A comprehensive workflow for optimizing RNA-seq data analysis.

BACKGROUND: Current RNA-seq analysis software for RNA-seq data tends to use similar parameters across different species without considering species-specific differences. However, the suitability and accuracy of these tools may vary when analyzing data from different species, such as humans, animals, plants, fungi, and bacteria. For most laboratory researchers lacking a background in information science, determining how to construct an analysis workflow that meets their specific needs from the array of complex analytical tools available poses a significant challenge. RESULTS: By utilizing RNA-seq data from plants, animals, and fungi, it was observed that different analytical tools demonstrate some variations in performance when applied to different species. A comprehensive experiment was conducted specifically for analyzing plant pathogenic fungal data, focusing on differential gene analysis as the ultimate goal. In this study, 288 pipelines using different tools were applied to analyze five fungal RNA-seq datasets, and the performance of their results was evaluated based on simulation. This led to the establishment of a relatively universal and superior fungal RNA-seq analysis pipeline that can serve as a reference, and certain standards for selecting analysis tools were derived for reference. Additionally, we compared various tools for alternative splicing analysis. The results based on simulated data indicated that rMATS remained the optimal choice, although consideration could be given to supplementing with tools such as SpliceWiz. CONCLUSION: The experimental results demonstrate that, in comparison to the default software parameter configurations, the analysis combination results after tuning can provide more accurate biological insights. It is beneficial to carefully select suitable analysis software based on the data, rather than indiscriminately choosing tools, in order to achieve high-quality analysis results more efficiently.

PTI-ETI synergistic signal mechanisms in plant immunity.

Plants face a relentless onslaught from a diverse array of pathogens in their natural environment, to which they have evolved a myriad of strategies that unfold across various temporal scales. Cell surface pattern recognition receptors (PRRs) detect conserved elicitors from pathogens or endogenous molecules released during pathogen invasion, initiating the first line of defence in plants, known as pattern-triggered immunity (PTI), which imparts a baseline level of disease resistance. Inside host cells, pathogen effectors are sensed by the nucleotide-binding/leucine-rich repeat (NLR) receptors, which then activate the second line of defence: effector-triggered immunity (ETI), offering a more potent and enduring defence mechanism. Moreover, PTI and ETI collaborate synergistically to bolster disease resistance and collectively trigger a cascade of downstream defence responses. This article provides a comprehensive review of plant defence responses, offering an overview of the stepwise activation of plant immunity and the interactions between PTI-ETI synergistic signal transduction.

The miR6445-NAC029 module regulates drought tolerance by regulating the expression of glutathione S-transferase U23 and reactive oxygen species scavenging in Populus.

MicroRNAs are essential in plant development and stress resistance, but their specific roles in drought stress require further investigation. Here, we have uncovered that a Populus-specific microRNAs (miRNA), miR6445, targeting NAC (NAM, ATAF, and CUC) family genes, is involved in regulating drought tolerance of poplar. The expression level of miR6445 was significantly upregulated under drought stress; concomitantly, seven targeted NAC genes showed significant downregulation. Silencing the expression of miR6445 by short tandem target mimic technology significantly decreased the drought tolerance in poplar. Furthermore, 5' RACE experiments confirmed that miR6445 directly targeted NAC029. The overexpression lines of PtrNAC029 (OE-NAC029) showed increased sensitivity to drought compared with knockout lines (Crispr-NAC029), consistent with the drought-sensitive phenotype observed in miR6445-silenced strains. PtrNAC029 was further verified to directly bind to the promoters of glutathione S-transferase U23 (GSTU23) and inhibit its expression. Both Crispr-NAC029 and PtrGSTU23 overexpressing plants showed higher levels of PtrGSTU23 transcript and GST activity while accumulating less reactive oxygen species (ROS). Moreover, poplars overexpressing GSTU23 demonstrated enhanced drought tolerance. Taken together, our research reveals the crucial role of the miR6445-NAC029-GSTU23 module in enhancing poplar drought tolerance by regulating ROS homeostasis. This finding provides new molecular targets for improving the drought resistance of trees.

PeFUS3 Drives Lateral Root Growth Via Auxin and ABA Signalling Under Drought Stress in Populus.

