The plant endosomal system—its structure and role in signal transduction and plant development

Endosomes are highly dynamic membrane systems that receive endocytosed plasma membrane proteins and sort them for either degradation or recycling back to the cell surface. In addition, they receive newly synthesised proteins destined for vacuolar/lysosomal compartments. Sorting in the endosomes is necessary for the establishment and maintenance of cell polarity and it is needed to control levels and function of receptors and transporters at the cellular surface. Both processes are crucial for correct cell behaviour during tissue and organ development and for intercellular communication in general. It has therefore become an imperative to investigate structure and function of the endosomal system if we want to obtain a deeper mechanistic understanding of signal transduction and development. This review will compare our current understanding of endosomal trafficking in animals and yeast with what is known in plants, and will highlight some important breakthroughs in our understanding of the role of endosomes in signal transduction and multicellular development in Drosophila, as well as in Arabidopsis.Abbreviations ARF ADP ribosylation factor - BFA Brefeldin A - EGF Epidermal growth factor - GEF GDP/GTP exchange factor - MVB Multi-vesicular body - PCR Partially-coated reticulum - PI-3P Phosphatidylinositol-3-phosphate - TGN Trans-Golgi network     

Protective effect of tea against lead and cadmium-induced oxidative stress—a review

Exposure to Cd and Pb reduces the activity of antioxidant enzymes, which points to a decrease in the antioxidant potential of the body as a result of supplying factors which enhance cellular oxidation processes. Man is exposed to the effects of toxic metals because they are present in the environment, including in food. Since no effective ways to reduce the concentrations of Cd an Pb in food exist, studies are undertaken to develop methods of reducing their toxic effect on the body through chelating these metals using nutrients (which reduces their absorption by tissues) or increasing the oxidative capacity of the body (which decreases the possibility of inducing oxidative damage to internal organs). Studies performed on laboratory animals have shown that the use of tea infusions fulfil both functions.     

α-Aryl-N-aryl nitrones: Synthesis and screening of a new scaffold for cellular protection against an oxidative toxic stimulus

Nitrone-containing compounds are commonly employed as spin traps of free radical species in chemical and biological studies. Some molecules as α-phenyl-N-t-butyl nitrone (PBN) and its derivatives have been tested as potential drugs to treat oxidative stress related diseases, as Alzheimer and stroke for example. In this work we report the design and the synthesis of α-aryl-N-aryl nitrones and their cytoprotection profile on human neuroblastoma cells (SH-SY5Y) under induced oxidative stress. All the nine synthesized nitrones showed a significant response at low micromolar concentration. The selected compound 8 (α-phenyl-N-phenyl nitrone) increased the reduced glutathione (GSH) levels by 65% and lowered the necrotic cell death from 25.8% to 3.8%. Based on our data, the designed highly conjugated nitrone double-bond skeleton can be considered as a good scaffold for further studies regarding oxidative stress-related diseases.     

Heat generation and dissipation in plants: can the alternative oxidative phosphorylation pathway serve a thermoregulatory role in plant tissues other than specialized organs?

