Complete genome sequences of two Pantoea stewartii strains ATCC 8199 from maize and PSCN1 from sugarcane.

OBJECTIVES: The pathogen of Pantoea stewartii (Ps) is the causal agent of bacterial disease in corn and various graminaceous plants. Ps has two subspecies, Pantoea stewartii subsp. stewartia (Pss) and Pantoea stewartii subsp. indologenes (Psi). This study presents two complete genomes of Ps strains including ATCC 8199 isolated from maize and PSCN1 causing bacterial wilt in sugarcane. The two bacterial genomes information will be helpful for taxonomy analysis in this genus Pantoea at whole-genome levels and accurately discriminated the two subspecies of Pss and Psi. DATA DESCRIPTION: The reference strain ATCC 8199 isolated from maize was purchased from Beijing Biobw Biotechnology Co., Ltd. (China) and the strain of PSCN1 was isolated from sugarcane cultivar YZ08-1095 in Zhanjiang, Guangdong province of China. Two complete genomes were sequenced using Illumina Hiseq (second-generation) and Oxford Nanopore (third-generation) platforms. The genome of the strain ATCC 8199 comprised of 4.78 Mb with an average GC content of 54.03%, along with five plasmids, encoding a total of 4,846 gene with an average gene length of 827 bp. The genome of PSCN1 comprised of 5.03 Mb with an average GC content of 53.78%, along with two plasmids, encoding a total of 4,725 gene with an average gene length of 913 bp. The bacterial pan-genome analysis highlighted the strain ATCC 8199 was clustered into a subgroup with a Pss strain CCUG 26,359 from USA, while the strain PSCN1 was clustered into another subgroup with a Ps strain NRRLB-133 from USA. These findings will serve as a useful resource for further analyses of the evolution of Ps strains and corresponding disease epidemiology worldwide.

Ionic Liquid-Modified Copper for the Enhanced Thermal Conductivity and Mechanical Properties of Epoxy Resin/Expanded Graphite Composites.

In this study, diglycidylether of bisphenol A (DGEBA)/expanded graphite (EG)/copper (Cu) powder composites with high thermal conductivity were prepared for use as thermal interface materials. To construct an excellent thermally conductive network, the Cu surface was modified using the ionic liquid 1-ethyl-3-methyl imidazolium dicyanamide. In addition, the effect of the Cu content on the thermal conductivity, thermal stability, flexural properties, impact strength, and morphologies of the DGEBA/EG/Cu composites was investigated. The results indicated that the addition of 10 wt % Cu increased the thermal conductivity of the composites from 7.35 to 9.86 W/(m·K). Conversely, the thermal stability of the composites decreased with the addition of Cu. The flexural strength and impact strength of the composites increased from 27.9 MPa and 0.81 kJ/m2 to 39.6 MPa and 0.96 kJ/m2, respectively, as the Cu content increased from 0 to 10 wt %. Moreover, the flexural modulus of the composites increased from 9632 to 11,309 MPa with the addition of 10 wt % Cu. Scanning electron microscopy analysis of the DGEBA/EG/Cu composites revealed sheet-shaped blocks with numerous microcracks on the fracture surfaces.

Flow-electrode capacitive separation of organic acid products and recovery of alkali cations after acidic CO2 electrolysis.

Acidic CO2 electrolysis, enhanced by the introduction of alkali cations, presents a strategic approach for improving carbon efficiency compared to processes conducted in neutral and alkaline environments. However, a significant challenge arises from the dissolution of both organic acids and alkali cations in a strongly acidic feed stream, resulting in a considerable energy penalty for downstream separation. In this study, we investigate the feasibility of using flow-electrode capacitive deionization (FCDI) technology to separate organic acids and recover alkali cations from a strongly acidic feed stream (pH ~ 1). We show that organic acids, such as formic acid and acetic acid, are retained in molecular form in the separation chamber, achieving a rejection rate of over 90% under all conditions. Alkali cations, such as K+ and Cs+, migrate to the cathode chamber in ionic form, with their removal and recovery significantly influenced by their concentration and the pH of the feed stream, but responding differently to the types and concentrations of organic acids. The energy consumption for the removal and recovery of K+ is 4 to 8 times higher than for Cs+, and the charge efficiency is significantly influenced by the types of organic acid products and alkali cations. We conduct a series of electrochemical measurements and analyze the impedance spectroscopy, identifying that hindered mass transfer governed the electrode process. Our findings underscore the potential of FCDI as an advanced downstream separation technology for acidic electrocatalysis processes.

