Warsaw University of Life Sciences

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is thatthere is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure flux through the autophagy pathway (i.e., the completeprocess including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defined as increasedautophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in manycases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as forreviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multipleassays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation, it is imperative to target by gene knockout or RNA interference more than one autophagyrelated protein. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways implying that not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular assays, we hope to encourage technical innovation in the field.

Assessing Biodiversity Declines Understanding human impact on biodiversity depends on sound quantitative projection. Pereira et al. (p. 1496 , published online 26 October) review quantitative scenarios that have been developed for four main areas of concern: species extinctions, species abundances and community structure, habitat loss and degradation, and shifts in the distribution of species and biomes. Declines in biodiversity are projected for the whole of the 21st century in all scenarios, but with a wide range of variation. Hoffmann et al. (p. 1503 , published online 26 October) draw on the results of five decades' worth of data collection, managed by the International Union for Conservation of Nature Species Survival Commission. A comprehensive synthesis of the conservation status of the world's vertebrates, based on an analysis of 25,780 species (approximately half of total vertebrate diversity), is presented: Approximately 20% of all vertebrate species are at risk of extinction in the wild, and 11% of threatened birds and 17% of threatened mammals have moved closer to extinction over time. Despite these trends, overall declines would have been significantly worse in the absence of conservation actions.

The biodiversity-productivity relationship (BPR) is foundational to our understanding of the global extinction crisis and its impacts on ecosystem functioning. Understanding BPR is critical for the accurate valuation and effective conservation of biodiversity. Using ground-sourced data from 777,126 permanent plots, spanning 44 countries and most terrestrial biomes, we reveal a globally consistent positive concave-down BPR, showing that continued biodiversity loss would result in an accelerating decline in forest productivity worldwide. The value of biodiversity in maintaining commercial forest productivity alone-US$166 billion to 490 billion per year according to our estimation-is more than twice what it would cost to implement effective global conservation. This highlights the need for a worldwide reassessment of biodiversity values, forest management strategies, and conservation priorities.

Plants living under natural conditions are exposed to many adverse factors that interfere with the photosynthetic process, leading to declines in growth, development, and yield. The recent development of Chlorophyll a fluorescence (ChlF) represents a potentially valuable new approach to study the photochemical efficiency of leaves. Specifically, the analysis of fluorescence signals provides detailed information on the status and function of Photosystem II (PSII) reaction centers, light-harvesting antenna complexes, and both the donor and acceptor sides of PSII. Here, we review the results of fast ChlF analyses of photosynthetic responses to environmental stresses, and discuss the potential scientific and practical applications of this innovative methodology. The recent availability of portable devices has significantly expanded the potential utilization of ChlF techniques, especially for the purposes of crop phenotyping and monitoring.

L. (turmeric) rhizome, has been used for centuries for culinary and food coloring purposes, and as an ingredient for various medicinal preparations, widely used in Ayurveda and Chinese medicine. In recent decades, their biological activities have been extensively studied. Thus, this review aims to offer an in-depth discussion of curcumin applications for food and biotechnological industries, and on health promotion and disease prevention, with particular emphasis on its antioxidant, anti-inflammatory, neuroprotective, anticancer, hepatoprotective, and cardioprotective effects. Bioavailability, bioefficacy and safety features, side effects, and quality parameters of curcumin are also addressed. Finally, curcumin's multidimensional applications, food attractiveness optimization, agro-industrial procedures to offset its instability and low bioavailability, health concerns, and upcoming strategies for clinical application are also covered.

OBJECTIVE: Ageing is accompanied by deterioration of multiple bodily functions and inflammation, which collectively contribute to frailty. We and others have shown that frailty co-varies with alterations in the gut microbiota in a manner accelerated by consumption of a restricted diversity diet. The Mediterranean diet (MedDiet) is associated with health. In the NU-AGE project, we investigated if a 1-year MedDiet intervention could alter the gut microbiota and reduce frailty. DESIGN: We profiled the gut microbiota in 612 non-frail or pre-frail subjects across five European countries (UK, France, Netherlands, Italy and Poland) before and after the administration of a 12-month long MedDiet intervention tailored to elderly subjects (NU-AGE diet). RESULTS: Adherence to the diet was associated with specific microbiome alterations. Taxa enriched by adherence to the diet were positively associated with several markers of lower frailty and improved cognitive function, and negatively associated with inflammatory markers including C-reactive protein and interleukin-17. Analysis of the inferred microbial metabolite profiles indicated that the diet-modulated microbiome change was associated with an increase in short/branch chained fatty acid production and lower production of secondary bile acids, p-cresols, ethanol and carbon dioxide. Microbiome ecosystem network analysis showed that the bacterial taxa that responded positively to the MedDiet intervention occupy keystone interaction positions, whereas frailty-associated taxa are peripheral in the networks. CONCLUSION: Collectively, our findings support the feasibility of improving the habitual diet to modulate the gut microbiota which in turn has the potential to promote healthier ageing.

