Exosomes and retroviruses: the chicken or the egg?

Retroviruses appropriate pre‐existing cellular machineries to propagate. In the last decade, impressive similarities have been observed in the generation and dissemination in the host cells of retroviruses and small cellular vesicles known as exosomes. These cellular vesicles are thought to facilitate intercellular communication processes and mediate immune functions. However, their link to the retroviral life cycle has given rise to distinct hypotheses and puzzling dilemmas. Are exosomes the antecessors of retroviruses or do retroviruses merely exploit the same cellular machinery designated for exosome biosynthesis? Here, we address these fascinating evolutionary questions by reviewing recent discoveries and analysing the controversies surrounding them.     

Adaptation or exaptation? An experimental test of hypotheses on the origin of salinity tolerance in Bufo calamita

The natterjack toad (Bufo calamita) shows variation in embryonic and larval salinity tolerance across populations in southern Spain. However, its aquatic/terrestrial biphasic life cycle, together with remarkable differences in salinity tolerance between Spanish and UK freshwater populations suggest an alternative hypothesis to local adaptation. Drought resistance during the terrestrial phase and salinity tolerance during the aquatic phase are both related to osmotic stress tolerance, and if there were an association between them, one could have evolved as an exaptation from the other. To test such an association, we reared B. calamita juveniles from three populations known to differ genetically in their salinity tolerance, under either dry or humid conditions. Drought decreased growth rate, enhanced burying behaviour, and decreased foraging activity and efficiency. No significant population x treatment interaction was found for any variable, i.e. populations were equally affected by drought. These results do not support the hypothesis of a genetic association between salinity and drought tolerance.     

The chicken or the egg? Plastome evolution and an independent loss of the inverted repeat in papilionoid legumes

The plastid genome (plastome), while surprisingly constant in gene order and content across most photosynthetic angiosperms, exhibits variability in several unrelated lineages. During the diversification history of the legume family Fabaceae, plastomes have undergone many rearrangements, including inversions, expansion, contraction and loss of the typical inverted repeat (IR), gene loss and repeat accumulation in both shared and independent events. While legume plastomes have been the subject of study for some time, most work has focused on agricultural species in the IR-lacking clade (IRLC) and the plant model Medicago truncatula. The subfamily Papilionoideae, which contains virtually all of the agricultural legume species, also comprises most of the plastome variation detected thus far in the family. In this study three non-papilioniods were included among 34 newly sequenced legume plastomes, along with 33 publicly available sequences, to assess plastome structural evolution in the subfamily. In an effort to examine plastome variation across the subfamily, approximately 20% of the sampling represents the IRLC with the remainder selected to represent the early-branching papilionoid clades. A number of IR-related and repeat-mediated changes were identified and examined in a phylogenetic context. Recombination between direct repeats associated with ycf2 resulted in intraindividual plastome heteroplasmy. Although loss of the IR has not been reported in legumes outside of the IRLC, one genistoid taxon was found to completely lack the typical plastome IR. The role of the IR and non-IR repeats in the progression of plastome change is discussed.     

Somatic mutations in mitochondria: the chicken or the egg?

Somatic mutations of mitochondrial DNA have been detected in various pathologies such as cancer, neurodegenerative diseases, cardiac disorders and aging in general. Now it has been found that patients with rheumatoid arthritis also have a higher incidence of mitochondrial mutations in synoviocytes and synovial tissue compared with patients with osteoarthritis. Furthermore, it has been shown that these mutations possibly result in changed peptides that are presented by major histocompatibility complex II and thus might be recognized as non-self by the immune system. Further studies will show whether these mutations are actually able to trigger autoimmune inflammation in rheumatoid arthritis or whether they must be considered epiphenomena of cellular damage in chronic inflammation.     

Panic attacks and supraventricular tachycardias: the chicken or the egg?

Panic attacks occur in about 2 % of the population. Symptoms include a racing or pounding heart beat, chest pain, dizziness, light-headedness, nausea, difficulty in breathing, tingling or numbness in the hands, flushes or chills, dreamlike sensations or perceptual distortions. The symptoms of paroxysmal supraventricular tachycardia (PSVT) may be similar. A PSVT is often difficult to document on the ECG since it has often ceased before the patient comes to medical attention. Besides, a tachycardia may still be present and even be documented but interpreted as a phenomenon secondary to the panic attack. In addition, ECG abnormalities between episodes can often not be identified. The evidence that in some patients paroxysmal SVT is the cause, but not the consequence of a panic attack, is based on observations that catheter ablation was able to cure patients presenting with panic disorders. To better establish the prevalence of SVT as the underlying mechanism of a panic attack, there is a need for prospective studies and/or registries. Whereas gastric ulcer has in some patients changed from a psychosomatic disorder to an infectious disease, we may hypothesise that a certain proportion of panic disorders may mutate into an underlying arrhythmia rather than a primary psychiatric disorder.     