Changes in root system architecture are vital for plant adaptation to drought stress, yet the underlying molecular mechanisms of this process remain largely elusive. Here, FUSCA3 (FUS3), a B3 domain transcription factor isolated from Populus euphratica, was found to be an important gene of regulating lateral root (LR) development under drought stress. The expression of PeFUS3 was strongly induced by ABA and dehydration treatments. Overexpressing PeFUS3 in poplar 84 K (P. alba × P. glandulosa) positively regulated LR growth and enhanced drought tolerance, while the knockout lines, generated by the CRISPR/Cas9 system, displayed repressed LR growth and weakened drought tolerance. Further investigation demonstrated that PeFUS3 activated the expression of PIN2, PIN6a and AUX1, which were key genes involved in auxin transport, suggesting PeFUS3 modulated LR development under drought stress through auxin signalling. Moreover, PeFUS3 directly upregulated PePYL3 expression, and overexpressing PePYL3 poplar lines exhibited significantly increased drought resistance. In addition, PeABF2, an ABA responsive transcription factor, interacted with PeFUS3 and activated its transcription, indicating PeFUS3 was involved in ABA signalling pathway. Taken together, PeFUS3 is a key regulator, maintaining root growth of poplar by modulating the crosstalk of auxin and ABA signalling under drought stress.

An alternative splicing variant of PtRD26 delays leaf senescence by regulating multiple NAC transcription factors in Populus.

During leaf senescence, the final stage of leaf development, nutrients are recycled from leaves to other organs, and therefore proper control of senescence is thus critical for plant fitness. Although substantial progress has been achieved in understanding leaf senescence in annual plants, the molecular factors that control leaf senescence in perennial woody plants are largely unknown. Using RNA sequencing, we obtained a high-resolution temporal profile of gene expression during autumn leaf senescence in poplar (Populus tomentosa). Identification of hub transcription factors (TFs) by co-expression network analysis of genes revealed that senescence-associated NAC family TFs (Sen-NAC TFs) regulate autumn leaf senescence. Age-dependent alternative splicing (AS) caused an intron retention (IR) event in the pre-mRNA encoding PtRD26, a NAC-TF. This produced a truncated protein PtRD26IR, which functions as a dominant-negative regulator of senescence by interacting with multiple hub Sen-NAC TFs, thereby repressing their DNA-binding activities. Functional analysis of senescence-associated splicing factors identified two U2 auxiliary factors that are involved in AS of PtRD26IR. Correspondingly, silencing of these factors decreased PtRD26IR transcript abundance and induced early senescence. We propose that an age-dependent increase of IR splice variants derived from Sen-NAC TFs is a regulatory program to fine tune the molecular mechanisms that regulate leaf senescence in trees.

Single-cell transcriptome analysis of the mouse lungs during the injury and recovery periods after lipopolysaccharide administration.

OBJECTIVE: This study sought to investigate the cellular and molecular alterations during the injury and recovery periods of ALI and develop effective treatments for ALI. METHODS: Pulmonary histology at 1, 3, 6, and 9 days after lipopolysaccharide administration mice were assessed. An unbiased single-cell RNA sequencing was performed in alveoli tissues from injury (day 3) and recovery (day 6) mice after lipopolysaccharide administration. The roles of Fpr2 and Dpp4 in ALI were assessed. RESULTS: The most severe lung injury occurred on day 3, followed by recovery entirely on day 9 after lipopolysaccharide administration. The numbers of Il1a+ neutrophils, monocytes/macrophages, and Cd4+ and Cd8+ T cells significantly increased at day 3 after LPS administration; subsequently, the number of Il1a+ neutrophils greatly decreased, the numbers of monocytes/macrophages and Cd4+ and Cd8+ T cells continuously increased, and the number of resident alveolar macrophages significantly increased at day 6. The interactions between monocytes/macrophages and pneumocytes during the injury period were enhanced by the Cxcl10/Dpp4 pair, and inhibiting Dpp4 improved ALI significantly, while inhibiting Fpr2 did not. CONCLUSIONS: Our results offer valuable insights into the cellular and molecular mechanisms underlying its progression and identify Dpp4 as an effective therapeutic target for ALI.

