Zhejiang A & F University

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.

Phenolic compounds are an important class of plant secondary metabolites which play crucial physiological roles throughout the plant life cycle. Phenolics are produced under optimal and suboptimal conditions in plants and play key roles in developmental processes like cell division, hormonal regulation, photosynthetic activity, nutrient mineralization, and reproduction. Plants exhibit increased synthesis of polyphenols such as phenolic acids and flavonoids under abiotic stress conditions, which help the plant to cope with environmental constraints. Phenylpropanoid biosynthetic pathway is activated under abiotic stress conditions (drought, heavy metal, salinity, high/low temperature, and ultraviolet radiations) resulting in accumulation of various phenolic compounds which, among other roles, have the potential to scavenge harmful reactive oxygen species. Deepening the research focuses on the phenolic responses to abiotic stress is of great interest for the scientific community. In the present article, we discuss the biochemical and molecular mechanisms related to the activation of phenylpropanoid metabolism and we describe phenolic-mediated stress tolerance in plants. An attempt has been made to provide updated and brand-new information about the response of phenolics under a challenging environment.

The continental bio-cycling of silicon (Si) plays a key role in global Si cycle and as such partly controls global carbon (C) budget through nutrition of marine and terrestrial biota, accumulation of phytolith-occluded organic carbon (PhytOC) and weathering of silicate minerals. Despite the key role of elemental composition of phytoliths on their solubility in soils, the impact of plant cultivar and organ on the elemental composition of phytoliths in Si high-accumulator plants, such as rice (Oryza sativa) is not yet fully understood. Here we show that rice cultivar significantly impacts the elemental composition of phytoliths (Si, Al, Fe and C) in different organs of the shoot system (grains, sheath, leaf and stem). The amount of occluded OC within phytoliths is affected by contents of Si, Al and Fe in plants, while independent of the element composition of phytoliths. Our data document, for different cultivars, higher bio-available Si release from phytoliths of leaves and sheaths, which are characterized by higher enrichment with Al and Fe (i.e., lower Si/Al and Si/Fe ratios), compared to grains and stems. We indicate that phytolith solubility in soils may be controlled by rice cultivar and type of organs. Our results highlight that the role of the morphology, the hydration rate and the chemical composition in the solubility of phytoliths and the kinetic release of Si in soil solution needs to be studied further. This is central to a better understanding of the impact of soil amendment with different plant organs and cultivars on soil OC stock and on the delivery of dissolved Si as we show that sheath and leaf rice organs are both characterized by higher content of OC occluded in phytolith and higher phytolith solubility compared to grains and stems. Our study shows the importance of studying the impact of the agro-management on the evolution of sinks and sources of Si and C in soils used for Si-high accumulator plants.

Pharmaceuticals and personal care products (PPCPs) which contain diverse organic groups, such as antibiotics, hormones, antimicrobial agents, synthetic musks, etc., have raised significant concerns in recently years for their persistent input and potential threat to ecological environment and human health. China is a large country with high production and consumption of PPCPs for its economic development and population growth in recent years. This may result in PPCP contamination in different environmental media of China. This review summarizes the current contamination status of different environment media, including sewage, surface water, sludge, sediments, soil, and wild animals, in China by PPCPs. The human body burden and adverse effects derived from PPCPs are also evaluated. Based on this review, it has been concluded that more contamination information of aquatic environment and wildlife as well as human body burden of PPCPs in different areas of China is urgent. Studies about their environmental behavior and control technologies need to be conducted, and acute and chronic toxicities of different PPCP groups should be investigated for assessing their potential ecological and health risks.

The NLRP3 inflammasome is a multimeric protein complex that initiates an inflammatory form of cell death and triggers the release of proinflammatory cytokines IL-1β and IL-18. The NLRP3 inflammasome has been implicated in a wide range of diseases, including Alzheimer's disease, Prion diseases, type 2 diabetes, and some infectious diseases. It has been found that a variety of stimuli including danger-associated molecular patterns (DAMPs, such as silica and uric acid crystals) and pathogen-associated molecular patterns (PAMPs) can activate NLRP3 inflammasome, but the specific regulatory mechanisms of NLRP3 inflammasome activation remain unclear. Understanding the mechanisms of NLRP3 activation will enable the development of its specific inhibitors to treat NLRP3-related diseases. In this review, we summarize current understanding of the regulatory mechanisms of NLRP3 inflammasome activation as well as inhibitors that specifically and directly target NLRP3.