A number of hypothetical physiological roles have been proposed for the cyanide-insensitive alternative pathway in plants (Palmer, 1976; Laties, 1982; Meeuse, 1984; Purvis and Shewfelt, 1994; Wagner and Krab, 1995). The calorimetric observations of Raskin and co-workers (Ordentlich et al., 1991; Nevo et al., 1992; Moynihan et al., 1995) are significant contributions showing an interesting metabolic, chilling-induced response of the alternative pathway activity and differences in the low-temperature response among species adapted to different climates. Since different oxidative pathways do not have large differences in enthalpy, and observed heat rate increases are insufficient to cause significant temperature increases of physiological importance in nonthermogenic plants, other explanations must be developed for the relationship between the partitioning of electron flow and physiological conditions such as low temperature. The induction and engagement of the alternative respiratory pathway is involved in metabolic stasis, maintaining proper balance between carbon flow, ATP-ADP ratio, and electron flow during fluctuating or extreme temperature conditions. The alternative oxidase is engaged when ATP requirements are adequately met, as discussed by Palmer (1976), Meeuse (1983), Lambers (1985), and Wagner and Krab (1995). The expression and kinetic activity of the alternative oxidase are regulated by concentrations of key metabolites (Day and Wiskich, 1995; Siedow and Umbach, 1995; Wagner and Krab, 1995; Day et al., 1996). Dynamic partitioning of electron flow between Cyt oxidase and the alternative oxidase depends on the kinetic behavior of the two oxidases and the substrate dehydrogenases (Day and Wiskich, 1995; Siedow and Umbach, 1995; Wagner and Krab, 1995; Day et al., 1996). Furthermore, Moynihan et al. (1995) found that Episces cupreata Hook, adapted to the tropics, has very little alternative oxidase activity compared with wheat (Nevo et al., 1992), adapted to a large range of temperature climates. This results is consistent with the general relation between the apparent alternative oxidase activity and the climate of origin of the species.     

Attract and deter: a dual role for pyrrolizidine alkaloids in plant–insect interactions

Pyrrolizidine alkaloids (PAs) are the major defense compounds of plants in the Senecio genus. Here I will review the effects of PAs in Senecio on the preference and performance of specialist and generalist insect herbivores. Specialist herbivores have evolved adaptation to PAs in their host plant. They can use the alkaloids as cue to find their host plant and often they sequester PAs for their own defense against predators. Generalists, on the other hand, can be deterred by PAs. PAs can also affect survival of generalist herbivores. Usually generalist insects avoid feeding on young Senecio leaves, which contain a high concentration of alkaloids. Structurally related PAs can differ in their effects on insect herbivores, some are more toxic than others. The differences in effects of PAs on specialist and generalists could lead to opposing selection on PAs, which may maintain the genetic diversity in PA concentration and composition in Senecio species.     

The “minimal boundary curve for endothermy” as a predictor of heterothermy in mammals and birds: a review

According to the concept of the “minimal boundary curve for endothermy”, mammals and birds with a basal metabolic rate (BMR) that falls below the curve are obligate heterotherms and must enter torpor. We examined the reliability of the boundary curve (on a double log plot transformed to a line) for predicting torpor as a function of body mass and BMR for birds and several groups of mammals. The boundary line correctly predicted heterothermy in 87.5% of marsupials (n = 64), 94% of bats (n = 85) and 82.3% of rodents (n = 157). Our analysis shows that the boundary line is not a reliable predictor for use of torpor. A discriminate analysis using body mass and BMR had a similar predictive power as the boundary line. However, there are sufficient exceptions to both methods of analysis to suggest that the relationship between body mass, BMR and heterothermy is not a causal one. Some homeothermic birds (e.g. silvereyes) and rodents (e.g. hopping mice) fall below the boundary line, and there are many examples of heterothermic species that fall above the boundary line. For marsupials and bats, but not for rodents, there was a highly significant phylogenetic pattern for heterothermy, suggesting that taxonomic affiliation is the biggest determinant of heterothermy for these mammalian groups. For rodents, heterothermic species had lower BMRs than homeothermic species. Low BMR and use of torpor both contribute to reducing energy expenditure and both physiological traits appear to be a response to the same selective pressure of fluctuating food supply, increasing fitness in endothermic species that are constrained by limited energy availability. Both the minimal boundary line and discriminate analysis were of little value for predicting the use of daily torpor or hibernation in heterotherms, presumably as both daily torpor and hibernation are precisely controlled processes, not an inability to thermoregulate.     