Rational design of waste anode graphite-derived carbon catalyst to activate peroxymonosulfate for atrazine degradation.

As the rapidly growing number of waste lithium-ion batteries (LIBs), the recycling and reutilization of anode graphite is of increasing interest. Converting waste anode graphite into functional materials may be a sensible option. Herein, a series of carbonaceous catalysts (TG) were successfully prepared using spent anode graphite calcined at various temperatures and applied for activating peroxymonosulfate (PMS) to degrade atrazine (ATZ). The catalyst obtained at 800 °C (TG-800) showed the optimum performance for ATZ removal (99.2% in 6 min). Various experimental conditions were explored to achieve the optimum efficiency of the system. In the TG-800/PMS system, free radicals (e.g., SO4·-, HO·), singlet oxygen (1O2), together with a direct electron transfer pathway all participated in ATZ degradation, and the ketonic (CO) group was proved as the leading catalytic site for PMS activation. The potential degradation routes of ATZ have also been presented. According to the toxicity assessment experiments, the toxicity of the intermediate products decreased. The reusability and universal applicability of the TG-800 were also confirmed. This research not only provides an efficient PMS activator for pollutant degradation, but also offers a meaningful reference for the recovery of waste anode graphite to develop environmentally functional materials.

Yield stress Measurement of municipal sludge: A comprehensive evaluation of testing methods and concentration effects using a rotational rheometer.

Accurate prediction and measurement of yield stress are crucial for optimizing sludge treatment and disposal. However, the differences and applicability of various methods for measuring yield stress are subjects of ongoing debate. Meanwhile, literature on measuring sludge yield stress is limited to low solid concentrations (TS <10%), understanding and studying the yield stress of medium to high solid concentration sludge is crucial due to increasingly stringent standards for sludge treatment and disposal. So, this study employed a rotational rheometer to measure sludge yield stress across a wide range of TS (4-50%) using steady shear, dynamic oscillatory shear, and transient shear. The study derived significant conclusions by comparing and summarizing the applicability and limitations of each testing method: Dynamic oscillatory shear methods, including G'-σ curve method, γ-σ curve method, and G**γc method can measure sludge yield stress ranging from 4% to 40% TS, while other methods are restricted to low or limited solid concentrations; The G' = G″ method, utilizing the intersection of G' and G″ curves, consistently yields the highest value for yield stress when 4%≤ TS ≤ 12%; The rotational rheometer cannot measure sludge yield stress when the solid concentration exceeds 40% TS; The relationship between sludge yield stress and solid concentration is stronger as a power-law for TS ≤ 25%, transitioning to linear for higher concentrations (28%≤ TS <40%). This study systematically explores the applicability and limitations of various measurement methods for characterizing sludge yield stress across a wide range of solid concentrations, providing valuable guidance for scientific measurement and highlighting challenging research issues.

Polystyrene nanoplastics induce apoptosis, autophagy, and steroidogenesis disruption in granulosa cells to reduce oocyte quality and fertility by inhibiting the PI3K/AKT pathway in female mice.

BACKGROUND: Nanoplastics (NPs) are emerging pollutants that pose risks to living organisms. Recent findings have unveiled the reproductive harm caused by polystyrene nanoparticles (PS-NPs) in female animals, yet the intricate mechanism remains incompletely understood. Under this research, we investigated whether sustained exposure to PS-NPs at certain concentrations in vivo can enter oocytes through the zona pellucida or through other routes that affect female reproduction. RESULTS: We show that PS-NPs disrupted ovarian functions and decreased oocyte quality, which may be a contributing factor to lower female fertility in mice. RNA sequencing of mouse ovaries illustrated that the PI3K-AKT signaling pathway emerged as the predominant environmental information processing pathway responding to PS-NPs. Western blotting results of ovaries in vivo and cells in vitro showed that PS-NPs deactivated PI3K-AKT signaling pathway by down-regulating the expression of PI3K and reducing AKT phosphorylation at the protein level, PI3K-AKT signaling pathway which was accompanied by the activation of autophagy and apoptosis and the disruption of steroidogenesis in granulosa cells. Since PS-NPs penetrate granulosa cells but not oocytes, we examined whether PS-NPs indirectly affect oocyte quality through granulosa cells using a granulosa cell-oocyte coculture system. Preincubation of granulosa cells with PS-NPs causes granulosa cell dysfunction, resulting in a decrease in the quality of the cocultured oocytes that can be reversed by the addition of 17ß-estradiol. CONCLUSIONS: This study provides findings on how PS-NPs impact ovarian function and include transcriptome sequencing analysis of ovarian tissue. The study demonstrates that PS-NPs impair oocyte quality by altering the functioning of ovarian granulosa cells. Therefore, it is necessary to focus on the research on the effects of PS-NPs on female reproduction and the related methods that may mitigate their toxicity.