Invariably, many agricultural soils of the world are deficient in one or more of the essential nutrients needed to support healthy plants. Acidity, alkalinity, salinity, anthropogenic processes, nature of farming, and erosion can lead to soil degradation. Additions of fertilizers and/or amendments are essential for a proper nutrient supply and maximum yields. Estimates of overall efficiency of applied fertilizer have been reported to be about or lower than 50% for N, less than 10% for P, and about 40% for K. Plants that are efficient in absorption and utilization of nutrients greatly enhance the efficiency of applied fertilizers, reducing cost of inputs, and preventing losses of nutrients to ecosystems. Inter- and intra-specific variation for plant growth and mineral nutrient use efficiency(NUE) are known to be under genetic and physiological control and are modified by plant interactions with environmental variables. There is need for breeding programs to focus on developing cultivars with high NUE. Identification of traits such as nutrient absorption, transport, utilization, and mobilization in plant cultivars should greatly enhance fertilizer use efficiency. The development of new cultivars with higher NUE, coupled with best management practices (BMPs) will contribute to sustainable agricultural systems that protect and promote soil, water and air quality.

With a pace of about twice the observed rate of global warming, the temperature on the Qinghai-Tibetan Plateau (Earth's 'third pole') has increased by 0.2 °C per decade over the past 50 years, which results in significant permafrost thawing and glacier retreat. Our review suggested that warming enhanced net primary production and soil respiration, decreased methane (CH(4)) emissions from wetlands and increased CH(4) consumption of meadows, but might increase CH(4) emissions from lakes. Warming-induced permafrost thawing and glaciers melting would also result in substantial emission of old carbon dioxide (CO(2)) and CH(4). Nitrous oxide (N(2)O) emission was not stimulated by warming itself, but might be slightly enhanced by wetting. However, there are many uncertainties in such biogeochemical cycles under climate change. Human activities (e.g. grazing, land cover changes) further modified the biogeochemical cycles and amplified such uncertainties on the plateau. If the projected warming and wetting continues, the future biogeochemical cycles will be more complicated. So facing research in this field is an ongoing challenge of integrating field observations with process-based ecosystem models to predict the impacts of future climate change and human activities at various temporal and spatial scales. To reduce the uncertainties and to improve the precision of the predictions of the impacts of climate change and human activities on biogeochemical cycles, efforts should focus on conducting more field observation studies, integrating data within improved models, and developing new knowledge about coupling among carbon, nitrogen, and phosphorus biogeochemical cycles as well as about the role of microbes in these cycles.

Water is polluted by increasing activities of population and the necessity to provide them with goods and services that use water as a vital resource. The contamination of water due to heavy metals (HMs) is a big concern for humankind; however, global studies related to this topic are scarce. Thus, the current review assesses the content of HMs in surface water bodies throughout the world from 1994 to 2019. To achieve this goal, multivariate analyses were applied in order to determine the possible sources of HMs. Among the analyzed HMs in a total of 147 publications, the average content of Cr, Mn, Co, Ni, As and Cd exceeded the permissible limits suggested by WHO and USEPA. The results of the heavy metal pollution index, evaluation index, the degree of contamination, water pollution and toxicity load showed that the examined water bodies are highly polluted by HMs. The results of median lethal toxicity index showed maximum toxicity in As, Co, Cr and Ni in the surface water bodies. Results of ingestion and dermal pathways for adults and children in the current analyzed review showed that As is the major contaminant. Moreover, Cr, Ni, As and Cd showed values that could be considered as a high risk for cancer generation via the ingestion pathway as compared to the dermal route. It is recommended that remediation techniques such as the introduction of aquatic phytoremediation plant species and adsorbents should be included in land management plans in order to reduce human risks.

Polyamines (PAs) are low molecular weight aliphatic nitrogenous bases containing two or more amino groups. They are produced by organisms during metabolism and are present in almost all cells. Because they play important roles in diverse plant growth and developmental processes and in environmental stress responses, they are considered as a new kind of plant biostimulant. With the development of molecular biotechnology techniques, there is increasing evidence that PAs, whether applied exogenously or produced endogenously via genetic engineering, can positively affect plant growth, productivity, and stress tolerance. However, it is still not fully understood how PAs regulate plant growth and stress responses. In this review, we attempt to cover these information gaps and provide a comprehensive and critical assessment of the published literature on the relationships between PAs and plant flowering, embryo development, senescence, and responses to several (mainly abiotic) stresses. The aim of this review is to summarize how PAs improve plants' productivity, and to provide a basis for future research on the mechanism of action of PAs in plant growth and development. Future perspectives for PA research are also suggested.