An increasing need of nanotechnology in various industries may cause a huge environment dispersion of nanoparticles in coming years. A concern about nanoparticles interaction with flora and fauna is raised due to a growing load of it in the environment. In recent years, several investigators have shown impact of nanoparticles on plant growth and their accumulation in food source. This review examines the research performed in the last decade to show how metal and metal oxide nanoparticles are influencing the plant metabolism. We addressed here, the impact of nanoparticle on plant in relation to its size, concentration, and exposure methodology. Based on the available reports, we proposed oxidative burst as a general mechanism through which the toxic effects of nanoparticles are spread in plants. This review summarizes the current understanding and the future possibilities of plant-nanoparticle research.

The aim of this educational review is to provide practical information on the hardware, methodology, and the hands on application of chlorophyll (Chl) a fluorescence technology. We present the paper in a question and answer format like frequently asked questions. Although nearly all information on the application of Chl a fluorescence can be found in the literature, it is not always easily accessible. This paper is primarily aimed at scientists who have some experience with the application of Chl a fluorescence but are still in the process of discovering what it all means and how it can be used. Topics discussed are (among other things) the kind of information that can be obtained using different fluorescence techniques, the interpretation of Chl a fluorescence signals, specific applications of these techniques, and practical advice on different subjects, such as on the length of dark adaptation before measurement of the Chl a fluorescence transient. The paper also provides the physiological background for some of the applied procedures. It also serves as a source of reference for experienced scientists.

Butyrate is a natural substance present in biological liquids and tissues. The present paper aims to give an update on the biological role of butyrate in mammals, when it is naturally produced by the gastrointestinal microbiota or orally ingested as a feed additive. Recent data concerning butyrate production delivery as well as absorption by the colonocytes are reported. Butyrate cannot be detected in the peripheral blood, which indicates fast metabolism in the gut wall and/or in the liver. In physiological conditions, the increase in performance in animals could be explained by the increased nutrient digestibility, the stimulation of the digestive enzyme secretions, a modification of intestinal luminal microbiota and an improvement of the epithelial integrity and defence systems. In the digestive tract, butyrate can act directly (upper gastrointestinal tract or hindgut) or indirectly (small intestine) on tissue development and repair. Direct trophic effects have been demonstrated mainly by cell proliferation studies, indicating a faster renewal of necrotic areas. Indirect actions of butyrate are believed to involve the hormono-neuro-immuno system. Butyrate has also been implicated in down-regulation of bacteria virulence, both by direct effects on virulence gene expression and by acting on cell proliferation of the host cells. In animal production, butyrate is a helpful feed additive, especially when ingested soon after birth, as it enhances performance and controls gut health disorders caused by bacterial pathogens. Such effects could be considered for new applications in human nutrition.

Demand for organic foods is partially driven by consumers' perceptions that they are more nutritious. However, scientific opinion is divided on whether there are significant nutritional differences between organic and non-organic foods, and two recent reviews have concluded that there are no differences. In the present study, we carried out meta-analyses based on 343 peer-reviewed publications that indicate statistically significant and meaningful differences in composition between organic and non-organic crops/crop-based foods. Most importantly, the concentrations of a range of antioxidants such as polyphenolics were found to be substantially higher in organic crops/crop-based foods, with those of phenolic acids, flavanones, stilbenes, flavones, flavonols and anthocyanins being an estimated 19 (95 % CI 5, 33) %, 69 (95 % CI 13, 125) %, 28 (95 % CI 12, 44) %, 26 (95 % CI 3, 48) %, 50 (95 % CI 28, 72) % and 51 (95 % CI 17, 86) % higher, respectively. Many of these compounds have previously been linked to a reduced risk of chronic diseases, including CVD and neurodegenerative diseases and certain cancers, in dietary intervention and epidemiological studies. Additionally, the frequency of occurrence of pesticide residues was found to be four times higher in conventional crops, which also contained significantly higher concentrations of the toxic metal Cd. Significant differences were also detected for some other (e.g. minerals and vitamins) compounds. There is evidence that higher antioxidant concentrations and lower Cd concentrations are linked to specific agronomic practices (e.g. non-use of mineral N and P fertilisers, respectively) prescribed in organic farming systems. In conclusion, organic crops, on average, have higher concentrations of antioxidants, lower concentrations of Cd and a lower incidence of pesticide residues than the non-organic comparators across regions and production seasons.