Performance and mechanism of diclofenac adsorption onto 3D poly(m-phenylenediamine)-grafted melamine foam via batch experiment and theoretical studies.

Seeking highly efficient adsorbents for pharmaceuticals and personal care products (PPCPs) removal has been a worldwide continuing endeavor. In this study, a new 3D composite material was synthesized by covalently anchoring Poly(m-Phenylenediamine) onto 3D polyvinyl alcohol modified foam framework (PmPD-MF-PVA). PmPD-MF-PVA was characterized and evaluated for its efficacy in removing diclofenac (DCF), a commonly detected PPCPs in both wastewater and surface water. Results showed that the adsorption capacity of PmPD-MF-PVA toward DCF was 1.5 times higher than that of PmPD-MF. The addition of PVA increased deposition area of PmPD, and promoted PmPD loading on the foam surface. Batch adsorption experiments exhibited that the adsorption of DCF was fitted well with Langmuir isotherm and pseudo-second-order kinetic models. The maximum adsorption capacity of PmPD-MF-PVA was 115 mg/g. Meanwhile, PmPD-MF-PVA exhibited better separation ability than the hard-to-separate PmPD. Characterization analysis and density functional theory (DFT) calculation elucidated the main mechanisms of DCF adsorption on PmPD-MF-PVA. Hydrogen bonding and π-π interactions were main drivers for DCF adsorption, followed by electrostatic attraction and hydrophobic forces. This study provides an effective strategy to overcome the drawbacks of PmPD, such as recycling difficulty and agglomeration problems, offering valuable insights for the design of polymers-based adsorbents.

Identification of WUSCHEL-related homeobox gene and truncated small peptides in transformation efficiency improvement in Eucalyptus.

BACKGROUND: The WUSCHEL-related Homeobox (WOX) genes, which encode plant-specific homeobox (HB) transcription factors, play crucial roles in regulating plant growth and development. However, the functions of WOX genes are little known in Eucalyptus, one of the fastest-growing tree resources with considerable widespread cultivation worldwide. RESULTS: A total of nine WOX genes named EgWOX1-EgWOX9 were retrieved and designated from Eucalyptus grandis. From the three divided clades marked as Modern/WUS, Intermediate and Ancient, the largest group Modern/WUS (6 EgWOXs) contains a specific domain with 8 amino acids: TLQLFPLR. The collinearity, cis-regulatory elements, protein-protein interaction network and gene expression analysis reveal that the WUS proteins in E. grandis involve in regulating meristems development and regeneration. Furthermore, by externally adding of truncated peptides isolated from WUS specific domain, the transformation efficiency in E. urophylla × E. grandis DH32-29 was significant enhanced. The transcriptomics data further reveals that the use of small peptides activates metabolism pathways such as starch and sucrose metabolism, phenylpropanoid biosynthesis and flavonoid biosynthesis. CONCLUSIONS: Peptides isolated from WUS protein can be utilized to enhance the transformation efficiency in Eucalyptus, thereby contributing to the high-efficiency breeding of Eucalyptus.

Spliceosomal protein U2B″ delays leaf senescence by enhancing splicing variant JAZ9ß expression to attenuate jasmonate signaling in Arabidopsis.