Tau phosphorylation, tangles, and neurodegeneration: the chicken or the egg?

Pathological aggregation of the microtubule-associated protein tau is a common feature of many neurodegenerative diseases. Although tau aggregation is associated with abnormal tau phosphorylation, the role of phosphorylation in the initiation of neurodegeneration has been unclear. Now, several animal models and data from human patients provide converging evidence that aberrant tau phosphorylation can cause a neurodegenerative phenotype similar to that seen in human neurodegenerative diseases.     

Dehydration-mediated activation of the xanthophyll cycle in darkness: is it related to desiccation tolerance?

The development of desiccation tolerance by vegetative tissues was an important step in the plants’ conquest of land. To counteract the oxidative stress generated under these conditions the xanthophyll cycle plays a key role. Recent reports have shown that desiccation itself induces de-epoxidation of xanthophyll cycle pigments, even in darkness. The aim of the present work was to study whether this trait is a common response of all desiccation-tolerant plants. The xanthophyll cycle activity and the maximal photochemical efficiency of PS II (F _v/F _m) as well as β-carotene and α-tocopherol contents were compared during slow and rapid desiccation and subsequent rehydration in six species pairs (with one desiccation-sensitive and one desiccation-tolerant species each) belonging to different taxa. Xanthophyll cycle pigments were de-epoxidised in darkness concomitantly with a decrease in F _v/F _m during slow dehydration in all the desiccation-tolerant species and in most of the desiccation-sensitive ones. De-epoxidation was reverted in darkness by re-watering in parallel with the recovery of the initial F _v/F _m. The stability of the β-carotene pool confirmed that its hydroxylation did not contribute to zeaxanthin formation. The α-tocopherol content of most of the species did not change during dehydration. Because it is a common mechanism present in all the desiccation-tolerant taxa and in some desiccation-sensitive species, and considering its role in antioxidant processes and in excess energy dissipation, the induction of the de-epoxidation of xanthophyll cycle pigments upon dehydration in the dark could be understood as a desiccation tolerance-related response maintained from the ancestral clades in the initial steps of land occupation by plants.     

Adaptation or exaptation? The case of the human hand

A controversy of relevance to the study of biological form involves the concept of adaptation. This controversy is illustrated by the structure and function of the human hand. A review of the principal definitions of adaptation points to two main problems: (1) they are qualitative and make reference to the whole structure (or substructural feature) and (2) they are based on the idea of natural selection as a moulding factor. The first problem would be solved by a definition that encompasses quantitative measures of the effects of selection, drawing on new advances in the comparative method. The second problem is deeper and presents greater conceptual difficulties. I will argue that the idea of natural selection as a moulding factor depends on the notion of a genetic program for development. But regarding the hand, experimental evidence on limb development challenges the idea of a genetic program for skeletal pattern formation, undermining a simple application of standard adaptationist concepts. These considerations lead to a revised definition of adaptation and interpretation of the evolutionary determinants of the hand’s form.     

Does tolerance of wheat to salinity and hypoxia correlate with root dehydrogenase activities or aerenchyma formation?

The effects of NaCl salinity (100 or 150 mol m^-3) and hypoxia on seedlings of several wheat varieties (Lyallpur-90, SARC-1, Pato, Tchere, Pb-85, Siete Cerros, Chinese Spring and a Chinese Spring × Thinopyrum elongatum amphidiploid) were studied in solution culture. In vivo studies of activities of different enzymes (alcohol dehydrogenase (ADH), lactate dehydrogenase (LDH) and cytochrome oxidase (COase)) extracted from Pato and Pb-85 included the effect of salinity with and without hypoxia, while during in vitro studies, NaCl, glycinebetaine and proline were added to the assay mixture. The extent of aerenchyma formation was also determined in Pato, Chinese Spring and a Chinese Spring × Thinopyrum elongatum amphidiploid. Imposition of hypoxia greatly induced ADH and LDH activity in roots of wheat seedlings after a week-long exposure. However, exposure of roots to salinity also slightly increased LDH and ADH activity compared with the non-saline control. On a relative basis, Pato had higher ADH activity under hypoxic (21×) or saline-hypoxic stress (20×) than in aerated conditions. Hypoxia alone or in the presence of salts decreased COase activity in both Pato and Pb-85. The in vitro studies revealed that NaCl (on an equimolar basis at up to 500 mol m^-3) is more disruptive than glycinebetaine or proline. LDH was more sensitive to NaCl than ADH. Aerenchyma development was higher near the root-shoot interface compared to near the root tip. Salinity under hypoxic conditions significantly reduced aerenchyma development near the root tip and root-shoot interface compared to hypoxia alone. Neither enzyme activity nor aerenchyma formation could account for varietal differences in tolerance to hypoxia alone or in combination with salinity.     