Polycystic ovary syndrome (PCOS) is a one of the most common endocrine disorders, with a prevalence rate of 5-10% in reproductive aged women. It's characterized by (1) chronic anovulation, (2) biochemical and/or clinical hyperandrogenism, and (3) polycystic ovarian morphology. PCOS has significant clinical implications and can lead to health problems related to the accumulation of adipose tissue, such as obesity, insulin resistance, metabolic syndrome, and type 2 diabetes. There is also evidence that PCOS patients are at higher risk of cardiovascular diseases, atherosclerosis, and high blood pressure. Several studies have reported the association between polycystic ovary syndrome (PCOS) and low-grade chronic inflammation. According to known data, inflammatory markers or their gene markers are higher in PCOS patients. Correlations have been found between increased levels of C-reactive protein (CRP), interleukin 18 (IL-18), tumor necrosis factor (TNF-α), interleukin 6 (IL-6), white blood cell count (WBC), monocyte chemoattractant protein-1 (MCP-1) and macrophage inflammatory protein-1α (MIP-1α) in the PCOS women compared with age- and BMI-matched controls. Women with PCOS present also elevated levels of AGEs and increased RAGE (receptor for advanced glycation end products) expression. This chronic inflammatory state is aggravating by obesity and hyperinsulinemia. There are studies describing mutual impact of hyperinsulinemia and obesity, hyperandrogenism, and inflammatory state. Endothelial cell dysfunction may be also triggered by inflammatory cytokines. Many factors involved in oxidative stress, inflammation, and thrombosis were proposed as cardiovascular risk markers showing the endothelial cell damage in PCOS. Those markers include asymmetric dimethylarginine (ADMA), C-reactive protein (CRP), homocysteine, plasminogen activator inhibitor-I (PAI-I), PAI-I activity, vascular endothelial growth factor (VEGF) etc. It was also proposed that the uterine hyperinflammatory state in polycystic ovary syndrome may be responsible for significant pregnancy complications ranging from miscarriage to placental insufficiency. In this review, we discuss the most importance evidence concerning the role of the process of chronic inflammation in pathogenesis of PCOS.