Stable construction and analysis of MDD modular networks based on multi-center EEG data.

BACKGROUND: The modular structure can reflect the activity pattern of the brain, and exploring it may help us understand the pathogenesis of major depressive disorder (MDD). However, little is known about how to build a stable modular structure in MDD patients and how modules are separated and integrated. METHOD: We used four independent resting state Electroencephalography (EEG) datasets. Different coupling methods, window lengths, and optimized community detection algorithms were used to find a reliable and robust modular structure, and the module differences of MDD were analyzed from the perspectives of global module attributes and local topology in multiple frequency bands. RESULTS: The combination of the Phase Lag Index (PLI) and the Louvain algorithm can achieve better results and can achieve stability at smaller window lengths. Compared with Healthy Controls (HC), MDD had higher Modularity (Q) values and the number of modules in low-frequency bands. In addition, MDD showed significant structural changes in the frontal and parietal-occipital lobes, which were confirmed by further correlation analysis. CONCLUSION: Our results provided a reliable validation of the modular structure construction method in MDD patients and contributed strong evidence for the changes in emotional cognition and visual system function in MDD patients from a new perspective. These results would afford valuable insights for further exploration of the pathogenesis of MDD.

Spatial and Temporal Analysis of Severe Fever with Thrombocytopenia Syndrome in Anhui Province from 2011 to 2023.

OBJECTIVE: To analyze the spatial autocorrelation and spatiotemporal clustering characteristics of severe fever with thrombocytopenia syndrome(SFTS) in Anhui Province from 2011 to 2023. METHODS: Data of SFTS in Anhui Province from 2011 to 2023 were collected. Spatial autocorrelation analysis was conducted using GeoDa software, while spatiotemporal scanning was performed using SaTScan 10.0.1 software to identify significant spatiotemporal clusters of SFTS. RESULTS: From 2011 to 2023, 5720 SFTS cases were reported in Anhui Province, with an average annual incidence rate of 0.7131/100,000. The incidence of SFTS in Anhui Province reached its peak mainly from April to May, with a small peak in October. The spatial autocorrelation results showed that from 2011 to 2023, there was a spatial positive correlation(P < 0.05) in the incidence of SFTS in all counties and districts of Anhui Province. Local autocorrelation high-high clustering areas are mainly located in the south of the Huaihe River. The spatiotemporal scanning results show three main clusters of SFTS in recent years: the first cluster located in the lower reaches of the Yangtze River, the eastern region of Anhui Province; the second cluster primarily focused on the region of the Dabie Mountain range, while the third cluster primarily focused on the region of the Huang Mountain range. CONCLUSIONS: The incidence of SFTS in Anhui Province in 2011-2023 was spatially clustered.

[Bone Metabolism of Multiple Myeloma Bone Disease Patients with Different Blood Separation Results].

