated to and do they influence clinical judgment?

Aims

Heart failure (HF) management is complicated by difficulties in clinical assessment. Biomarkers may help guide HF management, but the correspondence between clinical evaluation and biomarker serum levels has hardly been studied. We investigated the correlation between biomarkers and clinical signs and symptoms, the influence of patient characteristics and comorbidities on New York Heart Association (NYHA) classification and the effect of using biomarkers on clinical evaluation.

Methods and results

This post-hoc analysis comprised 622 patients (77 ± 8 years, 76 % NYHA class ≥3, 80 % LVEF ≤45 %) participating in TIME-CHF, randomising patients to either NT-proBNP-guided or symptom-guided therapy. Biomarker measurements and clinical evaluation were performed at baseline and after 1, 3, 6, 12 and 18 months. NT-proBNP, GDF-15, hs-TnT and to a lesser extent hs-CRP and cystatin-C were weakly correlated to NYHA, oedema, jugular vein distension and orthopnoea (ρ-range: 0.12–0.33; p < 0.01). NT-proBNP correlated more strongly to NYHA class in the NT-proBNP-guided group compared with the symptom-guided group. NYHA class was significantly influenced by age, body mass index, anaemia, and the presence of two or more comorbidities.

Conclusion

In HF, biomarkers correlate only weakly with clinical signs and symptoms. NYHA classification is influenced by several comorbidities and patient characteristics. Clinical judgement seems to be influenced by a clinician’s awareness of NT-proBNP concentrations.

Electronic supplementary material

The online version of this article (doi:10.1007/s12471-013-0503-y) contains supplementary material, which is available to authorized users.