CROWN ROOTLESS1 binds DNA with a relaxed specificity and activates OsROP and OsbHLH044 genes involved in crown root formation in rice.

In cereals, the root system is mainly composed of post-embryonic shoot-borne roots, named crown roots. The CROWN ROOTLESS1 (CRL1) transcription factor, belonging to the ASYMMETRIC LEAVES2-LIKE/LATERAL ORGAN BOUNDARIES DOMAIN (ASL/LBD) family, is a key regulator of crown root initiation in rice (Oryza sativa). Here, we show that CRL1 can bind, both in vitro and in vivo, not only the LBD-box, a DNA sequence recognized by several ASL/LBD transcription factors, but also another not previously identified DNA motif that was named CRL1-box. Using rice protoplast transient transactivation assays and a set of previously identified CRL1-regulated genes, we confirm that CRL1 transactivates these genes if they possess at least a CRL1-box or an LBD-box in their promoters. In planta, ChIP-qPCR experiments targeting two of these genes that include both a CRL1- and an LBD-box in their promoter show that CRL1 binds preferentially to the LBD-box in these promoter contexts. CRISPR/Cas9-targeted mutation of these two CRL1-regulated genes, which encode a plant Rho GTPase (OsROP) and a basic helix-loop-helix transcription factor (OsbHLH044), show that both promote crown root development. Finally, we show that OsbHLH044 represses a regulatory module, uncovering how CRL1 regulates specific processes during crown root formation.

Prediction of biogas production in anaerobic co-digestion of organic wastes using deep learning models.

Interest in anaerobic co-digestion (AcoD) has increased significantly in recent decades owing to enhanced biogas productivity due to the utilization of different organic wastes, such as food waste and sewage sludge. In this study, a robust AcoD model for biogas prediction is developed using deep learning (DL). We propose a hybrid DL architecture, i.e., DA-LSTM-VSN, wherein a dual-stage-attention (DA)-based long short-term memory (LSTM) network is integrated with variable selection networks (VSNs). To enhance the model predictability, we perform hyperparameter optimization. The model accuracy is validated using long-term AcoD monitoring data measured over two years of municipal wastewater treatment plant operation and then compared with those of two other DL-based models (i.e., DA-LSTM and the standard LSTM). In addition, the feature importance (FI) is analyzed to investigate the relative contribution of input variables to biogas production prediction. Finally, we demonstrate the successful application of the validated DL model to the AcoD process optimization. Results show that the model accuracy improved significantly by incorporating DA into LSTM, i.e., the coefficient of determination (R2) increased from 0.38 to 0.68; however, the R2 can be further increased to 0.76 by combining DA-LSTM with a VSN. For the biogas prediction of the AcoD model, the VSN contributes significantly by employing the discontinuous time series of measurement data on biodegradable organic-associated variables during AcoD. In addition, the VSN allows the AcoD model to be interpretable via FI analysis using its weighted input features. The FI results show that the relative importance is vital to variables associated with food waste leachate, whereas it is marginal for those associated with the primary and chemically assisted sedimentation sludges. In conclusion, the AcoD model proposed herein can be utilized in practical applications as a robust tool because it can provide the optimal sludge conditions to improve biogas production. This is because it facilitates the time-series biogas prediction at the full scale using unprocessed datasets with either missing value imputation or outlier removal.

Pharmaceutical removal at low energy consumption using membrane capacitive deionization.

The performance of the membrane capacitive deionization (MCDI) system was evaluated during the removal of three selected pharmaceuticals, neutral acetaminophen (APAP), cationic atenolol (ATN), and anionic sulfamethoxazole (SMX), in batch experiments (feed solution: 2 mM NaCl and 0.01 mM of each pharmaceutical). Upon charging, the cationic ATN showed the highest removal rate of 97.65 ± 1.71%, followed by anionic SMX (93.22 ± 1.66%) and neutral APAP (68.08 ± 5.24%) due to the difference in electrostatic charge and hydrophobicity. The performance parameters (salt adsorption capacity, specific capacity, and cycling efficiency) and energy factors (specific energy consumption and recoverable energy) were further evaluated over ten consecutive cycles depending on the pharmaceutical addition. A significant decrease in the specific adsorption capacity (from 24.6 to ∼3 mg-NaCl g-1) and specific capacity (from 17.6 to ∼2.5 mAh g-1) were observed mainly due to the shortened charging and discharging time by pharmaceutical adsorption onto the electrode. This shortened charging time also led to an immediate drop in specific energy consumption from 0.41 to 0.04 Wh L-1. Collectively, these findings suggest that MCDI can efficiently remove pharmaceuticals at a low energy demand; however, its performance changes dramatically as the pharmaceuticals are present in the target water.