The systemic response of plants to pathogen infection (systemic acquired resistance [SAR]), or wounding has been extensively studied with a network of numerous compounds and signals implicated (for review, see Dempsey and Klessig, 2012; Shah and Zeier, 2013). In recent years a new type of systemic response, termed systemic acquired acclimation (SAA), has emerged as an important acclimation response of plants to abiotic stresses (e.g. Karpiński et al., 1999; Szechyńska-Hebda et al., 2010; Suzuki et al., 2013). This response is characterized by a rapid spread of the systemic signal(s) that can reach the systemic tissue within minutes from the application of abiotic stress to a local tissue. A number of different signaling mechanisms were implicated in this response, including the reactive oxygen species (ROS) wave (Miller et al., 2009), the calcium (Ca2+) wave (Choi et al., 2014), and electric signals (Szechyńska-Hebda et al., 2010). In this review we will focus on recent findings regarding each of these signals, as well as their integration, and attempt to propose a model for the propagation of rapid systemic signals during SAA and SAR. Due to space limitations, we will not address many other important aspects of ROS signaling that have been covered by a number of recent excellent reviews (for review, see Foyer and Noctor, 2013; Vaahtera et al., 2014; Considine et al., 2015; Dietz, 2015; Mignolet-Spruyt et al., 2016). The ROS wave is an autopropagating wave of ROS production mediated via RESPIRATORY BURST OXIDASE HOMOLOG D (RBOHD) activation in each cell along its systemic path (Fig. 1). It was initially discovered by Miller et al. (2009), and was extensively reviewed by Mittler et al. (2011), Gilroy et al. (2014), and Mittler and Blumwald (2015). It can reach rates of up to 8.4 cm/min and is directly linked to the calcium wave (for review, see Gilroy et al., 2014) and possibly to electric signals (Suzuki et al., 2013; Fig. 2). It is required for SAA, but by itself it likely does not convey specificity to the systemic response of plants to different abiotic stresses (Suzuki et al., 2013; for review, see Mittler et al., 2011). The ROS wave is currently thought to be integrated with additional metabolic/signaling pathways and to enable rapid SAA responses and acclimation of plants, improving their overall fitness (Suzuki et al., 2013; for review, see Mittler et al., 2011; Mittler and Blumwald, 2015). Activation of the ROS wave by a local heat stress was shown, for example, to enhance the acclimation of systemic tissues to heat stress, and to be regulated by temporal and special interactions with ABA signaling (Suzuki et al., 2013; for review, see Mittler and Blumwald, 2015). In addition, local application of high light resulted in the activation of a ROS wave that enabled systemic tissues to withstand light stress, and was accompanied by the accumulation of photorespiratory amino acids, including Gly and Ser, in nonstressed systemic tissues (Suzuki et al., 2013). Integration of the ROS, Ca2+, and electric waves in and between cells via the function of RBOH proteins and superoxide dismutases (SODs; yellow), Ca2+-dependent protein kinases (CPK/CBL-CIPKs; green), calcium channels such as TPC1 and H2O2-activated plasma membrane calcium channels (red), and GLRs and/or plasma membrane H2O2 channels (blue). Activation of RBOHD is shown to be mediated by CPK/CBL-CIPKs, Cys-rich receptor kinases (CRKs), or directly by Ca2+. Activation of Ca2+ channels is shown to be mediated by H2O2 or by calcium via calcium-induced calcium release. Activation of GLRs is proposed to be mediated by H2O2 and/or calcium levels via calcium-induced calcium release. The level of ROS in cells is proposed to be regulated by NO-ROS and NO-RBOH interactions, retrograde signaling, and ROS removal/production in the chloroplast (Cp), mitochondria (Mt), and peroxisomes (Px). The regulation of gene expression in the nuclei is shown to be mediated via redox/ROS changes, LESION SIMULATING DISEASE1 (LSD), ENHANCED DISEASE SUSCEPTIBILITY1 (EDS), MITOGEN-ACTIVATED PROTEIN KINASEs (MPKs), WRKY, and RRTF1. The electric signal is depicted as a sinus-like wave that travels along the plasma membrane and through the plasmodesmata (PD). Copropagation of the ROS, calcium, hydraulic, and electric waves during rapid systemic signaling. The ROS wave is shown as a series of red arrows, the calcium wave is shown as a dashed green arrow, the hydraulic wave is shown as a dotted blue arrow, and the electric wave is shown as a dotted black arrow. Different sections along the path of the signal (yellow arrows) are also shown to have alternating levels of NPQ and ROS/APX1 levels, and JA is shown to accumulate in cells along the systemic path. The local tissue is shown to have alterations in ROS, calcium, and membrane depolarization potential, and the systemic tissue is shown to have accumulation of ROS and abscisic acid (ABA). Black arrows indicate accumulation or suppression in the level of a particular chemical or transcript/protein, and dashed, dotted, and wide red arrows indicate direction of the signal. The integration of different signaling pathways with ROS-dependent systemic responses has been extensively studied during pathogen-induced SAR, and research focusing on phloem-mobile SAR signals have identified several biologically active molecules, including methyl salicylate, a glycerol-3-P (G3P) derivative, a lipid-transfer protein (DIR1), azelaic acid (AzA), dehydroabietinal, jasmonic acid (JA), and pipecolic acid (Návarová et al., 2012; for review, see Dempsey and Klessig, 2012; Shah and Zeier, 2013). Among these, methyl salicylate, AzA, dehydroabietinal, and G3P were shown to induce SAR when applied to local tissues (Kachroo and Robin, 2013), and JA was shown to rapidly accumulate throughout the path of the systemic signal (Glauser et al., 2009). Recent studies demonstrated that the synthesis of these molecules could be regulated by ROS. Therefore, Arabidopsis (Arabidopsis thaliana) plants deficient in RBOHD or RBOHF showed lower accumulation of AzA and G3P, and exogenous application of G3P was able to rescue SAR in these plants (for review, see Wang et al., 2014). These findings could suggest that the ROS wave is also activated during SAR. Some of the most recent findings in SAR that may shed more light on how the ROS wave is mediated during SAA come from recent studies that focused on the interdependence of ROS signaling on nitric oxide (NO). The noa1/nia1 double mutant, deficient in NO accumulation, showed, for example, a fully compromised SAR accompanied by lower ROS accumulation in systemic tissues, that could be rescued by exogenous application of H2O2 (for review, see Wang et al., 2014). In addition, RBOHD was shown to be up-regulated through an NO-dependent process elicited by oligogalacturonides in response to pathogen attack (Rasul et al., 2012). Although these findings indicated that ROS could act downstream to NO in the SAR pathway, Arabidopsis deficient in RBOHD or RBOHF were unable to accumulate NO in response to pathogen attack (for review, see Wang et al., 2014; Wendehenne et al., 2014), suggesting that NO and ROS could operate in a feedback loop (Fig. 1). NO can react with reduced glutathione, by an S-nitrosylation reaction, to form S-nitrosoglutathione (GSNO; for review, see Considine et al., 2015; Del Río, 2015), and GSNO could function as a pool of NO ready to be used in ROS-NO interactions during SAR/SAA systemic signaling (Fig. 1). ROS, NO, and GSNO function as master-switches regulating various processes, including the SAR pathway and stomatal responses (for review, see Wang et al., 2014; Mittler and Blumwald, 2015; Considine et al., 2015). NO-dependent redox-based posttranslational modifications, such as addition of a glutathione to a protein Cys thiol in a glutathionylation reaction or a NO moiety to form a S-nitrosothiol, were shown to act as regulators of different processes (for review, see Zaffagnini et al., 2012; Considine et al., 2015), and