The regulatory framework of leaf senescence is gradually becoming clearer; however, the fine regulation of this process remains largely unknown. Here, genetic analysis revealed that U2 small nuclear ribonucleoprotein B (U2B″), a component of the spliceosome, is a negative regulator of leaf senescence. Mutation of U2B″ led to precocious leaf senescence, whereas overexpression of U2B″ extended leaf longevity. Transcriptome analysis revealed that the jasmonic acid (JA) signaling pathway was activated in the u2b″ mutant. U2B″ enhances the generation of splicing variant JASMONATE ZIM-DOMAIN 9ß (JAZ9ß) with an intron retention in the Jas motif, which compromises its interaction with CORONATINE INSENSITIVE1 and thus enhances the stability of JAZ9ß protein. Moreover, JAZ9ß could interact with MYC2 and obstruct its activity, thereby attenuating JA signaling. Correspondingly, overexpression of JAZ9ß rescued the early senescence phenotype of the u2b″ mutant. Furthermore, JA treatment promoted expression of U2B″ that was found to be a direct target of MYC2. Overexpression of MYC2 in the u2b″ mutant resulted in a more pronounced premature senescence than that in wild-type plants. Collectively, our findings reveal that the spliceosomal protein U2B″ fine-tunes leaf senescence by enhancing the expression of JAZ9ß and thereby attenuating JA signaling.

Histone variant HTB4 delays leaf senescence by epigenetic control of Ib bHLH transcription factor-mediated iron homeostasis.

Leaf senescence is an orderly process regulated by multiple internal factors and diverse environmental stresses including nutrient deficiency. Histone variants are involved in regulating plant growth and development. However, their functions and underlying regulatory mechanisms in leaf senescence remain largely unclear. Here, we found that H2B histone variant HTB4 functions as a negative regulator of leaf senescence. Loss of function of HTB4 led to early leaf senescence phenotypes that were rescued by functional complementation. RNA-seq analysis revealed that several Ib subgroup basic helix-loop-helix (bHLH) transcription factors (TFs) involved in iron (Fe) homeostasis, including bHLH038, bHLH039, bHLH100, and bHLH101, were suppressed in the htb4 mutant, thereby compromising the expressions of FERRIC REDUCTION OXIDASE 2 (FRO2) and IRON-REGULATED TRANSPORTER (IRT1), two important components of the Fe uptake machinery. Chromatin immunoprecipitation-quantitative polymerase chain reaction analysis revealed that HTB4 could bind to the promoter regions of Ib bHLH TFs and enhance their expression by promoting the enrichment of the active mark H3K4me3 near their transcriptional start sites. Moreover, overexpression of Ib bHLH TFs or IRT1 suppressed the premature senescence phenotype of the htb4 mutant. Our work established a signaling pathway, HTB4-bHLH TFs-FRO2/IRT1-Fe homeostasis, which regulates the onset and progression of leaf senescence.

Metabolic control of arginine and ornithine levels paces the progression of leaf senescence.

Leaf senescence can be induced by stress or aging, sometimes in a synergistic manner. It is generally acknowledged that the ability to withstand senescence-inducing conditions can provide plants with stress resilience. Although the signaling and transcriptional networks responsible for a delayed senescence phenotype, often referred to as a functional stay-green trait, have been actively investigated, very little is known about the subsequent metabolic adjustments conferring this aptitude to survival. First, using the individually darkened leaf (IDL) experimental setup, we compared IDLs of wild-type (WT) Arabidopsis (Arabidopsis thaliana) to several stay-green contexts, that is IDLs of two functional stay-green mutant lines, oresara1-2 (ore1-2) and an allele of phytochrome-interacting factor 5 (pif5), as well as to leaves from a WT plant entirely darkened (DP). We provide compelling evidence that arginine and ornithine, which accumulate in all stay-green contexts-likely due to the lack of induction of amino acids (AAs) transport-can delay the progression of senescence by fueling the Krebs cycle or the production of polyamines (PAs). Secondly, we show that the conversion of putrescine to spermidine (SPD) is controlled in an age-dependent manner. Thirdly, we demonstrate that SPD represses senescence via interference with ethylene signaling by stabilizing the ETHYLENE BINDING FACTOR1 and 2 (EBF1/2) complex. Taken together, our results identify arginine and ornithine as central metabolites influencing the stress- and age-dependent progression of leaf senescence. We propose that the regulatory loop between the pace of the AA export and the progression of leaf senescence provides the plant with a mechanism to fine-tune the induction of cell death in leaves, which, if triggered unnecessarily, can impede nutrient remobilization and thus plant growth and survival.