OBJECTIVE: To investigate the clinical significance of bone metabolic indexes for disease assessment and curative effect monitoring in multiple myeloma (MM) bone disease (MBD) patients with different blood separation results. METHODS: A total of 134 newly diagnosed MM patients treated in Cangzhou Hospital of Integrated TCM-WM-Hebei were enrolled and divided into control group [119 cases, serum, colloid and red blood cell (RBC) from top to bottom of sample] and abnormal group (15 cases, serum, mixed layer of RBC and serum, colloid and RBC from top to bottom of sample) according to the results of blood separation. According to the imaging findings, MBD was classified into grade 0-4, grade 0-2 was mild, and grade 3-4 was severe. The MBD grade of patients in the two groups was analyzed. The curative effect of MBD patients after chemotherapy and the changes of blood separation results and bone metabolic indexes before and after treatment were evaluated. The correlation between ß2-microglobulin (MG) and bone metabolic indexes was analyzed by Pearson correlation analysis. RESULTS: In the control group, there were 69 cases of grade 0-2 and 50 cases of grade 3-4, while in the abnormal group, there were 5 cases of grade 0-2 and 10 cases of grade 3-4, the difference was statistically significant (P < 0.05). The serum ß2-MG, ß-CTX levels in abnormal group were both significantly higher than those in control group, while the levels of P1NP and osteocalcin (OC) were significantly lower (all P < 0.001). In the control group, there were 95 patients with ≥ partial response (PR) and the blood separation results were not changed, while 24 patients with 0.05). Compared with before treatment, the levels of ß-CTX and ß2-MG in the control group with unchanged blood separation results were significantly decreased (both P < 0.001), while the levels of P1NP and OC were significantly increased (P < 0.01, P < 0.001), and the level of each index in the patients transformed to abnormal blood separation result after treatment did not significantly change (P >0.05); the levels of ß-CTX and ß2-MG in the abnormal group transformed to normal blood separation result were significantly decreased (both P < 0.01), while the levels of P1NP and OC were significantly increased (P < 0.001, P < 0.01), and the level of each index in patients with unchanged blood separation results did not significantly change (P>0.05). Pearson correlation analysis showed that serum ß2-MG was positively correlated with ß-CTX (r =0.709, P < 0.001), and negatively correlated with P1NP and OC (r =-0.410,r =-0.412, both P < 0.001). CONCLUSION: MBD patients with abnormal blood separation results have higher bone disease grade and poor prognosis, which is closely related to the significant increase of bone resorption index ß-CTX level and decrease of bone formation index P1NP and OC levels, leading to more serious bone metabolic homeostasis disorder. The results of blood separation combined with the changes of bone metabolic indexes can be used as one of the comprehensive predictors of disease condition, efficacy monitoring and prognosis evaluation of MBD patients.

Solid Electrolytes for Low-Temperature Carbon Dioxide Valorization: A Review.

One of the most promising approaches to address the global challenge of climate change is electrochemical carbon capture and utilization. Solid electrolytes can play a crucial role in establishing a chemical-free pathway for the electrochemical capture of CO2. Furthermore, they can be applied in electrocatalytic CO2 reduction reactions (CO2RR) to increase carbon utilization, produce high-purity liquid chemicals, and advance hybrid electro-biosystems. This review article begins by covering the fundamentals and processes of electrochemical CO2 capture, emphasizing the advantages of utilizing solid electrolytes. Additionally, it highlights recent advancements in the use of the solid polymer electrolyte or solid electrolyte layer for the CO2RR with multiple functions. The review also explores avenues for future research to fully harness the potential of solid electrolytes, including the integration of CO2 capture and the CO2RR and performance assessment under realistic conditions. Finally, this review discusses future opportunities and challenges, aiming to contribute to the establishment of a green and sustainable society through electrochemical CO2 valorization.

Insights into how characteristics of dissolved algal organic matter affect the efficiency of modified clay in controlling harmful algal blooms.

Dissolved algal organic matter (dAOM) originating from harmful algal blooms (HABs) can deteriorate the quality of municipal water supplies, threaten the health of aquatic environments, and interfere with modified clay (MC)-based HABs control measures. In this study, we explored the composition of dAOM from Prorocentrum donghaiense, a typical HAB organism, and assessed the influence of dAOM on MC flocculation. Our results suggested that dAOM composition was complex and had a wide molecular weight (MW) distribution. MW and electrical properties were important dAOM characteristics affecting flocculation and algal removal efficiency of MC. Negatively charged high-MW components (>50 kDa) critically affected algal removal efficiency, reducing the zeta potential of MC particles and leading to small and weak flocs. However, the effect of dAOM depended on its concentration. When the cell density of P. donghaiense reached HAB levels, the high-MW dAOM strongly decreased the algal removal efficiency of MC.

Role of Copper Nanoparticles in the Thermal and Mechanical Properties of Expanded Graphite-Reinforced Epoxy Hybrids.