these could also function during SAR or SAA to amplify or dampen the signal. In contrast to the up-regulation of RBOHD through an NO-dependent process enhanced by oligogalacturonides (Rasul et al., 2012), S-nitrosylation of RBOHD at Cys-890 was found to inhibit its enzymatic activity by impeding FAD binding (Yun et al., 2011), indicating a possible dual role for NO in the regulation of RBOHD. NO-mediated S-nitrosylation was also shown to inhibit ROS scavenging enzymes such as catalase and ascorbate peroxidase (Ortega-Galisteo et al., 2012; de Pinto et al., 2013), suggesting that NO could also promote an increase in H2O2 by reducing its decay (Suzuki et al., 2013). Moreover, glutaredoxin S12 in the chloroplast and Gly decarboxylase in the mitochondria were shown to be targets of glutathionylation, and these posttranslational modifications might also contribute to the regulation of ROS levels in cells (Palmieri et al., 2010; for review, see Zaffagnini et al., 2012). Although the involvement of NO in SAA has not been thoroughly studied, the regulation of RBOHD via NO signaling could implicate NO as a key player in modulating the ROS wave (Fig. 1). Furthermore, peroxisomes, mitochondria, and chloroplasts, known as sources of ROS, were also shown to generate NO that might regulate signal transduction involved in various biological processes (for review, see Del Río, 2015). Recent studies uncovered a possible integration between a hub of regulatory genes involved in programmed cell death, retrograde signaling, and hormone regulation, and ROS-dependent systemic responses to high light stress. Thus, genes such as LESION SIMULATING DISEASE1, ENHANCED DISEASE SUSCEPTIBILITY1, PHYTOALEXIN DEFICIENT4, ETHYLENE INSENSITIVE2, and MITOGEN-ACTIVATED PROTEIN KINASE 4 were shown to play important roles in the simultaneous regulation of SAA via ROS- and salicylic acid-dependent pathways (Mühlenbock et al., 2008; Szechyńska-Hebda et al., 2010; Wituszyńska et al., 2013; Gawroński et al., 2014; for review, see Karpiński et al., 2013; Mignolet-Spruyt et al., 2016). In addition, PHOTOSYSTEM II SUBUNIT S-dependent local and systemic wave-like regulation of nonphotochemical quenching (NPQ) and chlorophyll fluorescence decay time, important dissipation and quenching mechanisms of light absorbed in excess, were also proposed to be dependent on ROS and salicylic acid signaling during SAA (Szechyńska-Hebda et al., 2010; Gawroński et al., 2013, 2014; Ciszak et al., 2015; Fig. 2). Although a possible cross talk between ROS and retrograde signaling involving some of the genes indicated above has been proposed, and could explain how the systemic signal is integrated with redox and photosynthesis/respiration control, further studies are required to uncover how these pathways and the RBOHD-dependent ROS wave are coordinated during SAA and possibly SAR (for review, see Mignolet-Spruyt et al., 2016). For example, it is not clear if retrograde signaling functions downstream to rapid systemic signaling, or whether it is directly involved in attenuating or amplifying the signal. A recent study demonstrated that REDOX RESPONSIVE TRANSCRIPTION FACTOR1 (RRTF1) might function as a key regulator of systemic ROS-dependent responses during high light stress (Matsuo et al., 2015). RRTF1-dependent systemic signaling was shown to be regulated by WRKY transcription factors (Matsuo et al., 2015), whose expression is enhanced during RBOHD-dependent SAA (Miller et al., 2009), but its rate of systemic response is slower than that of the ROS wave. RRTF1 could therefore play a role in the regulation of gene expression downstream to the ROS wave during SAA (Fig. 1). Taken together, SAA might be regulated by a complex network linking NO, retrograde signaling, and RBOH-dependent ROS signaling that could function to amplify or attenuate the systemic signal (Fig. 1). Further studies are of course required to determine the mode of integration of NO and ROS signals in SAA that could be a key aspect of systemic signaling during abiotic stress. Along with ROS, changes in Ca2+ have also been linked to systemic signaling activity throughout the is a regulator involved in a wide of processes and responses to and abiotic stresses (for review, see et al., 2010; and 2014). Ca2+ through has been proposed as of this Ca2+-dependent response network et al., in addition to this for a of Ca2+ signals, is also for the systemic spread of a Ca2+ This Ca2+ to local of such as wounding or stress to responses and 2). Thus, local stress has been shown to a Ca2+ increase that from of local in and in Arabidopsis (Choi et al., 2014; et al., 2014). This Ca2+ through the and cell in the (Choi et al., 2014), but to spread more the et al., 2014). directly with cell can mechanisms to in the and cell wounding and signals et al., 2013; et al., 2014) that are likely to a Ca2+ wave et al., that from to with at of the tissues used for of the signal et al., 2014). signaling in the has been linked to responses (for review, see et al., 2016). of Ca2+ channels at the and to cells has also been proposed as a key player in systemic propagation of Ca2+ linked to these responses et al., also see in et al., 2014). Although the channels involved in the processes above at the level a recent the role of the and channels have to shed some light on mechanisms (Fig. 1). Thus, propagation of and Ca2+ waves are dependent on the by TPC1 (Choi et al., 2014; et al., 2015). in the of this et al., et al., 2011; et al., also to up-regulation of a hormone linked to systemic responses (e.g. et al., the that the regulation of this might be linked to these of systemic response The of a TPC1 Ca2+ response to a of and abiotic stresses when at the level et al., is with a role for this as a systemic of Ca2+ Thus, the spread of Ca2+ increase is in the in response to local and Ca2+ are et al., 2014) or et al., 2015). TPC1 also as an of the complex of interactions we can to contribute to and/or these systemic propagation Thus, in addition to its Ca2+ TPC1 on its may be in Ca2+ et al., 2011; et al., and and and Ca2+ levels are thought to activity through on the et al., for review, see and 2011). In addition, roles for a of other regulatory likely on the from (e.g. and see also in and and ROS et al., 2009), to et al., 2012), proteins et al., and an of interactions that (for review, see and 2011). The of these regulatory mechanisms may in activity a signal increase it to a to rapidly amplify the signal. whether of these other regulators an important role in modulating the Ca2+ wave has to be In addition, TPC1 is to a of including Ca2+ (e.g. and for review, see and 2011; 2011), whether it directly Ca2+ or by modulating other to be In addition to the GLRs have also emerged as key in systemic signaling The GLRs are a of channels et al., 2013; for review, see et al., that linked to rapid signaling. Thus, in and attenuate systemic signaling et al., 2013; et al., 2014; 2016). has been to play a role in the spread of the signal the that the of channels to signal to some and to to the systemic signal can of the and Ca2+ signals does with between of et al., 2015). of likely between but it is of if for example, in response to of a indicating a more in its the spread of the Ca2+ increase in the of the by local of with in the of propagation et al., 2014). such in the pathways of within the or response between different an important to be more fully the double signaling from to it does not in the et al., the of the likely of the systemic signaling The GLRs have binding and are by a of amino (e.g. et al., 2008; et al., 2012). whether such amino acid an important role in their in propagation of systemic signals to be It is also important to that the role for these channels in processes such as regulation et al., and hormone signaling et al., may be on their in systemic signal and functions in signaling will of The of of Ca2+ and other systemic signals has also propagation a hydraulic signal through the could the signal (e.g. et al., 2014). In this a wave of