What affects the accuracy and applicability of determining wastewater sludge water content via low-field nuclear magnetic resonance?

The accurate determination of waster sludge water content is crucial to sludge dewatering treatment and its disposal management. Though previous studies highlight the great advantages of low-field nuclear magnetic resonance (LF-NMR) in the determination of sludge water content, its accuracy and applicability are not well studied. Herein, this study investigated the settling of operating parameters and the properties of sludge samples on the accuracy and applicability of LF-NMR method in measuring sludge water content. The results showed that the setting of basic parameters such as standard curve, number of scanning times (NS) and sample weight affected the accuracy of sludge water content by LF-NMR. The standard calibration curve constructed by 3 g/L CuSO4, NS = 8 and the sample weight of about 5 g, were suitable for the accurate determination of sludge water content. Furthermore, the existence of magnetic substances in sludge can affect the distribution gradient of main magnetic field, and thus restricted the applicability of LF-NMR. The saturation magnetization of chemical reagents strongly correlated with the measured relative errors of sludge water content (r = 0.995, p < 0.01), the greater the saturation magnetization of the magnetic material, the greater the error of the test results. On the whole, it is necessary to fully consider the influence of process parameters and sludge properties to evaluate the accuracy and applicability of the LF-NMR method, rather than simply copying the parameters in literatures.

Enantioseparation of amino acid and mandelic acid enantiomers using Josiphos-metal complexes as chiral extractants.

The development of new and efficient chiral extractants has always been the research hotspot and difficulty in the field of chiral extraction. Josiphos, a famous ferrocene derivative catalyst, is employed as a chiral extractant in enantioseparation of amino acid and mandelic acid enantiomers. The influences of metal ions, organic solvents, pH of the aqueous solution, extractant concentrations, and extraction temperature on enantioselectivities are systematically studied. The result reveals that Josiphos-Pd has good capabilities to enantioseparate 4-nitro-phenylalanine (Nphe), 3-chloro-phenylglycine (Cpheg), and mandelic acid (MA) with separation factors (α) of 3.30, 2.65, and 2.18, respectively. The pH of the aqueous phase and Josiphos-Pd concentration affect the extraction significantly, whereas extraction temperature shows little influence. After optimizing by response surface method, the mathematical models for extractions are established. And the highest experimental performance factors (pf) for Nphe, Cpheg, and MA are 0.1843, 0.1335, and 0.08884, respectively.

Cuprous-mediated peroxymonosulfate activation for Fenton-like removal of micropollutants: The function of co-catalyst and the accelerated degradation mechanism.

Introducing co-catalysts to enhance the activation of cuprous-mediated peroxymonosulfate (PMS) and induce the continuous generation of highly reactive oxygen species is promising. The function, effectiveness, and acceleration mechanism of co-catalysts in the cuprous-mediated PMS activation process were fully explored in this work, which focused on rhodamine B as the target contaminants. The results demonstrated that molybdenum (Mo) powder was a superb co-catalyst, and that the reaction of cuprous-mediated PMS system was carried out by surface Mo species as opposed to Mo ions in the solution. The Cu (II)/Cu(I) cycle was primarily encouraged by the Mo0, which also caused abundant ·HO and 1O2 and minimal SO4·- and ·O2- to be produced from PMS. The Mo/Cu2+/PMS system exhibited high removal efficiency towards typical pollutants, especially ciprofloxacin, methyl orange, malachite green, and crystal violet, with removal rates up to 93%, 99%, 97%, and 92%, respectively. Additionally, this system showed excellent adaptability to complex water environments. After four cycles, the Mo powder retained its properties and morphology, and the target pollutants could still maintain an 82% degradation efficiency. This study provides a basis for enhancing cuprous-mediated PMS activation for wastewater treatment.