Epoxy resin is extensively applied in the electronics and electrical fields because of its outstanding comprehensive performance. However, the low thermal conductivity (TC) limits its application in thermal interface materials. In the present work, epoxy-based hybrid composites with high TC were prepared by using expanded graphite (EG) and copper (Cu) nanoparticles as thermally conductive hybrid fillers via hot blending and compression-curing processes. Additionally, the influence of the Cu content on the thermal properties, mechanical properties, and morphology of each epoxy/EG/Cu composite was investigated. According to the results, the epoxy/EG/Cu composite showed a maximum TC of 9.74 W/(m·K) at a fixed EG content of 60 wt % owing to the addition of 10 wt % Cu. After the addition of 10 wt % Cu, the flexural strength, flexural modulus, and impact strengths of epoxy/EG/Cu composites were improved from 27.9 MPa, 9.72 GPa, and 0.81 kJ/m2 to 37.5 MPa, 10.88 GPa, and 0.91 kJ/m2, respectively. Hence, this study offers a feasible strategy for the design of epoxy hybrid composites with excellent TC that can be applied to thermal interface materials.

Delineating cathodic extracellular electron transfer pathways in microbial electrosynthesis: Modulation of polarized potential and Pt@C addition.

Microbial electrosynthesis (MES) is an innovative technology that employs microbes to synthesize chemicals by reducing CO2. A comprehensive understanding of cathodic extracellular electron transfer (CEET) is essential for the advancement of this technology. This study explores the impact of different cathodic potentials on CEET and its response to introduction of hydrogen evolution materials (Pt@C). Without the addition of Pt@C, H2-mediated CEET contributed up to 94.4 % at -1.05 V. With the addition of Pt@C, H2-mediated CEET contributions were 76.6 % (-1.05 V) and 19.9 % (-0.85 V), respectively. BRH-c20a was enriched as the dominated microbe (>80 %), and its relative abundance was largely affected by the addition of Pt@C NPs. This study highlights the tunability of MES performance through cathodic potential control and the addition of metal nanoparticles.

Tandem Acidic CO2 Electrolysis Coupled with Syngas Fermentation: A Two-Stage Process for Producing Medium-Chain Fatty Acids.

The tandem application of CO2 electrolysis with syngas fermentation holds promise for achieving heightened production rates and improved product quality. However, the significant impact of syngas composition on mixed culture-based microbial chain elongation remains unclear. Additionally, effective methods for generating syngas with an adjustable composition from acidic CO2 electrolysis are currently lacking. This study successfully demonstrated the production of medium-chain fatty acids from CO2 through tandem acidic electrolysis with syngas fermentation. CO could serve as the sole energy source or as the electron donor (when cofed with acetate) for caproate generation. Furthermore, the results of gas diffusion electrode structure engineering highlighted that the use of carbon black, either alone or in combination with graphite, enabled consistent syngas generation with an adjustable composition from acidic CO2 electrolysis (pH 1). The carbon black layer significantly improved the CO selectivity, increasing from 0% to 43.5% (0.05 M K+) and further to 92.4% (0.5 M K+). This enhancement in performance was attributed to the promotion of K+ accumulation, stabilizing catalytically active sites, rather than creating a localized alkaline environment for CO2-to-CO conversion. This research contributes to the advancement of hybrid technology for sustainable CO2 reduction and chemical production.

Surface coating combined with in situ cyclic voltammetry to enhance the stability of gas diffusion electrodes for electrochemical CO2 reduction.

Electrochemical CO2 reduction (CO2RR), fueled by clean and renewable energy, presents a promising method for utilizing CO2 effectively. The electrocatalytic reduction of CO2 to CO using a gas diffusion electrode (GDE) has shown great potential for industrial applications due to its high reaction rate and selectivity. However, guaranteeing its long-term stability still poses a significant challenge. In this study, we conducted a comprehensive investigation into various strategies to enhance the stability of the GDE. These strategies involved modifying the structure of the substrate, such as the gas diffusion layer (GDL) and the back side of the GDL (macroporous layer side). Additionally, we explored modifications to the catalyst layer (CL) and the front of the CL. To address these stability concerns, we proposed a practical approach that involved surface coating using carbon black in combination with in situ cyclic voltammetry (CV) cycles on Ag/Ag300/polytetrafluoroethylene (PTFE). The partial Faradaic efficiency exceeded 80 % within a span of 70 h. Electron microscopy and electrochemical characterization revealed that the implementation of in situ CV led to a reduction in catalyst particle size and the formation of a porous surface structure. By enhancing the stability of the GDE, this research opens up possibilities for the advancement of hybrid systems that focus on the production and utilization of syngas.