that in act to an Ca2+ to cells or (Fig. This the cell for further and Although Ca2+ are linked to signaling in plants (for review, see and 2013), and an of likely such as et al., 2014), kinases et al., 2014), and the and channels (for review, see et al., have been the possible roles of such and channels in rapid systemic signaling have to be fully Integration of the different waves that rapid systemic signaling during are shown to the as well as a hydraulic wave that in the calcium wave via The calcium and ROS waves are shown to be linked via RBOH and the ROS and electric waves are shown to be linked through RBOHD and and the calcium and electric waves are shown to be linked via channels such as GLRs or The different waves are shown to the propagation of each other and to a response in the systemic tissue. further of proposed of the Ca2+ wave propagation from the of a role for ROS and the in signal These suggest a for propagation of a Ca2+ increase ROS by activation could channels Ca2+ at the plasma Ca2+ channels and in the plasma membrane have been identified at the (e.g. et al., et al., et al., and levels (e.g. the or et al., 2010; et al., 2014; Fig. to the channels to systemic signaling have not been such an Ca2+ has the Ca2+ increase could be through a Ca2+ involving and a loop of RBOH activation further of Ca2+ and propagation to cells (Fig. 1). are known to be by Ca2+-dependent signaling directly through their et al., 2008; et al., and through posttranslational such as Ca2+-dependent protein activity (e.g. et al., 2012; et al., 2013; et al., 2013; et al., 2014; et al., 2014). In such a model ROS and Ca2+ to a whether Ca2+ or ROS of the other of a as the response of ROS production that are linked to ROS-dependent Ca2+ (Fig. 1). to ROS-dependent could a for of the to the wave-like of the Ca2+ changes from cell to For example, the ROS production has elicited rapid to the and the of responses in a slower of ROS to the cell (e.g. through et al., could to of important as et al., and of the signal in that The propagation to cells to a wave-like of the Ca2+ Further regulatory that could contribute to this increase and in Ca2+ are also at in the For example, have been to attenuate Ca2+ in the in et al., 2014). the known between Ca2+, stress response, and NO (for review, see et al., and the above of between ROS, NO, and signaling, of the interactions between these may be a to the systemic signal propagation and signals in plants are et al., by (e.g. and spread rapidly in various plants from a to several by (e.g. through the and regulated by hydraulic (for review, see and and that on the pool and et al., 2009). cell to signals can along the cell membrane likely via plasmodesmata (Fig. 1). between cells via plasmodesmata has been shown in species and Arabidopsis is known the of plasmodesmata that regulate signals is that the of a local on cell membrane could to depolarization of the cell membrane of an cell et al., In resistance be high for signals to than For signal throughout the the are more a pathway to their and plasma membrane In addition, channels that are in the plasma membrane of the are with propagation of by and abiotic stresses (for review, see et al., 2014). may also be involved in systemic signal for example, in wounding the in changes, to changes in the cells that membrane changes via et al., for review, see et al., 2014; et al., 2014). of the signal between and is thought to be mediated by cells (Szechyńska-Hebda et al., 2010; et al., 2013). signal propagation along the tissue in the of was shown by et al., 2014). the of the channels various of signals is currently it was that genes channels could signals et al., 2013; Fig. 1). numerous studies have shown a systemic of signals on various processes in The most are in and These on of et al., 2010). the elicited by are and it was discovered that are required for to be that is able to et al., 2016). additional of in is via regulation of the reaction and et al., 2011). of a was shown to that a of of II and et al., 2014). of on were found in other species such as and et al., 2013). In addition, studies of or pathogen attack indicated that signaling an important role in the of systemic such as the activation of various genes (for review, see and and including JA et al., 2013), and et al., 2010). it was demonstrated that chloroplast ROS, and NPQ play an important role in signaling in plants and Szechyńska-Hebda et al., 2010). signaling was also shown to generate a wave-like systemic in ROS, and and systemic changes in ROS and gene expression were found to be in a contrast to the waves of NPQ changes (Fig. Szechyńska-Hebda et al., 2010). Although changes in light or from light to was found to induce systemic signals that were by Ca2+ and were light (Szechyńska-Hebda et al., 2010; for review, see et al., the involved in and regulating these waves during SAA at (Fig. 1). A number of different waves are proposed to be involved in rapid systemic signaling during SAA and SAR (Fig. and are some of the mechanisms these waves could be and regulate each other (Fig. The integration of the Ca2+ wave with the ROS wave could be mediated via the of such as kinases and RBOHD (Fig. 1). The recent of GLRs as of systemic electric signals et al., 2013; et al., 2014; and the findings that in the of RBOHD electric signaling is (Suzuki et al., could to a between ROS signaling and electric signaling mediated via GLRs and Fig. 1). GLRs could therefore be regulated by interactions and regulate Ca2+ or electric In addition, hydraulic waves that could at the local tissue to wounding (for review, see et al., 2014), rapid changes in stomatal and/or local stress (for review, see Mittler and Blumwald, 2015), could also be or integrated Ca2+ and ROS waves by that Ca2+ and/or ROS production (e.g. et al., 2009). A model could therefore the different waves (Fig. shown in local could directly Ca2+ or a hydraulic wave that be a Ca2+ signal via The Ca2+ wave in be integrated with the ROS wave via the activation of RBOH proteins by Ca2+ binding or RBOH that enhanced ROS production in will further or inhibit Ca2+ channels such as TPC1 and/or plasma membrane The ROS wave could be integrated with the electric wave via activation of GLRs or other channels that will membrane and regulate electric signals could of course further via Ca2+ The Ca2+ wave could be integrated with the electric wave via GLRs and TPC1 in a calcium-induced calcium The waves could therefore amplify and regulate each other and the systemic signal the to the systemic tissue (Fig. It be that the different waves the of an activated between and not the of a particular systemic from cell to the The ROS wave is mediated by the of an RBOH activation between the Ca2+ wave by the of a Ca2+ activation as through regulation of GLRs or and the electric signal is mediated by the of an activation or each of these processes likely a complex of regulators that each the activated cell along the path of the signal on therefore a particular of in response to a signal that is to it by the cells in the production of a signal that is to the cells it in the pathway (Fig. 1). The signal not be the and of the wave could feedback or the course a new activated is within the different cells along the pathway, each of these cells could be a particular or hormone (e.g. JA or et al., Suzuki et al., 2013), or a particular or that more to abiotic stress (e.g. the accumulation of Gly and Suzuki et al., 2013). This autopropagating wave signal therefore be more a of each other the the systemic tissue to a particular that is from cell to cell it the systemic It is possible that the integration of the different signals with to their and specificity to the or that an or signal is for a response in the systemic tissue (Suzuki et al., 2013; for review, see Mittler et al., 2011). Further studies are of course to this important systemic acquired resistance systemic acquired acclimation nitric oxide glycerol-3-P azelaic acid S-nitrosoglutathione nonphotochemical quenching