The Lake Victoria environment: Its fisheries and wetlands — a review

Recent ecological changes in the Lake Victoria ecosystem have been attributed to the effects of species stockings and, in particular, from predation pressure by the Nile perch. Evidence for the decline of haplochromines due to predation by the Nile perch, while overwhelming, does not necessarily account for these gross ecological changes. Ecological theory predicts that natural fluctuation would occur in a fisheries where predator and prey species could alternate in abundance. The absence of a substantial recovery of the endemic species within cyclical abundance patterns in Lake Victoria (even though they could be delayed), particularly in the pelagic and profundal zones, points to other causal factors.Ecological changes have occurred in Lake Victoria since the turn of the century when modern fishing methods and techniques were introduced. As the human population increased and the catchment became more exposed to diverse socio-economic activities, further pressure on the ecological functioning of the lake was compounded by exotic species stockings. Thus, declining fisheries, wetland degradation and eutrophication are part of gross environmental changes that are likely to become more manifest with the increasing impact of the water hyacinth. It therefore seems appropriate to consider the ecological changes at both temporal and spatial scales and to re-examine some of the paradigms for ecological change.Although cataclysmic impacts may have occurred between the 1960's and the early 1980's, the basic cause of ecological changes, at least in the inshore zone, appears to result from human activities partly associated with a degradation of the riparian wetlands that exposes the aquatic ecosystem to catchment activities. Overexploitation and a reduction in habitat quality and quantity in this zone could be major factors in the ecological transformations. However, the importance of the littoral zone and the ecological impact of the Nile tilapia, another stocked species, are hardly known. An additional hypothesis is therefore put forward to determine whether or not wetland vegetation types in Lake Victoria are important fish habitats. This hypothesis allows for testing several interrelated sub-hypotheses about the relationships between wetland vegetation and the ecology of Nile tilapia. The water hyacinth, a recent feature of the shoreline and an additional strain to the already endangered buffer zone, may have to be regarded as a dynamic, but permanent, part of most of the littoral zone.Corresponding Editor: Prof. P. Denny     

Does an animal peptide:N-glycanase have the dual role as an enzyme and a carbohydrate-binding protein?

Recently, we have reported purification and characterization of a de-N-glycosylating enzyme, peptide:N-glycanase (PNGase) found in C3H mouse fibroblast L-929 cells, and designated L-929 PNGase [Suzuki T, Seko A, Kitajima K, Inoue Y, Inoue S (1994)J Biol Chem 269, 17611–18]. The unique properties of L-929 PNGase are that the enzyme had a high affinity to the substrate glycopeptide (e.g.K _m=114 µm for fetuin derived glycopentapeptide) and that the PNGase-catalysed reaction is strongly inhibited by the released free oligosaccharides but not by the free peptides formed, suggesting that L-929 PNGase is able to bind to a certain type of carbohydrate chain. In this study, we report the new findings of the mannan-binding property of L-929 PNGase; the de-N-glycosylating enzyme activity of L-929 PNGase was inhibited by yeast mannan and triomannose, Man1 3(Man1 6)Man, but not by mannose and -methyl-d-mannoside. Furthermore, L-929 PNGase was revealed to bind to the glycan moiety of yeast mannan by using mannan-conjugated Sepharose 4B gel as a ligand, suggesting that L-929 PNGase could serve not only as an enzyme but also as a carbohydrate recognition proteinin vivo. Such dual properties found for animal-derived L-929 PNGase are unique and are not shared with other previously characterized plant- and bacterial-origin PNGases — PNGase A and PNGase F, respectively.Abbreviations GLC gas liquid chromatography - GlcNAc-Asn 2-acetamido-1--(l-aspartamido)-1,2-dideoxy-d-glucose - BSA bovine serum albumin - DTT dithiothreitol - EDTA ethylenediaminetetraacetic acid - Gal d-galactose - GlcNAc N-acetyl-d-glucosamine - Man d-mannose; triomannose, Man1 3(Man1 6)Man; - MES 2-(N-morphorino)ethanesulfonic acid - NeuAc N-acetyl-neuraminic acid - PNGase peptide:N ⁴-(N-accetyl-glucosaminyl)asparagine amidase (peptide:N-glycanase,EC 3.5.1.52) - PNP p-nitrophenyl     

The origin of dystrophin-glycoprotein complex(DGC)-related muscular dystrophies: the need for protection against an ancestral pathogen?