Influence of natural organic matter on membrane capacitive deionization performance.

Membrane capacitive deionization (MCDI) is a prospective desalination technology that removes ions using an electric potential difference across charged porous carbon electrodes. Natural organic matter (NOM) in feed water could influence the electrochemical process by leading to pore-blockages or forming a cake layer on the ion-exchange membrane-coated porous carbon electrode, thereby hindering ion removal. In this study, we explored the influence of different types of NOM, namely, humic acid (HA) and tannic acid (TA), on the MCDI desalination process for feed waters with inorganic salts (NaCl and CaCl2). HA significantly interfered with the adsorption process and reduced the salt removal rate by up to 68% in the case of NaCl-based feed water. However, the influence of HA on salt removal in the case of CaCl2-based feed water was marginal owing to the formation of a charge-neutralized complex, which was caused by the egg-box effect between Ca2+ and HA. TA reduced removal rates of salts (NaCl and CaCl2) by 37% and 60%, respectively. This is because of the lower molecular weight and smaller hydrodynamic diameter of TA relative to that of HA, owing to which TA exhibits a stronger adhesion to the electrode pore structure. Furthermore, as TA substantially reduces MCDI performance with regard to the adsorption of inorganic salts, its presence in feed water results in higher electrical resistance and energy consumption.

Membrane and Electrochemical Processes for Water Desalination: A Short Perspective and the Role of Nanotechnology.

In the past few decades, membrane-based processes have become mainstream in water desalination because of their relatively high water flux, salt rejection, and reasonable operating cost over thermal-based desalination processes. The energy consumption of the membrane process has been continuously lowered (from >10 kWh m-3 to ~3 kWh m-3) over the past decades but remains higher than the theoretical minimum value (~0.8 kWh m-3) for seawater desalination. Thus, the high energy consumption of membrane processes has led to the development of alternative processes, such as the electrochemical, that use relatively less energy. Decades of research have revealed that the low energy consumption of the electrochemical process is closely coupled with a relatively low extent of desalination. Recent studies indicate that electrochemical process must overcome efficiency rather than energy consumption hurdles. This short perspective aims to provide platforms to compare the energy efficiency of the representative membrane and electrochemical processes based on the working principle of each process. Future water desalination methods and the potential role of nanotechnology as an efficient tool to overcome current limitations are also discussed.

Influences of Combined Organic Fouling and Inorganic Scaling on Flux and Fouling Behaviors in Forward Osmosis.

This study investigated the influence of combined organic fouling and inorganic scaling on the flux and fouling behaviors of thin-film composite (TFC) forward osmosis (FO) membranes. Two organic macromolecules, namely, bovine serum albumin (BSA) and sodium alginate (SA), and gypsum (GS), as an inorganic scaling agent, were selected as model foulants. It was found that GS scaling alone caused the most severe flux decline. When a mixture of organic and inorganic foulants was employed, the flux decline was retarded, compared with when the filtration was performed with only the inorganic scaling agent (GS). The early onset of the conditioning layer formation, which was due to the organics, was probably the underlying mechanism for this inhibitory phenomenon, which had suppressed the deposition and growth of the GS crystals. Although the combined fouling resulted in less flux decline, compared with GS scaling alone, the concoction of SA and GS resulted in more fouling and flux decline, compared with the mixture of BSA and GS. This was because of the carboxyl acidity of the alginate, which attracted calcium ions and formed an intermolecular bridge.

Impact of salt accumulation in the bioreactor on the performance of nanofiltration membrane bioreactor (NF-MBR)+Reverse osmosis (RO) process for water reclamation.

The impacts of salt accumulation, through adjusting the solid retention time (SRT), in the bioreactor on the bioprocess as well as membrane performance of a high retention nanofiltration membrane bioreactor (NF-MBR) and subsequent reverse osmosis (RO) process for water reclamation are addressed in this study. The build-up of salts (i.e., Ca, Mg, PO4) is a function of SRT, hydraulic retention time (HRT) and membrane rejection. Despite the accumulation of salts, both NF-MBRs at SRT of 30 and 60 days, achieved (i) similar biodegradation efficiency; (ii) excellent organic removal (> 97%); and (iii) excellent ammonia removal (> 98%). Extending the SRT could improve the microbial bio-flocculation capability, but did not influence the microbial activity, viability, and community structure. However, more severe membrane fouling was observed in the NF-MBR with elevated salt levels, which was attributed to the greater formation of calcium phosphate scale and Ca-polysaccharides complex (i.e., irreversible fouling layer) as well as the cake-enhanced-osmotic-pressure (CEOP) effect. Although both NF-MBRs produced comparable quality of permeate, a higher RO membrane fouling rate was observed when the permeate of NF-MBR with SRT at 60 days was fed to the RO system, implying organic compositions in NF-MBR permeate may influence RO performance.