Using chlorophyll (Chl) a fluorescence many aspects of the photosynthetic apparatus can be studied, both in vitro and, noninvasively, in vivo. Complementary techniques can help to interpret changes in the Chl a fluorescence kinetics. Kalaji et al. (Photosynth Res 122:121-158, 2014a) addressed several questions about instruments, methods and applications based on Chl a fluorescence. Here, additional Chl a fluorescence-related topics are discussed again in a question and answer format. Examples are the effect of connectivity on photochemical quenching, the correction of F V /F M values for PSI fluorescence, the energy partitioning concept, the interpretation of the complementary area, probing the donor side of PSII, the assignment of bands of 77 K fluorescence emission spectra to fluorescence emitters, the relationship between prompt and delayed fluorescence, potential problems when sampling tree canopies, the use of fluorescence parameters in QTL studies, the use of Chl a fluorescence in biosensor

Abstract Silicon (Si) is the second‐most abundant element in the earth's crust. In the pedosphere, however, huge spans of Si contents occur mainly caused by Si redistribution in soil profiles and landscapes. Here, we summarize the current knowledge on the different pools and fluxes of Si in soils and terrestrial biogeosystems. Weathering and subsequent release of soluble Si may lead to (1) secondarily bound Si in newly formed Al silicates, (2) amorphous silica precipitation on surfaces of other minerals, (3) plant uptake, formation of phytogenic Si, and subsequent retranslocation to soils, (4) translocation within soil profiles and formation of new horizons, or (5) translocation out of soils (desilication). The research carried out hitherto focused on the participation of Si in weathering processes, especially in clay neoformation, buffering mechanisms for acids in soils or chemical denudation of landscapes. There are, however, only few investigations on the characteristics and controls of the low‐crystalline, almost pure silica compounds formed during pedogenesis. Further, there is strong demand to improve the knowledge of (micro)biological and rhizosphere processes contributing to Si mobilization, plant uptake, and formation of phytogenic Si in plants, and release due to microbial decomposition. The contribution of the biogenic Si sources to Si redistribution within soil profiles and desilication remains unknown concerning the pools, rates, processes, and driving forces. Comprehensive studies considering soil hydrological, chemical, and biological processes as well as their interactions at the scale of pedons and landscapes are necessary to make up and model the Si balance and to couple terrestrial processes with Si cycle of limnic, fluvial, or marine biogeosystems.