Because of its crucial role during the early stages of morphogenesis, no genetic defects associated to dystroglycan have been reported so far. Dystroglycan is an important member of the dystrophin-glycoprotein complex (DGC) and in several muscular dystrophies, depending on abnormalities of proteins belonging to or associated with the DGC, it is frequently observed a significant reduction of dystroglycan levels at the sarcolemma. Recently, it has been demonstrated that dystroglycan acts as a receptor for pathogens such as M. leprae and arenaviruses. It is well-known that mutated alleles causing diseases can be selected in order to confer an additional genetic advantage. Herein it is discussed the possibility that mutations leading to a certain number of muscular dystrophies might have been originally selected to indirectly gain a specific advantage: the absence or the lower levels of dystroglycan could have greatly reduced the risk of some ancestral lethal infections specifically directed against muscles.     

Cysteine residues as catalysts for covalent peptide and protein modification: a role for thiyl radicals?

Cysteine thiyl radicals engage in reversible intramolecular hydrogen-transfer reactions with amino acid residues in peptides and proteins. These reactions can be experimentally demonstrated through covalent hydrogen-deuterium exchange when experiments are carried out in (2)H2O. To this end, hydrogen-transfer reactions have been observed between cysteine thiyl radicals and glycine, alanine, serine, valine and leucine in both model peptides and a protein, insulin. The relevance of such reactions for protein oxidation under conditions of oxidative stress is discussed.     

Impact of a resistance gene against a fungal pathogen on the plant host residue microbiome: The case of the Leptosphaeria maculans–Brassica napus pathosystem

Oilseed rape residues are a crucial determinant of stem canker epidemiology as they support the sexual reproduction of the fungal pathogen Leptosphaeria maculans. The aim of this study was to characterize the impact of a resistance gene against L. maculans infection on residue microbial communities and to identify microorganisms interacting with this pathogen during residue degradation. We used near-isogenic lines to obtain healthy and infected host plants. The microbiome associated with the two types of plant residues was characterized by metabarcoding. A combination of linear discriminant analysis and ecological network analysis was used to compare the microbial communities and to identify microorganisms interacting with L. maculans. Fungal community structure differed between the two lines at harvest, but not subsequently, suggesting that the presence/absence of the resistance gene influences the microbiome at the base of the stem whilst the plant is alive, but that this does not necessarily lead to differential colonization of the residues by fungi. Direct interactions with other members of the community involved many fungal and bacterial amplicon sequence variants (ASVs). L. maculans appeared to play a minor role in networks, whereas one ASV affiliated to Plenodomus biglobosus (synonym Leptosphaeria biglobosa) from the Leptosphaeria species complex may be considered a keystone taxon in the networks at harvest. This approach could be used to identify and promote microorganisms with beneficial effects against residue-borne pathogens and, more broadly, to decipher the complex interactions between multispecies pathosystems and other microbial components in crop residues.     

Plasma cytokines and oxidative damage in HIV-positive and HIV-negative adolescents and young adults: a protective role for IL-10?

HIV infection causes immune activation that leads to oxidative damage. Proinflammatory cytokines may promote such damage and the regulatory cytokine IL-10 may protect against such damage. To examine the relation of these cytokines to oxidative damage, 67 cases of oxidative damage and 67 matched controls were selected from the reaching for excellence in adolescent health (REACH) study. Subjects were young (15-23 years), largely female (76%), HIV-positive (73%) and black (69%). Proinflammatory cytokines were not significantly associated with oxidative damage but plasma IL-10 had a significant, negative association with oxidative damage. This finding is consistent with a protective role for IL-10 in diminishing oxidative damage during immune activation.     