CRISPR elements provide a new framework for the genealogy of the citrus canker pathogen Xanthomonas citri pv. citri.

BACKGROUND: Xanthomonads are an important clade of Gram-negative bacteria infecting a plethora of economically important host plants, including citrus. Knowledge about the pathogen's diversity and population structure are prerequisite for epidemiological surveillance and efficient disease management. Rapidly evolving genetic loci, such as Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), are of special interest to develop new molecular typing tools. RESULTS: We analyzed CRISPR loci of 56 Xanthomonas citri pv. citri strains of world-wide origin, a regulated pathogen causing Asiatic citrus canker in several regions of the world. With one exception, 23 unique sequences built up the repertoire of spacers, suggesting that this set of strains originated from a common ancestor that already harbored these 23 spacers. One isolate originating from Pakistan contained a string of 14 additional, probably more recently acquired spacers indicating that this genetic lineage has or had until recently the capacity to acquire new spacers. Comparison of CRISPR arrays with previously obtained molecular typing data, such as amplified fragment length polymorphisms (AFLP), variable-number of tandem-repeats (VNTR) and genome-wide single-nucleotide polymorphisms (SNP), demonstrated that these methods reveal similar evolutionary trajectories. Notably, genome analyses allowed to generate a model for CRISPR array evolution in X. citri pv. citri, which provides a new framework for the genealogy of the citrus canker pathogen. CONCLUSIONS: CRISPR-based typing will further improve the accuracy of the genetic identification of X. citri pv. citri outbreak strains in molecular epidemiology analyses, especially when used concomitantly with another genotyping method.

Transcriptional response of rice flag leaves to restricted external phosphorus supply during grain filling in rice cv. IR64.

Plant phosphorus (P) remobilisation during leaf senescence has fundamental implications for global P cycle fluxes. Hypothesising that genes involved in remobilisation of P from leaves during grain filling would show altered expression in response to P deprivation, we investigated gene expression in rice flag leaves at 8 days after anthesis (DAA) and 16 DAA in plants that received a continuous supply of P in the nutrient solution vs plants where P was omitted from the nutrient solution for 8 consecutive days prior to measurement. The transcriptional response to growth in the absence of P differed between the early stage (8 DAA) and the later stage (16 DAA) of grain filling. At 8 DAA, rice plants maintained production of energy substrates through upregulation of genes involved in photosynthesis. In contrast, at 16 DAA carbon substrates were produced by degradation of structural polysaccharides and over 50% of highly upregulated genes in P-deprived plants were associated with protein degradation and nitrogen/amino acid transport, suggesting withdrawal of P from the nutrient solution led to accelerated senescence. Genes involved in liberating inorganic P from the organic P compounds and vacuolar P transporters displayed differential expression depending on the stage of grain filling stage and timing of P withdrawal.

Phosphorus uptake commences at the earliest stages of seedling development in rice.

Seed phosphorus (P) reserves are essential for seedling development; however, we hypothesise that the quantity of P in seeds will lose importance in cultivars that rapidly acquire it via their roots. Our objective in this study was therefore to investigate the onset of seedling P uptake in rice (Oryza sativa). This was addressed through 33P-labelled supply and through measuring P depletion in combination with the detection of P transporter activity in the root tissue of three rice cultivars during early development. 33P supplied to roots 4 d after germination (DAG) was detected in shoots 2 d later, indicating that P was taken up and translocated to shoots during early seedling development. Measurements of P depletion from the growth medium indicated that uptake occurred even at 2 DAG when roots were only 3 cm long. By day 3, P depletion was rapid and P transporter activity was detected in roots, regardless of the levels of seed P reserves present. We conclude that P uptake commences at the earliest stages of seedling development in rice, that the amount taken up will be limited by root size, and that genotypes with more rapid root development should more rapidly complement seed-P reserves by root uptake.

Remobilisation of phosphorus fractions in rice flag leaves during grain filling: Implications for photosynthesis and grain yields.