Remote sensing-based methods of aboveground biomass (AGB) estimation in forest ecosystems have gained increased attention, and substantial research has been conducted in the past three decades. This paper provides a survey of current biomass estimation methods using remote sensing data and discusses four critical issues – collection of field-based biomass reference data, extraction and selection of suitable variables from remote sensing data, identification of proper algorithms to develop biomass estimation models, and uncertainty analysis to refine the estimation procedure. Additionally, we discuss the impacts of scales on biomass estimation performance and describe a general biomass estimation procedure. Although optical sensor and radar data have been primary sources for AGB estimation, data saturation is an important factor resulting in estimation uncertainty. LIght Detection and Ranging (lidar) can remove data saturation, but limited availability of lidar data prevents its extensive application. This literature survey has indicated the limitations of using single-sensor data for biomass estimation and the importance of integrating multi-sensor/scale remote sensing data to produce accurate estimates over large areas. More research is needed to extract a vertical vegetation structure (e.g. canopy height) from interferometry synthetic aperture radar (InSAR) or optical stereo images to incorporate it into horizontal structures (e.g. canopy cover) in biomass estimation modeling.

The massive consumption of a wide range plastic products has generated a huge amount of plastic waste. There is a need to provide awareness of their uses and routine management as a part of our lifestyle. Nowadays, plastics are increasingly being used in our daily life activities, including the packaging in different food and brewing companies, cosmetics, pharmaceutical, and other production sectors need to pack their end products for efficient and safer product's delivery to the community. Plastics are produced through the biochemical process of polymerization or polycondensation. The post-use of generated plastic waste has many adverse impacts on the environment if not processed and managed in a proper way. This review aims to discuss the lifecycle of plastic products according to their different categories, including polyvinyl chloride (PVC–U), polystyrene or styrofoam (PS), polypropylene (PP), high-density polyethylene (HDPE), polyethylene terephthalate (PETE), and others. Herein, we have also discussed the problems caused by the inadequate processing of plastic waste and the possible solutions that can be provided to ensure a good atmosphere and to reduce the causes of climate changes, which is challenging to life on this planet.

Plants face a variety of abiotic stresses, which generate reactive oxygen species (ROS), and ultimately obstruct normal growth and development of plants. To prevent cellular damage caused by oxidative stress, plants accumulate certain compatible solutes known as osmolytes to safeguard the cellular machinery. The most common osmolytes that play crucial role in osmoregulation are proline, glycine-betaine, polyamines, and sugars. These compounds stabilize the osmotic differences between surroundings of cell and the cytosol. Besides, they also protect the plant cells from oxidative stress by inhibiting the production of harmful ROS like hydroxyl ions, superoxide ions, hydrogen peroxide, and other free radicals. The accumulation of osmolytes is further modulated by phytohormones like abscisic acid, brassinosteroids, cytokinins, ethylene, jasmonates, and salicylic acid. It is thus important to understand the mechanisms regulating the phytohormone-mediated accumulation of osmolytes in plants during abiotic stresses. In this review, we have discussed the underlying mechanisms of phytohormone-regulated osmolyte accumulation along with their various functions in plants under stress conditions.

The plant-Trichoderma-pathogen triangle is a complicated web of numerous processes. Trichoderma spp. are avirulent opportunistic plant symbionts. In addition to being successful plant symbiotic organisms, Trichoderma spp. also behave as a low cost, effective and ecofriendly biocontrol agent. They can set themselves up in various patho-systems, have minimal impact on the soil equilibrium and do not impair useful organisms that contribute to the control of pathogens. This symbiotic association in plants leads to the acquisition of plant resistance to pathogens, improves developmental processes and yields and promotes absorption of nutrient and fertilizer use efficiency. Among other biocontrol mechanisms, antibiosis, competition and mycoparasitism are among the main features through which microorganisms, including Thrichoderma, react to the presence of other competitive pathogenic organisms, thereby preventing or obstructing their development. Stimulation of every process involves the biosynthesis of targeted metabolites like plant growth regulators, enzymes, siderophores, antibiotics, etc. This review summarizes the biological control activity exerted by Trichoderma spp. and sheds light on the recent progress in pinpointing the ecological significance of Trichoderma at the biochemical and molecular level in the rhizosphere as well as the benefits of symbiosis to the plant host in terms of physiological and biochemical mechanisms. From an applicative point of view, the evidence provided herein strongly supports the possibility to use Trichoderma as a safe, ecofriendly and effective biocontrol agent for different crop species.

