Root exudation is a key plant function with a large influence on soil organic matter dynamics and plant–soil feedbacks in forest ecosystems. Yet despite its importance, the main ecological drivers of ...root exudation in mature forest trees remain to be identified.
During two growing seasons, we analyzed the dependence of in situ collected root exudates on root morphology, soil chemistry and nutrient availability in six mature European beech (Fagus sylvatica L.) forests on a broad range of bedrock types.
Root morphology was a major driver of root exudation across the nutrient availability gradient. A doubling of specific root length exponentially increased exudation rates of mature trees by c. 5-fold. Root exudation was also closely negatively related to soil pH and nitrogen (N) availability. At acidic and N-poor sites, where fungal biomass was reduced, exudation rates were c. 3-fold higher than at N- and base-richer sites and correlated negatively with the activity of enzymes degrading less bioavailable carbon (C) and N in the bulk soil.
We conclude that root exudation increases on highly acidic, N-poor soils, in which fungal activity is reduced and a greater portion of the assimilated plant C is shifted to the external ecosystem C cycle.
C₄ photosynthesis outperforms the ancestral C₃ state in a wide range of natural and agro-ecosystems by affording higher water-use and nitrogen-use efficiencies. It therefore represents a prime target ...for engineering novel, high-yielding crops by introducing the trait into C₃ backgrounds. However, the genetic architecture of C₄ photosynthesis remains largely unknown. To define the divergence in gene expression modules between C₃ and C₄ photosynthesis during leaf ontogeny, we generated comprehensive transcriptome atlases of two Cleomaceae species, Gynandropsis gynandra (C₄) and Tarenaya hassleriana (C₃), by RNA sequencing. Overall, the gene expression profiles appear remarkably similar between the C₃ and C₄ species. We found that known C₄ genes were recruited to photosynthesis from different expression domains in C₃, including typical housekeeping gene expression patterns in various tissues as well as individual heterotrophic tissues. Furthermore, we identified a structure-related module recruited from the C₃ root. Comparison of gene expression patterns with anatomy during leaf ontogeny provided insight into genetic features of Kranz anatomy. Altered expression of developmental factors and cell cycle genes is associated with a higher degree of endoreduplication in enlarged C₄ bundle sheath cells. A delay in mesophyll differentiation apparent both in the leaf anatomy and the transcriptome allows for extended vein formation in the C₄ leaf.
Abstract
Crassulacean acid metabolism (CAM) has evolved as a water-saving strategy, and its engineering into crops offers an opportunity to improve their water use efficiency. This requires a ...comprehensive understanding of the regulation of the CAM pathway. Here, we use the facultative CAM species Talinum triangulare as a model in which CAM can be induced rapidly by exogenous abscisic acid. RNA sequencing and metabolite measurements were employed to analyse the changes underlying CAM induction and identify potential CAM regulators. Non-negative matrix factorization followed by k-means clustering identified an early CAM-specific cluster and a late one, which was specific for the early light phase. Enrichment analysis revealed abscisic acid metabolism, WRKY-regulated transcription, sugar and nutrient transport, and protein degradation in these clusters. Activation of the CAM pathway was supported by up-regulation of phosphoenolpyruvate carboxylase, cytosolic and chloroplastic malic enzymes, and several transport proteins, as well as by increased end-of-night titratable acidity and malate accumulation. The transcription factors HSFA2, NF-YA9, and JMJ27 were identified as candidate regulators of CAM induction. With this study we promote the model species T. triangulare, in which CAM can be induced in a controlled way, enabling further deciphering of CAM regulation.
Exogenous abscisic acid leads to fast transcriptome reprogramming, which translates into altered metabolome composition. This includes nocturnal acidification, indicating induction of the CAM pathway.