Phosphorus (P) is translocated from vegetative tissues to developing seeds during senescence in annual crop plants, but the impact of this P mobilisation on photosynthesis and plant performance is poorly understood. This study investigated rice (Oryza sativa L.) flag leaf photosynthesis and P remobilisation in a hydroponic study where P was either supplied until maturity or withdrawn permanently from the nutrient solution at anthesis, 8 days after anthesis (DAA) or 16 DAA. Prior to anthesis, plants received either the minimum level of P in nutrient solution required to achieve maximum grain yield ('adequate P treatment'), or received luxury levels of P in the nutrient solution ('luxury P treatment'). Flag leaf photosynthesis was impaired at 16 DAA when P was withdrawn at anthesis or 8 DAA under adequate P supply but only when P was withdrawn at anthesis under luxury P supply. Ultimately, reduced photosynthesis did not translate into grain yield reductions. There was some evidence plants remobilised less essential P pools (e.g. Pi) or replaceable P pools (e.g. phospholipid-P) prior to remobilisation of P in pools critical to leaf function such as nucleic acid-P and cytosolic Pi. Competition for P between vegetative tissues and developing grains can impair photosynthesis when P supply is withdrawn during early grain filling. A reduction in the P sink strength of grains by genetic manipulation may enable leaves to sustain high rates of photosynthesis until the later stages of grain filling.

Phosphorus remobilization from rice flag leaves during grain filling: an RNA-seq study.

The physiology and molecular regulation of phosphorus (P) remobilization from vegetative tissues to grains during grain filling is poorly understood, despite the pivotal role it plays in the global P cycle. To test the hypothesis that a subset of genes involved in the P starvation response are involved in remobilization of P from flag leaves to developing grains, we conducted an RNA-seq analysis of rice flag leaves during the preremobilization phase (6 DAA) and when the leaves were acting as a P source (15 DAA). Several genes that respond to phosphate starvation, including three purple acid phosphatases (OsPAP3, OsPAP9b and OsPAP10a), were significantly up-regulated at 15 DAA, consistent with a role in remobilization of P from flag leaves during grain filling. A number of genes that have not been implicated in the phosphate starvation response, OsPAP26, SPX-MFS1 (a putative P transporter) and SPX-MFS2, also showed expression profiles consistent with involvement in P remobilization from senescing flag leaves. Metabolic pathway analysis using the KEGG system suggested plastid membrane lipid synthesis is a critical process during the P remobilization phase. In particular, the up-regulation of OsPLDz2 and OsSQD2 at 15 DAA suggested phospholipids were being degraded and replaced by other lipids to enable continued cellular function while liberating P for export to developing grains. Three genes associated with RNA degradation that have not previously been implicated in the P starvation response also showed expression profiles consistent with a role in P mobilization from senescing flag leaves.

Phosphorus uptake, partitioning and redistribution during grain filling in rice.

BACKGROUNDS AND AIMS: In cultivated rice, phosphorus (P) in grains originates from two possible sources, namely exogenous (post-flowering root P uptake from soil) or endogenous (P remobilization from vegetative parts) sources. This study investigates P partitioning and remobilization in rice plants throughout grain filling to resolve contributions of P sources to grain P levels in rice. METHODS: Rice plants (Oryza sativa 'IR64') were grown under P-sufficient or P-deficient conditions in the field and in hydroponics. Post-flowering uptake, partitioning and re-partitioning of P was investigated by quantifying tissue P levels over the grain filling period in the field conditions, and by employing 33P isotope as a tracer in the hydroponic study. KEY RESULTS: Post-flowering P uptake represented 40-70 % of the aerial plant P accumulation at maturity. The panicle was the main P sink in all studies, and the amount of P potentially remobilized from vegetative tissues to the panicle during grain filling was around 20 % of the total aerial P measured at flowering. In hydroponics, less than 20 % of the P tracer taken up at 9 d after flowering (DAF) was found in the above-ground tissues at 14 DAF and half of it was partitioned to the panicle in both P treatments. CONCLUSIONS: The results demonstrate that P uptake from the soil during grain filling is a critical contributor to the P content in grains in irrigated rice. The P tracer study suggests that the mechanism of P loading into grains involves little direct transfer of post-flowering P uptake to the grain but rather substantial mobilization of P that was previously taken up and stored in vegetative tissues.

The knowns and unknowns of phosphorus loading into grains, and implications for phosphorus efficiency in cropping systems.