Perturbations in gut and respiratory microbiota in COVID-19 and influenza patients: a systematic review and meta-analysis.

Objectives: Coronavirus disease-19 (COVID-19)/influenza poses unprecedented challenges to the global economy and healthcare services. Numerous studies have described alterations in the microbiome of COVID-19/influenza patients, but further investigation is needed to understand the relationship between the microbiome and these diseases. Herein, through systematic comparison between COVID-19 patients, long COVID-19 patients, influenza patients, no COVID-19/influenza controls and no COVID-19/influenza patients, we conducted a comprehensive review to describe the microbial change of respiratory tract/digestive tract in COVID-19/influenza patients. Methods: We systematically reviewed relevant literature by searching the PubMed, Embase, and Cochrane Library databases from inception to August 12, 2023. We conducted a comprehensive review to explore microbial alterations in patients with COVID-19/influenza. In addition, the data on α-diversity were summarized and analyzed by meta-analysis. Results: A total of 134 studies comparing COVID-19 patients with controls and 18 studies comparing influenza patients with controls were included. The Shannon indices of the gut and respiratory tract microbiome were slightly decreased in COVID-19/influenza patients compared to no COVID-19/influenza controls. Meanwhile, COVID-19 patients with more severe symptoms also exhibited a lower Shannon index versus COVID-19 patients with milder symptoms. The intestinal microbiome of COVID-19 patients was characterized by elevated opportunistic pathogens along with reduced short-chain fatty acid (SCFAs)-producing microbiota. Moreover, Enterobacteriaceae (including Escherichia and Enterococcus) and Lactococcus, were enriched in the gut and respiratory tract of COVID-19 patients. Conversely, Haemophilus and Neisseria showed reduced abundance in the respiratory tract of both COVID-19 and influenza patients. Conclusion: In this systematic review, we identified the microbiome in COVID-19/influenza patients in comparison with controls. The microbial changes in influenza and COVID-19 are partly similar.

Super-fast Charging Biohybrid Batteries through a Power-to-formate-to-bioelectricity Process by Combining Microbial Electrochemistry and CO2 Electrolysis.

Extensive study on renewable energy storage has been sparked by the growing worries regarding global warming. In this study, incorporating the latest advancements in microbial electrochemistry and electrochemical CO2 reduction, a super-fast charging biohybrid battery was introduced by using pure formic acid as an energy carrier. CO2 electrolyser with a slim-catholyte layer and a solid electrolyte layer was built, which made it possible to use affordable anion exchange membranes and electrocatalysts that are readily accessible. The biohybrid battery only required a 3-minute charging to accomplish an astounding 25-hour discharging phase. In the power-to-formate-to-bioelectricity process, bioconversion played a vital role in restricting both the overall Faradaic efficiency and Energy efficiency. The CO2 electrolyser was able to operate continuously for an impressive total duration of 164 hours under Gas Stand-By model, by storing N2 gas in the extraction chamber during stand-by periods. Additionally, the electric signal generated during the discharging phase was utilized for monitoring water biotoxicity. Functional genes related to formate metabolism were identified in the bioanode and electrochemically active bacteria were discovered. On the other hand, Paracoccus was predominantly found in the used air cathode. These results advance our current knowledge of exploiting biohybrid technology.

Identification of ARF transcription factor gene family and its defense responses to bacterial infection and salicylic acid treatment in sugarcane.