Biochar is produced as a charred material with high surface area and abundant functional groups by pyrolysis, which refers to the process of thermochemical decomposition of organic material at elevated temperatures in the absence of oxygen. The carbon component in biochar is relatively stable, and, hence, biochar was originally proposed as a soil amendment to store carbon in the soil. Biochar has multifunctional values that include the use of it for the following purposes: soil amendment to improve soil health, nutrient and microbial carrier, immobilising agent for remediation of toxic metals and organic contaminants in soil and water, catalyst for industrial applications, porous material for mitigating greenhouse gas emissions and odorous compounds, and feed supplement to improve animal health and nutrient intake efficiency and, thus, productivity. This article provides for the first time an overview of the multifunctional values and unintended consequences of biochar applications.

It has always been critical to develop high-performance polymeric materials with exceptional mechanical strength and toughness, thermal stability, and even healable properties for meeting performance requirements in industry. Conventional chemical cross-linking leads to enhanced mechanical strength and thermostability at the expense of extensibility due to mutually exclusive mechanisms. Such major challenges have recently been addressed by using noncovalent cross-linking of reversible multiple hydrogen-bonds (H-bonds) that widely exist in biological materials, such as silk and muscle. Recent decades have witnessed the development of many tailor-made high-performance H-bond cross-linked polymeric materials. Here, recent advances in H-bond cross-linking strategies are reviewed for creating high-performance polymeric materials. H-bond cross-linking of polymers can be realized via i) self-association of interchain multiple H-bonding interactions or specific H-bond cross-linking motifs, such as 2-ureido-4-pyrimidone units with self-complementary quadruple H-bonds and ii) addition of external cross-linkers, including small molecules, nanoparticles, and polymer aggregates. The resultant cross-linked polymers normally exhibit tunable high strength, large extensibility, improved thermostability, and healable capability. Such performance portfolios enable these advanced polymers to find many significant cutting-edge applications. Major challenges facing existing H-bond cross-linking strategies are discussed, and some promising approaches for designing H-bond cross-linked polymeric materials in the future are also proposed.

Plants are often exposed to unfavorable environmental conditions, for instance abiotic stresses, which dramatically alter distribution of plant species among ecological niches and limit the yields of crop species. Among these, drought stress is one of the most impacting factors which alter seriously the plant physiology, finally leading to the decline of the crop productivity. Drought stress causes in plants a set of morpho-anatomical, physiological and biochemical changes, mainly addressed to limit the loss of water by transpiration with the attempt to increase the plant water use efficiency. The stomata closure, one of the first consistent reactions observed under drought, results in a series of consequent physiological/biochemical adjustments aimed at balancing the photosynthetic process as well as at enhancing the plant defense barriers against drought-promoted stress (e.g., stimulation of antioxidant systems, accumulation of osmolytes and stimulation of aquaporin synthesis), all representing an attempt by the plant to overcome the unfavorable period of limited water availability. In view of the severe changes in water availability imposed by climate change factors and considering the increasing human population, it is therefore of outmost importance to highlight: (i) how plants react to drought; (ii) the mechanisms of tolerance exhibited by some species/cultivars; and (iii) the techniques aimed at increasing the tolerance of crop species against limited water availability. All these aspects are necessary to respond to the continuously increasing demand for food, which unfortunately parallels the loss of arable land due to changes in rainfall dynamics and prolonged period of drought provoked by climate change factors. This review summarizes the most updated findings on the impact of drought stress on plant morphological, biochemical and physiological features and highlights plant mechanisms of tolerance which could be exploited to increase the plant capability to survive under limited water availability. In addition, possible applicative strategies to help the plant in counteracting unfavorable drought periods are also discussed.