The ‘chicken or the egg’: which comes first,forest tree decline or loss of mycorrhizae?

Forest trees are experiencing massive declines globally caused by a multitude of stressors, both abiotic (pollution, fragmentation and climate change) and biotic (fungi, bacteria, viruses and insects). Mycorrhizal fungi aid plants in the requisition of nutrients through their mutualistic relationship with plant roots and are integral to tree health. Stresses affecting tree health will also influence mycorrhizal fungi directly or indirectly, and thus alter the pathways responsible for nutrient absorption. Such an intimate association is a true chicken or egg quandary; do external stressors cause a loss of mycorrhizae which leads to tree decline, does tree decline result in a loss of mycorrhizae, or is it a combination of both? A review of literature has identified six stressors known to contribute to tree decline and to impact directly on mycorrhizae; global climate change, pesticides, heavy metals, excess fertilizer, pathogens and habitat fragmentation. A few review papers have highlighted the link; however, what is missing is irrefutable empirical research. This review documents the known direct impacts of the six stressors on mycorrhizal communities and places this in the context of decline syndromes in long-lived forest trees. We also discuss methodologies available to identify fungi and future research needed to unravel the complex relationships between forest tree declines and their associated mycorrhizal fungi.     

The physiology and proteomics of drought tolerance in maize: early stomatal closure as a cause of lower tolerance to short-term dehydration?

Understanding the response of a crop to drought is the first step in the breeding of tolerant genotypes. In our study, two maize (Zea mays L.) genotypes with contrasting sensitivity to dehydration were subjected to moderate drought conditions. The subsequent analysis of their physiological parameters revealed a decreased stomatal conductance accompanied by a slighter decrease in the relative water content in the sensitive genotype. In contrast, the tolerant genotype maintained open stomata and active photosynthesis, even under dehydration conditions. Drought-induced changes in the leaf proteome were analyzed by two independent approaches, 2D gel electrophoresis and iTRAQ analysis, which provided compatible but only partially overlapping results. Drought caused the up-regulation of protective and stress-related proteins (mainly chaperones and dehydrins) in both genotypes. The differences in the levels of various detoxification proteins corresponded well with the observed changes in the activities of antioxidant enzymes. The number and levels of up-regulated protective proteins were generally lower in the sensitive genotype, implying a reduced level of proteosynthesis, which was also indicated by specific changes in the components of the translation machinery. Based on these results, we propose that the hypersensitive early stomatal closure in the sensitive genotype leads to the inhibition of photosynthesis and, subsequently, to a less efficient synthesis of the protective/detoxification proteins that are associated with drought tolerance.     

How do salinity and water stress affect transport of water,assimilates and ions to tomato fruits?

The study was conducted in order to determine whether water stress affects the accumulation of dry matter in tomato fruits similarly to salinity, and whether the increase in fruit dry matter content is solely a result of the decrease in water content. Although the rate of water transport to tomato fruits decreased throughout the entire season in saline water irrigated plants, accumulation rates of dry matter increased significantly. Phloem water transport contributed 80–85% of the total water transport in the control and water-stressed plants, and over 90% under salinity. The concentration of organic compounds in the phloem sap was increased by 40% by salinity. The rate of ions transported via the xylem was also significantly increased by salinity, but their contribution to fruit osmotic adjustment was less. The rate of fruit transpiration was also markedly reduced by salinity. Water stress also decreased the rate of water transport to the tomato fruit and increased the rate of dry matter accumulation, but much less than salinity. The similar changes, 10–15%, indicate that the rise in dry matter accumulation was a result of the decrease in water transport. Other parameters such as fruit transpiration rates, phloem and xylem sap concentration, relative transport via phloem and xylem, solutes contributing to osmotic adjustment of fruits and leaves, were only slightly affected by water stress. The smaller response of these parameters to water stress as compared to salinity could not be attributed to milder stress intensity, as leaf water potential was found to be more negative. Measuring fruit growth of girdled trusses, in which phloem flow was inactive, and comparing it with ungirdled trusses validated the mechanistic model. The relative transport of girdled as compared to ungirdled fruits resembled the calculated values of xylem transport.     

Are patterns in the taxonomic,biological and ecological traits of water beetles congruent in Mediterranean ecosystems?