Auxin response factor (ARF) is a critical regulator in the auxin signaling pathway, involved in a variety of plant biological processes. Here, gene members of 24 SpapARFs and 39 SpnpARFs were identified in two genomes of Saccharum spontaneum clones AP85-441 and Np-X, respectively. Phylogenetic analysis showed that all ARF genes were clustered into four clades, which is identical to those ARF genes in maize (Zea mays) and sorghum (Sorghum bicolor). The gene structure and domain composition of this ARF family are conserved to a large degree across plant species. The SpapARF and SpnpARF genes were unevenly distributed on chromosomes 1-8 and 1-10 in the two genomes of AP85-441 and Np-X, respectively. Segmental duplication events may also contribute to this gene family expansion in S. spontaneum. The post-transcriptional regulation of ARF genes likely involves sugarcane against various stressors through a miRNA-medicated pathway. Expression levels of six representative ShARF genes were analyzed by qRT-PCR assays on two sugarcane cultivars [LCP85-384 (resistant to leaf scald) and ROC20 (susceptible to leaf scald)] triggered by Acidovorax avenae subsp. avenae (Aaa) and Xanthomonas albilineans (Xa) infections and salicylic acid (SA) treatment. ShARF04 functioned as a positive regulator under Xa and Aaa stress, whereas it was a negative regulator under SA treatment. ShARF07/17 genes played positive roles against both pathogenic bacteria and SA stresses. Additionally, ShARF22 was negatively modulated by Xa and Aaa stimuli in both cultivars, particularly LCP85-384. These findings imply that sugarcane ARFs exhibit functional redundancy and divergence against stressful conditions. This work lays the foundation for further research on ARF gene functions in sugarcane against diverse environmental stressors.

Electricity-Driven Microbial Metabolism of Carbon and Nitrogen: A Waste-to-Resource Solution.

Electricity-driven microbial metabolism relies on the extracellular electron transfer (EET) process between microbes and electrodes and provides promise for resource recovery from wastewater and industrial discharges. Over the past decades, tremendous efforts have been dedicated to designing electrocatalysts and microbes, as well as hybrid systems to push this approach toward industrial adoption. This paper summarizes these advances in order to facilitate a better understanding of electricity-driven microbial metabolism as a sustainable waste-to-resource solution. Quantitative comparisons of microbial electrosynthesis and abiotic electrosynthesis are made, and the strategy of electrocatalyst-assisted microbial electrosynthesis is critically discussed. Nitrogen recovery processes including microbial electrochemical N2 fixation, electrocatalytic N2 reduction, dissimilatory nitrate reduction to ammonium (DNRA), and abiotic electrochemical nitrate reduction to ammonia (Abio-NRA) are systematically reviewed. Furthermore, the synchronous metabolism of carbon and nitrogen using hybrid inorganic-biological systems is discussed, including advanced physicochemical, microbial, and electrochemical characterizations involved in this field. Finally, perspectives for future trends are presented. The paper provides valuable insights on the potential contribution of electricity-driven microbial valorization of waste carbon and nitrogen toward a green and sustainable society.

Global Responses of Autopolyploid Sugarcane Badila (Saccharum officinarum L.) to Drought Stress Based on Comparative Transcriptome and Metabolome Profiling.

Sugarcane (Saccharum spp. hybrid) is frequently affected by seasonal drought, which causes substantial declines in quality and yield. To understand the drought resistance mechanisms of S. officinarum, the main species of modern sugarcane, at a molecular level, we carried out a comparative analysis of transcriptome and metabolome profiling of the sugarcane variety Badila under drought stress (DS). Compared with control group (CG) plants, plants exposed to DS had 13,744 (6663 up-regulated and 7081 down-regulated) differentially expressed genes (DEGs). GO and KEGG analysis showed that the DEGs were enriched in photosynthesis-related pathways and most DEGs had down-regulated expression. Moreover, the chlorophyll content, photosynthesis (Photo), stomatal conductance (Cond), intercellular carbon dioxide concentration (Ci) and transpiration rate (Trmmol) were sharply decreased under DS. These results indicate that DS has a significant negative influence on photosynthesis in sugarcane. Metabolome analysis identified 166 (37 down-regulated and 129 up-regulated) significantly regulated metabolites (SRMs). Over 50% of SRMs were alkaloids, amino acids and their derivatives, and lipids. The five most significantly enriched KEGG pathways among SRMs were Aminoacyl-tRNA biosynthesis, 2-Oxocarboxylic acid metabolism, Biosynthesis of amino acids, Phenylalanine metabolism, and Arginine and proline metabolism (p < 0.05). Comparing CG with DS for transcriptome and metabolome profiling (T_CG/DS and M_CG/DS, respectively), we found three of the same KEGG-enriched pathways, namely Biosynthesis of amino acids, Phenylalanine metabolism and Arginine and proline metabolism. The potential importance of Phenylalanine metabolism and Arginine and proline metabolism was further analyzed for response to DS in sugarcane. Seven SRMs (five up-regulated and two down-regulated) and 60 DEGs (17 up-regulated and 43 down-regulated) were enriched in Phenylalanine metabolism under DS, of which novel.31261, Sspon.04G0008060-1A, Sspon.04G0008060-2B and Sspon.04G0008060-3C were significantly correlated with 7 SRMs. In Arginine and proline metabolism, eight SRMs (seven up-regulated and one down-regulated) and 63 DEGs (32 up-regulated and 31 down-regulated) were enriched, of which Sspon.01G0026110-1A (OAT) and Sspon.03G0002750-3D (P5CS) were strongly associated with proline (r > 0.99). These findings present the dynamic changes and possible molecular mechanisms of Phenylalanine metabolism as well as Arginine and proline metabolism under DS and provide a foundation for future research and sugarcane improvement.