In this work, we studied castor-oil plant
Ricinus communis
as a classical system for endosperm reserve breakdown. The seeds of castor beans consist of a centrally located embryo with the two thin ...cotyledons surrounded by the endosperm. The endosperm functions as major storage tissue and is packed with nutritional reserves, such as oil, proteins, and starch. Upon germination, mobilization of the storage reserves requires inter-organellar interplay of plastids, mitochondria, and peroxisomes to optimize growth for the developing seedling. To understand their metabolic interactions, we performed a large-scale organellar proteomic study on castor bean endosperm. Organelles from endosperm of etiolated seedlings were isolated and subjected to liquid chromatography-tandem mass spectrometry (LC-MS/MS). Computer-assisted deconvolution algorithms were applied to reliably assign the identified proteins to their correct subcellular localization and to determine the abundance of the different organelles in the heterogeneous protein samples. The data obtained were used to build a comprehensive metabolic model for plastids, mitochondria, and peroxisomes during storage reserve mobilization in castor bean endosperm.
Liver X receptors (LXRs) are ligand-activated transcription factors that coordinate regulation of gene expression involved in several cellular functions but most notably cholesterol homeostasis ...encompassing cholesterol transport, catabolism, and absorption. WAY-252623 (LXR-623) is a highly selective and orally bioavailable synthetic modulator of LXR, which demonstrated efficacy for reducing lesion progression in the murine LDLR−/− atherosclerosis model with no associated increase in hepatic lipogenesis either in this model or Syrian hamsters. In nonhuman primates with normal lipid levels, WAY-252623 significantly reduced total (50–55%) and LDL-cholesterol (LDLc) (70–77%) in a time- and dose-dependent manner as well as increased expression of the target genes ABCA1/G1 in peripheral blood cells. Statistically significant decreases in LDLc were noted as early as day 7, reached a maximum by day 28, and exceeded reductions observed for simvastatin alone (20 mg/kg). Transient increases in circulating triglycerides and liver enzymes reverted to baseline levels over the course of the study. Complementary microarray analysis of duodenum and liver gene expression revealed differential activation of LXR target genes and suggested no direct activation of hepatic lipogenesis.
Cyanidioschyzon merolae (C. merolae) is an acidophilic red alga growing in a naturally low carbon dioxide (CO
) environment. Although it uses a ribulose 1,5-bisphosphate carboxylase/oxygenase with ...high affinity for CO
, the survival of C. merolae relies on functional photorespiratory metabolism. In this study, we quantified the transcriptomic response of C. merolae to changes in CO
conditions. We found distinct changes upon shifts between CO
conditions, such as a concerted up-regulation of photorespiratory genes and responses to carbon starvation. We used the transcriptome data set to explore a hypothetical CO
concentrating mechanism in C. merolae, based on the assumption that photorespiratory genes and possible candidate genes involved in a CO
concentrating mechanism are co-expressed. A putative bicarbonate transport protein and two α-carbonic anhydrases were identified, which showed enhanced transcript levels under reduced CO
conditions. Genes encoding enzymes of a PEPCK-type C
pathway were co-regulated with the photorespiratory gene cluster. We propose a model of a hypothetical low CO
compensation mechanism in C. merolae integrating these low CO
-inducible components.
Cyanidioschyzon merolae (C. merolae) is an acidophilic red alga growing in a naturally low carbon dioxide (CO2) environment. Although it uses a ribulose 1,5-bisphosphate carboxylase/oxygenase with ...high affinity for CO2, the survival of C. merolae relies on functional photorespiratory metabolism. In this study, we quantified the transcriptomic response of C. merolae to changes in CO2 conditions. We found distinct changes upon shifts between CO2 conditions, such as a concerted up-regulation of photorespiratory genes and responses to carbon starvation. We used the transcriptome data set to explore a hypothetical CO2 concentrating mechanism in C. merolae, based on the assumption that photorespiratory genes and possible candidate genes involved in a CO2 concentrating mechanism are co-expressed. A putative bicarbonate transport protein and two α-carbonic anhydrases were identified, which showed enhanced transcript levels under reduced CO2 conditions. Genes encoding enzymes of a PEPCK-type C4 pathway were co-regulated with the photorespiratory gene cluster. We propose a model of a hypothetical low CO2 compensation mechanism in C. merolae integrating these low CO2-inducible components.