Atrial fibrillation in β-thalassemia patients with a focus on the role of iron-overload and oxidative stress: A review

Cardiac complications including arrhythmia and especially atrial fibrillation (AF) are common causes of death in β-thalassemia patients. The main factor in the etiopathogenesis of these complications is iron overload, which results in increased oxidative stress. Although there is a known association between cardiac complications and iron overload in β-thalassemia patients, there is no comprehensive review on AF and excessive iron with a focus on oxidative stress in these patients. The aim of this article was to review the different aspects of AF in β-thalassemia patients with a focus on the prevention and treatment of AF by using iron chelators and/or anti-oxidants. AF in β-thalassemia patients is more common than in the general population. One of the most important causes of AF is cardiac iron overload and the harmful effects of increased oxidative stress. Iron-induced AF can be reversed by using an intensive iron chelation regimen. Based on a few experimental studies, the combination of iron chelators with some anti-oxidants, including NAC, vitamin C, and acetaminophen, can lead to improved cardiac protection. However, the effect of such combinations on cardiac arrhythmias should be further evaluated with animal and human studies.     

The evolution of peer review as a basis for scientific publication: directional selection towards a robust discipline?

Peer review is pivotal to science and academia, as it represents a widely accepted strategy for ensuring quality control in scientific research. Yet, the peer‐review system is poorly adapted to recent changes in the discipline and current societal needs. We provide historical context for the cultural lag that governs peer review that has eventually led to the system's current structural weaknesses (voluntary review, unstandardized review criteria, decentralized process). We argue that some current attempts to upgrade or otherwise modify the peer‐review system are merely sticking‐plaster solutions to these fundamental flaws, and therefore are unlikely to resolve them in the long term. We claim that for peer review to be relevant, effective, and contemporary with today's publishing demands across scientific disciplines, its main components need to be redesigned. We propose directional changes that are likely to improve the quality, rigour, and timeliness of peer review, and thereby ensure that this critical process serves the community it was created for.     

Monk parakeet invasion success: a role for nest thermoregulation and bactericidal potential of plant nest material?

Invasive species are a global threat to biodiversity, economy and human wellbeing. To mitigate these threats, identifying and halting the introduction of potentially invasive species is crucial. Although progress has been made in elucidating mechanisms underlying invasion success, the role of species behavioral strategies has only received scant attention. Here, we use the invasion of monk parakeets in Santa Catarina state, southern Brazil to study whether behavioral strategies such as nest thermoregulation and the ability to self-medicate against pathogens contribute to the establishment success of invading species. We relate data on monk parakeet reproductive success to ambient temperatures in- and outside nesting chambers and test the bactericidal potential of plants transported to the nest by breeding monk parakeets. Compared to breeding data from other invaded ranges and parts of the species’ native range, our results suggest both thermoregulation and the use of bactericidal plants could potentially influence monk parakeet reproductive success. Thermoregulation maintains stable temperatures of incubator chambers compared to large fluctuations (especially hotter extremes) outside the nest. At least one of the plants brought to the nest effectively inhibited growth of pathogenic bacteria. The union of these two factors could increase reproductive rates and may consequently aid the expansion of the species in new non-native environments.     

The evolution and maintenance of virulence in Staphylococcus aureus: a role for host-to-host transmission?

Despite progress in our understanding of infectious disease biology and prevention, the conditions that select for the establishment and maintenance of microbial virulence remain enigmatic. To address this aspect of pathogen biology, we focus on two members of the Staphylococcus genus - Staphylococcus aureus and Staphylococcus epidermidis - and consider why S. aureus has evolved to become more virulent than S. epidermidis. Several hypotheses to explain this phenomenon are discussed and a mathematical model is used to argue that a complex transmission pathway is the key factor in explaining the evolution and maintenance of virulence in S. aureus. In the case of S. epidermidis, where skin contact affords easier transmission between hosts, high levels of virulence do not offer an advantage to this pathogen.     