Recently, biochar has received significant attention, especially for the removal of potentially toxic elements (PTEs) from water and wastewater. No review has been focused on the potential use of wood-based biochar (WB) for the removal of PTEs in water and wastewater. Here, we have critically reviewed the (i) preparation and characterisation of WB; (ii) removal efficiency of WB for PTEs in water with respect to its physicochemical characteristics, biochar/water ratio, pH, and sorption system; (iii) removal mechanisms of PTEs by WB; (iv) fate of the sorbed PTEs onto WB; and (v) recovery of the sorbed PTEs from the resultant sludge of WB. We also discussed the removal of PTEs by engineered/designer WB as compared to pristine WB. This review demonstrates the overarching scientific opportunities for a comprehensive understanding of using WB as an emerging biosorbent and a promising low-cost and effective material for the remediation of PTEs contaminated water.

It has long been established that premature leaf senescence negatively impacts the yield stability of rice, but the underlying molecular mechanism driving this relationship remains largely unknown. Here, we identified a dominant premature leaf senescence mutant, prematurely senile 1 (ps1-D). PS1 encodes a plant-specific NAC (no apical meristem, Arabidopsis ATAF1/2, and cup-shaped cotyledon2) transcriptional activator, Oryza sativa NAC-like, activated by apetala3/pistillata (OsNAP). Overexpression of OsNAP significantly promoted senescence, whereas knockdown of OsNAP produced a marked delay of senescence, confirming the role of this gene in the development of rice senescence. OsNAP expression was tightly linked with the onset of leaf senescence in an age-dependent manner. Similarly, ChIP-PCR and yeast one-hybrid assays demonstrated that OsNAP positively regulates leaf senescence by directly targeting genes related to chlorophyll degradation and nutrient transport and other genes associated with senescence, suggesting that OsNAP is an ideal marker of senescence onset in rice. Further analysis determined that OsNAP is induced specifically by abscisic acid (ABA), whereas its expression is repressed in both aba1 and aba2, two ABA biosynthetic mutants. Moreover, ABA content is reduced significantly in ps1-D mutants, indicating a feedback repression of OsNAP on ABA biosynthesis. Our data suggest that OsNAP serves as an important link between ABA and leaf senescence. Additionally, reduced OsNAP expression leads to delayed leaf senescence and an extended grain-filling period, resulting in a 6.3% and 10.3% increase in the grain yield of two independent representative RNAi lines, respectively. Thus, fine-tuning OsNAP expression should be a useful strategy for improving rice yield in the future.

In this work, torrefaction of hemicellulose, cellulose, and lignin were studied at a series of torrefaction temperatures (210, 240, 270, and 300 °C) based on the properties of their three-phase products, namely solid, liquid (water and tar), and gaseous products. Among the three biomass components, significant difference of torrefaction characteristics was found due to their different molecular structures. For the solid product, hemicellulose presented lowest yield from 85.65% to 41.54% as the temperature increased because of the poor thermostability, thereby showing obvious variations in carbon and oxygen contents. For the gaseous product, CO2, followed by CO, were the dominant gaseous components in all torrefaction conditions including different feedstock and temperatures; also a small number of other components (H2 and CH4) were produced during torrefaction of lignin. The liquid product was composed of water and a small amount of tar. For the tar product, acids and ketones were the dominant components in the torrefaction of hemicellulose, while anhydrosugar in the torrefaction of cellulose, and phenols in the torrefaction of lignin. As the temperature increased from 210 °C to 300 °C, about 19.76–71.11%, 5.85–33.27%, and 16.28–44.89% of oxygen from hemicellulose, cellulose, and lignin, respectively, was transformed into the liquid and gaseous products. Dehydration reaction and volatilization of the oxygenated gaseous product were the two dominant deoxygenation pathways, and the water, CO2, and CO were the dominant carriers of oxygen migration. In contrast to oxygen, only a small amount of carbon was transferred into tar product, followed by gaseous product, consequently the solid samples still retained most of the energy.

Chromium (Cr) is an element naturally occurring in rocky soils and volcanic dust. It has been classified as a carcinogen agent according to the International Agency for Research on Cancer. Therefore, this metal needs an accurate understanding and thorough investigation in soil-plant systems. Due to its high solubility, Cr (VI) is regarded as a hazardous ion, which contaminates groundwater and can be transferred through the food chain. Cr also negatively impacts the growth of plants by impairing their essential metabolic processes. The toxic effects of Cr are correlated with the generation of reactive oxygen species (ROS), which cause oxidative stress in plants. The current review summarizes the understanding of Cr toxicity in plants via discussing the possible mechanisms involved in its uptake, translocation and sub-cellular distribution, along with its interference with the other plant metabolic processes such as chlorophyll biosynthesis, photosynthesis and plant defensive system.