•Peroxisomes are favorable targets for metabolic engineering.•Peroxisomes can be manipulated to increase oilseed yield and produce designer oils.•Modified peroxisomal metabolism might improve stress ...tolerance in plants.•Artificial metabolic pathways can be implemented into peroxisomes to gain novel peroxisomal functions.
Plant metabolic engineering is a promising tool for biotechnological applications. Major goals include enhancing plant fitness for an increased product yield and improving or introducing novel pathways to synthesize industrially relevant products. Plant peroxisomes are favorable targets for metabolic engineering, because they are involved in diverse functions, including primary and secondary metabolism, development, abiotic stress response, and pathogen defense. This review discusses targets for manipulating endogenous peroxisomal pathways, such as fatty acid β-oxidation, or introducing novel pathways, such as the synthesis of biodegradable polymers. Furthermore, strategies to bypass peroxisomal pathways for improved energy efficiency and detoxification of environmental pollutants are discussed. In sum, we highlight the biotechnological potential of plant peroxisomes and indicate future perspectives to exploit peroxisomes as biofactories.
Background
Inconsistencies in the nomenclature of structures of the frontal sinus have impeded the development of a validated “reference standard” classification system that surgeons can reliably ...agree upon. The International Frontal Sinus Anatomy Classification (IFAC) system was developed as a consensus document, based on expert opinion, attempting to address this issue. The purposes of this study are to: establish the reliability of the IFAC as a tool for classifying cells in the frontal recess among an international group of rhinologists; and improve communication and teaching of frontal endoscopic sinus surgery (ESS).
Methods
Forty‐two computed tomography (CT) scans, each with a marked frontal cell, were reviewed by 15 international fellowship‐trained rhinologists. Each marked cell was classified into 1 of 7 categories described in the IFAC, on 2 occasions separated by 2 weeks. Inter‐ and intrarater reliability were evaluated using Light's kappa (κ), the interclass correlation coefficient (ICC), and simple proportion of agreement.
Results
Interrater reliability showed pairwise κ values ranging from 0.7248 to 1.0, with a mean of 0.9162 (SD, 0.0537). The ICC was 0.98. Intrarater reliability showed κ values ranging from 0.8613 to 1.0, with a mean of 0.9407 (SD, 0.0376). The within‐rater ICC was 0.98.
Conclusion
Among a diverse sample of rhinologists (raters), there was substantial to almost perfect agreement between raters, and among individual raters at different timepoints. The IFAC is a reliable tool for classification of cells in the frontal sinus. Further outcome studies are still needed to determine the validity of the IFAC.
The study explored the suitability of unfractionated extracts from the seeds of the
Moringa oleifera
tree as a coagulant for water treatment. The coagulant was obtained by soaking crushed and sieved ...seeds in a low salinity aqueous solution: a simple and inexpensive alternative to conventional coagulants in settings where specialized expertise and equipment are lacking. The performance of
M. oleifera
-derived coagulants was quantified in terms of turbidity removal, bacteriophage clearance, concentration of residual organics, as well as meta-parameters such as floc size and fractal dimension. Treating high turbidity clay suspensions at the optimal coagulant dosage (14.7 mg(DOC)/L) and flocculation mixing conditions (
G
¯
= 22.4 s
−1
) removed > 94% of turbidity, similar to that recorded in reference tests with alum. Floc size distribution shifted to larger sizes during the first 10 min of flocculation with no change afterwards, while the floc fractal dimension,
D
f
, continued to increase, pointing to the gradual formation of denser (
D
f
= 2.1 to 2.2), more settleable flocs. Preliminary tests with MS2 bacteriophage showed that coagulation with
M. oleifera
decreased the viable MS2 titre by ~ 1.3 log, which was significantly above the turbidity removal (~ 1 log). The extraction process, however, allowed a large amount of residual organics (> 78% of extracted DOC) into the treated water. Combining the coagulants with downstream filtration and adsorption, employing UV or solar disinfection, or limiting applications to non-potable reuse is suggested for mitigating the concerns related to residual DOC.
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