Genome-Wide Analysis of the FBA Subfamily of the Poplar F-Box Gene Family and Its Role under Drought Stress.

F-box proteins are important components of eukaryotic SCF E3 ubiquitin ligase complexes, which specifically determine protein substrate proteasomal degradation during plant growth and development, as well as biotic and abiotic stress. It has been found that the FBA (F-box associated) protein family is one of the largest subgroups of the widely prevalent F-box family and plays significant roles in plant development and stress response. However, the FBA gene family in poplar has not been systematically studied to date. In this study, a total of 337 F-box candidate genes were discovered based on the fourth-generation genome resequencing of P. trichocarpa. The domain analysis and classification of candidate genes revealed that 74 of these candidate genes belong to the FBA protein family. The poplar F-box genes have undergone multiple gene replication events, particularly in the FBA subfamily, and their evolution can be attributed to genome-wide duplication (WGD) and tandem duplication (TD). In addition, we investigated the P. trichocarpa FBA subfamily using the PlantGenIE database and quantitative real-time PCR (qRT-PCR); the results showed that they are expressed in the cambium, phloem and mature tissues, but rarely expressed in young leaves and flowers. Moreover, they are also widely involved in the drought stress response. At last, we selected and cloned PtrFBA60 for physiological function analysis and found that it played an important role in coping with drought stress. Taken together, the family analysis of FBA genes in P. trichocarpa provides a new opportunity for the identification of P. trichocarpa candidate FBA genes and elucidation of their functions in growth, development and stress response, thus demonstrating their utility in the improvement of P. trichocarpa.

Prediction of arsenic adsorption onto metal organic frameworks and adsorption mechanisms interpretation by machine learning.

Metal-organic frameworks (MOFs) are promising adsorbents for the removal of arsenic (As) from wastewater. The As removal efficiency is influenced by several factors, such as the textural properties of MOFs, adsorption conditions, and As species. Examining all of the relevant factors through traditional experiments is challenging. To predict the As adsorption capacities of MOFs toward organic, inorganic, and total As and reveal the adsorption mechanisms, four machine learning-based models were developed, with the adsorption conditions, MOF properties, and characteristics of different As species as inputs. The results demonstrated that the extreme gradient boosting (XGBoost) model exhibited the best predictive performance (test R2 = 0.93-0.96). The validation experiments demonstrated the high accuracy of the inorganic As-based XGBoost model. The feature importance analysis showed that the concentration of As, the surface area of MOFs, and the pH of the solution were the three key factors governing inorganic-As adsorption, while those governing organic-As adsorption were the concentration of As, the pHpzc value of MOFs, and the oxidation state of the metal clusters. The formation of coordination complexes between As and MOFs is possibly the major adsorption mechanism for both inorganic and organic As. However, electrostatic interaction may have a greater effect on organic-As adsorption than on inorganic-As adsorption. Overall, this study provides a new strategy for evaluating As adsorption on MOFs and discovering the underlying decisive factors and adsorption mechanisms, thereby facilitating the investigation of As wastewater treatment.

Enhancing data reliability in quantitative characterization of moisture distribution in sludge using DSC: Impact of sample attributes and test parameters.

Exploring moisture distribution, especially bound water content, is vital for studying and applying sludge dewatering. The differential scanning calorimetry (DSC) method has been extensively utilized for the quantitative characterization of moisture distribution in sludge. However, this method has certain limitations, such as low reproducibility of results, leading to controversial parameter values in different papers and hindering result comparison. In this study, we investigated the influence of key sample attributes on measuring sludge bound water using the DSC method.The findings demonstrated that the moisture content and mass of sludge samples substantially influenced the reproducibility and stability of DSC test results. To ensure data reliability, the moisture content of the sludge sample should be minimized and kept below 84%, with the mass not exceeding 10 mg. Compared to the influence of sludge moisture content and sample mass, the heating rate (1⁓5 °C/min) minimally affected DSC test results. This study offers a comprehensive insight into how sample attributes and test parameters affect the quantitative characterization of bound water in sludge using the DSC method. Furthermore, practical strategies are presented to enhance the method's applicability in sludge bound water characterization.