Inefficient use of phosphorus (P) in agriculture adds to production costs, increases the risk of eutrophication of waterways, and contributes to the rapid depletion of the world's non-renewable rock phosphate supplies. The removal of large quantities of P from fields in harvested grains is a major driver in the global P cycle, but opportunities exist to reduce the amount of P in harvested grains through plant breeding. Using rice (Oryza sativa L.) as a model crop, we examine our current understanding of the process of P loading into grain and its regulation by genetic and environmental factors. We expose a dearth of knowledge on the physiological processes involved in loading P into grains, poor resolution of the genes and networks involved in P mobilization from vegetative tissues to grains, and limited understanding of genetic versus environmental contributions to variation in grain P concentrations observed among genotypes. We discuss potential breeding strategies and highlight key research gaps that should be addressed to facilitate these breeding approaches. Given the strong economic and environmental incentives for a low grain P trait, we suggest that some of the investment and resources currently directed to determining the molecular regulation of P starvation responses in model plant species should be diverted to resolving the physiology, genetics, and molecular regulation of P loading into cereal grains.

Genetic diversity for mycorrhizal symbiosis and phosphate transporters in rice.

Phosphorus (P) is a major plant nutrient and developing crops with higher P-use efficiency is an important breeding goal. In this context we have conducted a comparative study of irrigated and rainfed rice varieties to assess genotypic differences in colonization with arbuscular mycorrhizal (AM) fungi and expression of different P transporter genes. Plants were grown in three different soil samples from a rice farm in the Philippines. The data show that AM symbiosis in all varieties was established after 4 weeks of growth under aerobic conditions and that, in soil derived from a rice paddy, natural AM populations recovered within 6 weeks. The analysis of AM marker genes (AM1, AM3, AM14) and P transporter genes for the direct Pi uptake (PT2, PT6) and AM-mediated pathway (PT11, PT13) were largely in agreement with the observed root AM colonization providing a useful tool for diversity studies. Interestingly, delayed AM colonization was observed in the aus-type rice varieties which might be due to their different root structure and might confer an advantage for weed competition in the field. The data further showed that P-starvation induced root growth and expression of the high-affinity P transporter PT6 was highest in the irrigated variety IR66 which also maintained grain yield under P-deficient field conditions.

Prediction of effluent concentration in a wastewater treatment plant using machine learning models.

Of growing amount of food waste, the integrated food waste and waste water treatment was regarded as one of the efficient modeling method. However, the load of food waste to the conventional waste treatment process might lead to the high concentration of total nitrogen (T-N) impact on the effluent water quality. The objective of this study is to establish two machine learning models-artificial neural networks (ANNs) and support vector machines (SVMs), in order to predict 1-day interval T-N concentration of effluent from a wastewater treatment plant in Ulsan, Korea. Daily water quality data and meteorological data were used and the performance of both models was evaluated in terms of the coefficient of determination (R2), Nash-Sutcliff efficiency (NSE), relative efficiency criteria (drel). Additionally, Latin-Hypercube one-factor-at-a-time (LH-OAT) and a pattern search algorithm were applied to sensitivity analysis and model parameter optimization, respectively. Results showed that both models could be effectively applied to the 1-day interval prediction of T-N concentration of effluent. SVM model showed a higher prediction accuracy in the training stage and similar result in the validation stage. However, the sensitivity analysis demonstrated that the ANN model was a superior model for 1-day interval T-N concentration prediction in terms of the cause-and-effect relationship between T-N concentration and modeling input values to integrated food waste and waste water treatment. This study suggested the efficient and robust nonlinear time-series modeling method for an early prediction of the water quality of integrated food waste and waste water treatment process.

Notch intracellular domain expression in various skin fibroproliferative diseases.

BACKGROUND: The effects of the Notch signaling pathway in fibroproliferative skin diseases have not been fully elucidated. OBJECTIVE: The aim of this study was to investigate the expression of activated Notch signaling molecules in various skin fibroproliferative diseases. METHODS: Immunohistochemical analysis of Notch intracellular domain (NICD) expression in keloid, hypertrophic scar, morphea, dermatofibroma, and normal control skin specimens was performed, and the clinical characteristics of patients with various skin fibroproliferative diseases were analyzed. RESULTS: NICD was highly expressed in fibroblasts of keloids and moderately to highly expressed in hypertrophic scars and dermatofibromas, whereas low or no expression was detected in the fibroblasts of normal skin specimens and morpheas. NICD was constitutively expressed in keratinocytes, endothelial cells, and immune cells in normal skin specimens. CONCLUSION: NICD was significantly expressed in human fibroproliferative skin disorders, especially keloids, suggesting that an activated Notch signaling pathway is involved in the pathogenesis of skin fibrosis.