Genome-wide characterization of cys-tathionine-ß-synthase domain-containing proteins in sugarcane reveals their role in defense responses under multiple stressors.

Cys-tathionine-ß-synthase (CBS) domain-containing proteins (CDCPs) are essential for regulating plant responses to various biotic and abiotic stressors. This study describes the systematic identification and characterization of CDCP family genes in Saccharum spontaneum. A total of 95 SsCDCP genes and eight phylogenetic groups were identified that were distributed over 29 chromosomes of the AP85-441 genome. Most (78/95) SsCDCPs underwent fragment duplication events, and 64 gene pairs were located in synteny blocks. Expression profiling of nine ShCDCPs was also carried out in the Saccharum spp. cultivars ROC22 and MT11-611 that are resistant and susceptible to red stripe, respectively, in response to: (i) Infection by the bacterial pathogen Acidovorax avenue subsp. avenae (Aaa); (ii) abiotic stressors (drought and salinity); and (iii) exogenous salicylic acid (SA) treatment. Members of one gene pair (ShCBSD-PB1-5A and ShCBSD-PB1-7A-1) with a fragment duplication event acted as negative regulators in sugarcane under four stresses, as supported by the significantly decreased expression levels of ShCBSD-PB1-5A (23-83%) and ShCBSD-PB1-7A-1 (15-75%) at all-time points, suggesting that they have functional redundancy. Genes in another pair, ShCBS-4C and ShCBS-4D-1, which have a fragment duplication event, play opposing regulatory roles in sugarcane exposed to multiple stresses, particularly Aaa and NaCl treatments. ShCBS-4C expression was significantly decreased by 32-77%, but ShCBS-4D-1 expression was dramatically upregulated by 1.2-6.2-fold in response to Aaa treatment of both cultivars across all-time points. This result suggested that both genes exhibited functional divergence. Meanwhile, the expression of SsCBSDCBS-5A was significantly upregulated in ROC22 by 1.4-4.6-fold in response to the four stressors. These findings provide important clues for further elucidating the function of ShCDCP genes in sugarcane responding to a diverse range of stresses.

Integrated Analysis of Transcriptome and Metabolome Reveals the Regulation of Chitooligosaccharide on Drought Tolerance in Sugarcane (Saccharum spp. Hybrid) under Drought Stress.