1. Coleoptera species show considerable diversity in life histories and ecological strategies, which makes possible their wide distribution in freshwater habitats, including highly stressed ones such as saline or temporary waterbodies. Explaining how particular combinations of traits allow species to occupy distinctive habitats is a central question in ecology. 2. A total of 212 sites, sampled over a wide range of inland aquatic habitats in the south‐eastern Iberian Peninsula, yielded 272 species belonging to 68 genera and 11 families. The affinities of genera for 11 biological and 11 ecological traits, gathered from literature and the authors’ own expertise, were used to assess the degree of congruence between taxonomic, biological and ecological traits. 3. Taxonomic richness was significantly related to the number of both biological and ecological trait categories, with the richest families also showing the highest functional and ecological diversity. A fuzzy correspondence analysis performed on the abundance‐weighed array of biological traits separated genera according to categories of diet, feeding habits, respiration, reproduction and locomotion. A similar analysis of ecological traits revealed that preferences related to longitudinal distribution (headwater to mouth), local habitat and current velocity best discriminated genera. At the family level, there was a distinctive functional grouping of genera based on biological traits. Only Elmidae showed noticeable homogeneity across genera for both biological and ecological traits. 4. Co‐inertia analysis demonstrated a significant match between biological and ecological traits (Rv‐correlation = 0.35, P < 0.001). Elmidae genera displayed the highest concordance, whereas Hydraenidae demonstrated the lowest. 5. These results indicate that the predominance of habitat filtering processes in headwater streams yields biological trait conservatism (as shown by Elmidae genera), as well as trait convergence for some specific traits (for instance, respiration) among certain Dytiscidae genera and other typical rheophilic taxa, whereas other biotic factors, such as competition among species, appear more prominent in less stressed habitats. Further knowledge of traits, especially regarding physiological capabilities, is needed to better understand water beetle life history strategies.     

The policy chicken and the science egg. Has applied ecology failed the transgenic crops debate?

Ecology has a long history of research relevant to and impacting on real-world issues. Nonetheless problems of communication remain between policy-makers and scientists because they tend to work at different levels of generality (policy deals with broad issues, science prefers specific questions), and complexity (policy-makers want simple answers, ecologists tend to offer multi-factorial solutions) and to different timescales (policy-makers want answers tomorrow, ecologists always seem to want more time). These differences are not unique to the debate about the cultivation of transgenic crops. Research on gene flow is used to illustrate how science and policy are intimately bound together in a value-laden, iterative and messy process unlike that characterised by the ‘encounter problem—do science—make policy’ model. It also demonstrates how the gap between science and policy is often characterised by value-laden language. Scientists involved in ERA for transgenic crops may find their engagement with policy- and decision-makers clouded by misunderstanding about what one should expect from the other. Not the least of these, that science can define harm, is explored in a discussion of the UK Farm Scale Evaluations of herbicide-tolerant GM crops. The varied responses to these extensive trials highlight the problems of linking specific scientific experiments with broad policy objectives. The problems of applied ecology in the transgenic crops debate are not unique but may differ from other areas of environmental policy in the intense politicisation of the debate, the emphasis on assessment of risk and the particularly broad policy objectives.     

The serpent and the egg: unidirectional evolution of reproductive mode in vipers?

Dollo’s law, that complex characters are not regained in evolution, is a pattern applied to many systems. Recent work has evaluated unidirectional evolution in a number of contexts, and several violations of this law have been documented. These methods have also been criticized for potentially overestimating reversals. We test the hypothesis that the ancestral reproductive mode of oviparity can be regained in vipers, in opposition to Dollo’s law. We use model comparison and ancestral character state reconstruction methods that address recent criticisms, and find evidence both supporting and refuting Dollo’s predictions from different analyses. We discuss our results in the context of unidirectional evolution and review factors required for strong inference of violations of Dollo’s law.     

An integrin chicken and egg problem: which comes first, the extracellular matrix or the cytoskeleton?

Integrins have the ability to organise macromolecular structures both inside and outside the cell. Analysis of integrin function in the developing embryos of worms and flies suggests that, although the extracellular matrix directs integrins to organise intracellular proteins, the cytoskeleton may have the first word.     

Adaptation to stress in yeast: to translate or not?

For most eukaryotic organisms, including Saccharomyces cerevisiae, the rapid inhibition of protein synthesis forms part of a response to stress. In order to balance the changing conditions, precise stress-specific alterations to the cell's proteome are required. Therefore, in the background of a global down-regulation in protein synthesis, specific proteins are induced. Given the level of plasticity required to enable stress-specific alterations of this kind, it is surprising that the mechanisms of translational regulation are not more diverse. In the present review, we summarize the impact of stress on translation initiation, highlighting both the similarities and distinctions between various stress responses. Finally, we speculate as to how yeast cells generate stress-responsive programmes of protein production when regulation is focused on the same steps in the translation pathway.