Selenium is a micronutrient that is essential for the proper functioning of all organisms. Studies on the functions of selenium are rapidly developing. This element is a cofactor of many enzymes, for example, glutathione peroxidase or thioredoxin reductase. Insufficient supplementation of this element results in the increased risk of developing many chronic degenerative diseases. Selenium is important for the protection against oxidative stress, demonstrating the highest activity as a free radical scavenger and anti-cancer agent. In food, it is present in organic forms, as exemplified by selenomethionine and selenocysteine. In dietary supplementation, the inorganic forms of selenium (selenite and selenate) are used. Organic compounds are more easily absorbed by human organisms in comparison with inorganic compounds. Currently, selenium is considered an essential trace element of fundamental importance for human health. Extreme selenium deficiencies are widespread among people all over the world. Therefore, it is essential to supplement the deficiency of this micronutrient with selenium-enriched food or yeast cell biomass in the diet.

Particulate matter (PM) is an air contaminant in urban and industrial areas that often exceeds limit values, creating serious problems due to its harmful effects on health. Planting trees and shrubs as air filters is a way to improve air quality in these areas. However,further knowledge on species effectiveness in air purification is essential This study compared four species of tree (Acer campestre L, Fraxinus excelsior L, Platanus x hispanica Mill. ex Muenchh. 'Acerifolia', Tilia cordata Mill.), three species of shrub (Forsythia x intermedia Zabel, Physocarpus opulifolius (L.) Maxim., Spiraea japonica L.), and one climber species (Hedera helix L) that are commonly cultivated along streets in Poland to capture fine, coarse and larger particles from air. Separate gravimetric analyses were performed to quantify PM deposited on surfaces and trapped in waxes. Significant differences were found between the plant species tested. The distribution of different particle size fractions differed between and within species and also between leaf surfaces and in waxes.

At harvest, sunflower (Helianthus annuus L.) seeds are dormant and unable to germinate at temperatures below 15 degrees C. Seed storage in the dry state, known as after-ripening, is associated with an alleviation of embryonic dormancy allowing subsequent germination at suboptimal temperatures. To identify the process by which dormancy is broken during after-ripening, we focused on the role of reactive oxygen species (ROS) in this phenomenon. After-ripening entailed a progressive accumulation of ROS, namely superoxide anions and hydrogen peroxide, in cells of embryonic axes. This accumulation, which was investigated at the cellular level by electron microscopy, occurred concomitantly with lipid peroxidation and oxidation (carbonylation) of specific embryo proteins. Incubation of dormant seeds for 3 h in the presence of hydrogen cyanide (a compound that breaks dormancy) or methylviologen (a ROS-generating compound) also released dormancy and caused the oxidation of a specific set of embryo proteins. From these observations, we propose a novel mechanism for seed dormancy alleviation. This mechanism involves ROS production and targeted changes in protein carbonylation patterns.

This review summarises existing evidence on the impact of organic food on human health. It compares organic vs. conventional food production with respect to parameters important to human health and discusses the potential impact of organic management practices with an emphasis on EU conditions. Organic food consumption may reduce the risk of allergic disease and of overweight and obesity, but the evidence is not conclusive due to likely residual confounding, as consumers of organic food tend to have healthier lifestyles overall. However, animal experiments suggest that identically composed feed from organic or conventional production impacts in different ways on growth and development. In organic agriculture, the use of pesticides is restricted, while residues in conventional fruits and vegetables constitute the main source of human pesticide exposures. Epidemiological studies have reported adverse effects of certain pesticides on children's cognitive development at current levels of exposure, but these data have so far not been applied in formal risk assessments of individual pesticides. Differences in the composition between organic and conventional crops are limited, such as a modestly higher content of phenolic compounds in organic fruit and vegetables, and likely also a lower content of cadmium in organic cereal crops. Organic dairy products, and perhaps also meats, have a higher content of omega-3 fatty acids compared to conventional products. However, these differences are likely of marginal nutritional significance. Of greater concern is the prevalent use of antibiotics in conventional animal production as a key driver of antibiotic resistance in society; antibiotic use is less intensive in organic production. Overall, this review emphasises several documented and likely human health benefits associated with organic food production, and application of such production methods is likely to be beneficial within conventional agriculture, e.g., in integrated pest management.

Freeze-drying, also known as lyophilization, is a process in which water in the form of ice under low pressure is removed from a material by sublimation. This process has found many applications for the production of high quality food and pharmaceuticals. The main steps of the freeze-drying process, such as the freezing of the product and primary and secondary drying, are described in this paper. The problems and mechanisms of each step of the freeze-drying process are also analyzed. The methods necessary for the selection of the primary and secondary end processes are characterized. The review contains a description of the effects of process conditions and the selected physical properties of freeze-dried materials, such as structural properties (shrinkage and density porosity), color, and texture. The study shows that little attention is given to the mechanical properties and texture of freeze-dried materials obtained from different conditions of the lyophilization process.

Selenium is one of the elements classified within the group of micronutrients which are necessary in trace amounts for the proper functioning of organisms. Selenium participates in the protection of cells against excess H₂O₂, in heavy metal detoxification, and regulation of the immune and reproductive systems as well. It also ensures the proper functioning of the thyroid gland. Selenium induces the occurrence of the selenoprotein synthesis process involved in the antioxidant defense mechanism of the organism. Recent years have brought much success in the studies on selenium. Anticarcinogenic properties of selenium against some cancers have been reported. Supplementation is increasingly becoming a solution to this problem. A large number of different supplementation methods are promoting studies in this area. Slight differences in the selenium content can result in excess or deficiency, therefore supplementation has to be done carefully and cautiously.