Sugarcane (Saccharum spp. hybrid) is an important crop for sugar and biofuels, and often suffers from water shortages during growth. Currently, there is limited knowledge concerning the molecular mechanism involved in sugarcane response to drought stress (DS) and whether chitooligosaccharide could alleviate DS. Here, we carried out a combined transcriptome and metabolome of sugarcane in three different treatment groups: control group (CG), DS group, and DS + chitooligosaccharide group (COS). A total of 12,275 (6404 up-regulated and 5871 down-regulated) differentially expressed genes (DEGs) were identified when comparing the CG and DS transcriptomes (T_CG/DS), and 2525 (1261 up-regulated and 1264 down-regulated) DEGs were identified in comparing the DS and COS transcriptomes (T_DS/COS). GO and KEGG analysis showed that DEGs associated with photosynthesis were significantly enriched and had down-regulated expression. For T_DS/COS, photosynthesis DEGs were also significantly enriched but had up-regulated expression. Together, these results indicate that DS of sugarcane has a significantly negative influence on photosynthesis, and that COS can alleviate these negative effects. In metabolome analysis, lipids, others, amino acids and derivatives and alkaloids were the main significantly different metabolites (SDMs) observed in sugarcane response to DS, and COS treatment reduced the content of these metabolites. KEGG analysis of the metabolome showed that 2-oxocarboxylic acid metabolism, ABC transporters, biosynthesis of amino acids, glucosinolate biosynthesis and valine, leucine and isoleucine biosynthesis were the top-5 KEGG enriched pathways when comparing the CG and DS metabolome (M_CG/DS). Comparing DS with COS (M_DS/COS) showed that purine metabolism and phenylalanine metabolism were enriched. Combined transcriptome and metabolome analysis revealed that pyruvate and phenylalanine metabolism were KEGG-enriched pathways for CG/DS and DS/COS, respectively. For pyruvate metabolism, 87 DEGs (47 up-regulated and 40 down-regulated) and five SDMs (1 up-regulated and 4 down-regulated) were enriched. Pyruvate was closely related with 14 DEGs (|r| > 0.99) after Pearson's correlation analysis, and only 1 DEG (Sspon.02G0043670-1B) was positively correlated. For phenylalanine metabolism, 13 DEGs (7 up-regulated and 6 down-regulated) and 6 SDMs (1 up-regulated and 5 down-regulated) were identified. Five PAL genes were closely related with 6 SDMs through Pearson's correlation analysis, and the novel.31257 gene had significantly up-regulated expression. Collectively, our results showed that DS has significant adverse effects on the physiology, transcriptome, and metabolome of sugarcane, particularly genes involved in photosynthesis. We further show that COS treatment can alleviate these negative effects.

Combined transcriptome and metabolome reveal glutathione metabolism plays a critical role in resistance to salinity in rice landraces HD961.

Rice (Oryza sativa) is one of the most important food crops around the world, which is sensitive to salt stress, especially in the seedling and booting stage. HD961 is a salt-tolerant rice landrace that grows along coastal beaches and has disease and insect pest resistance, salt tolerance, and vigorous growth characteristics. We performed a combined transcriptome and metabolome analysis to clarify salinity resistance mechanisms in cultivar HD961, which has adapted to salinity soil at the early seedling stage. The results showed that the growth and antioxidant capacity of HD961 were stronger than 9311 under salt stress (SS). Transcriptomic analysis showed that a total of 6,145, 3,309, 1,819, and 1,296 differentially expressed genes (DEGs) were identified in the groups of TH60 (control group vs. 60 mM group of HD961 for transcriptome), TH120 (control group vs. 120 mM group of HD961 for transcriptome), T60 (control group vs. 60 mM group of 9311 for transcriptome), and T120 (control group vs. 120 mM group of 9311 for transcriptome), respectively. Starch and sucrose metabolism and phenylpropanoid biosynthesis were shared in the four treatment groups based on a KEGG enrichment analysis of DEGs. In addition, alpha-linolenic acid metabolism, plant hormone signal transduction, plant-pathogen interaction, and fatty acid elongation were specific and significantly different in HD961. A total of 92, 158, 151, and 179 significantly regulated metabolites (SRMs) responded to SS in MH60 (control group vs. 60 mM group of HD961 for metabolome), MH120 (control group vs. 120 mM group of HD961 for metabolome), M60 (control group vs. 60 mM group of 9311 for metabolome), and M120 (control group vs. 120 mM group of 9311 for metabolome), respectively. The KEGG analysis showed that eight common metabolic pathways were identified in the four treatment groups, of which biosynthesis of amino acids was the most significant. Three specific metabolic pathways were identified in the HD961, including glutathione metabolism, ascorbate and aldarate metabolism, and pantothenate and CoA biosynthesis. Integrative analysis between the transcriptome and metabolome showed that glutathione metabolism was specific and significantly affected under SS in HD961. A total of seven SRMs and 48 DEGs and four SRMs and 15 DEGs were identified in the glutathione metabolism pathway in HD961 and 9311, respectively. The Pearson correlation analysis showed a significant correlation between reduced glutathione and 16 genes (12 upregulated and four downregulated genes), suggesting these genes could be candidates as salt-tolerance regulation genes. Collectively, our data show that glutathione metabolism plays a critical role in response to SS in rice. Moreover, the stronger regulative ability of related common genes and metabolites might contribute to salt resistance in HD961.