Pines and oaks in the restoration of Mediterranean landscapes of Spain: New perspectives for an old practice — a review

Pines have been extensively used for land restoration in the Mediterranean basin and in other parts of the world, since the late 19^th century. The theoretical basis supporting pine utilisation was its stress-tolerant and pioneer features, and their attributed role of facilitating the development of late-successional hardwoods in the long-term. In the present work, the use of pines and hardwoods in forest restoration is discussed in the frame of the current disturbance regime and social demands for Mediterranean forests. Large pine plantations have recently disappeared because of their sensitivity to fire (e.g., Pinus nigra) or because of the short fire-intervals (e.g., Pinus halepensis). Combined pine and oak plantations are proposed for degraded land restoration on the basis of the complementary features of both groups of species. Seeding and containerised seedling plantation, soil amendments and plantation techniques to reduce transplant shock are evaluated for reforestation under water-stressing conditions, on the basis of several experiments performed in eastern Spain. Both P. halepensis and Quercus ilex are tested.     

When considering no man is an island—assessing bioenergy systems in a regional and LCA context: a review

Purpose

With many environmental burdens associated with bioenergy production occurring at the regional level, there is a need to produce more regional and spatially representative life cycle assessment of bioenergy systems. On the other hand, such assessments also need to account for the global and cumulative impacts along the full bioenergy life cycle in order to support effective regional policy measures and decision making. Therefore, the challenge is to find a balance. In other words, how should we define the regional context for bioenergy system assessments in order to complement life cycle thinking? The aim of this review is to answer this question by providing an overview of important considerations when assessing bioenergy systems in a regional and LCA context and how these two contexts intersect. It also aims to help guide and orientate LCA practitioners interested in including more regional aspects in their bioenergy studies. Until now, such a review which explores the integration of regional and life cycle contexts in relation to bioenergy systems and their products has not been done.

Methods

As a first step, we define what we mean by the term region. We then look at the potential burdens relating to bioenergy systems and their relationship with the regional context. In a next step, we explore life cycle thinking and the intersection between the regional and LCA contexts by providing some examples from the literature. We then discuss the benefits and limitations of such regionally contextualized life cycle approaches in relation to bioenergy production systems and indeed other alternative biomass uses.

Results and discussion

Three regional contexts were identified to help orientate life cycle thinking aiming to assess the regional and nonregional environmental implications of bioenergy production. These contexts were as follows: “within regional,” “regional and ROW,” and “regionalized.” The added value of implementing a regionally contextualized life cycle approach is the ability, therefore, to include greater regional and spatial details in the assessments of bioenergy production systems, without losing the links to the diversity of global supply chains. Thus, providing greater geographical and regional insight into how such potential burdens can be reduced or shifted burdens avoided or how associated regional production activities could be optimized to mitigate such burdens.

Conclusions

The use of different regional contexts as proposed in this paper is not only useful to orientate life cycle thinking in relation to bioenergy systems but also for the assessment of alternative novel bio-based systems.

     

The involvement of cell death and survival in neural tube defects: a distinct role for apoptosis and autophagy?

Neural tube defects (NTDs), such as spina bifida (SB) or exencephaly, are common congenital malformations leading to infant mortality or severe disability. The etiology of NTDs is multifactorial with a strong genetic component. More than 70 NTD mouse models have been reported, suggesting the involvement of distinct pathogenetic mechanisms, including faulty cell death regulation. In this review, we focus on the contribution of functional genomics in elucidating the role of apoptosis and autophagy genes in neurodevelopment. On the basis of compared phenotypical analysis, here we discuss the relative importance of a tuned control of both apoptosome-mediated cell death and basal autophagy for regulating the correct morphogenesis and cell number in developing central nervous system (CNS). The pharmacological modulation of genes involved in these processes may thus represent a novel strategy for interfering with the occurrence of NTDs.