Phenotyping of single plant cells on a microfluidic cytometry platform with fluorescent, mechanical, and electrical modules.

Compared to animal cells, phenotypic characterization of single plant cells on microfluidic platforms is still rare. In this work, we collated population statistics on the morphological, biochemical, physical and electrical properties of Arabidopsis protoplasts under different external and internal conditions, using progressively improved microfluidic platforms. First, we analyzed the different effects of three phytohormones (auxin, cytokinin and gibberellin) on the primary cell wall (PCW) regeneration process using a microfluidic flow cytometry platform equipped with a single-channel fluorescence sensor. Second, we correlated the intracellular reactive oxygen species (ROS) level induced by heavy metal stress with the concurrent PCW regeneration process by using a dual-channel fluorescence sensor. Third, by integrating contraction channels, we were able to effectively discriminate variations in cell size while monitoring the intensity of intracellular ROS signaling. Fourth, by combining an electrical impedance electrode with the contraction channel, we analyzed the differences in electrical and mechanical properties of wild-type and mutant plant cells before and after primary cell wall regeneration. Overall, our work demonstrates the feasibility and sensitivity of microfluidic flow cytometry in high-throughput phenotyping of plant cells and provides a reference for assessing metabolic and physiological indicators of individual plant cells in multiple dimensions.

Effects of intensive psychological intervention on treatment compliance, psychological status, and quality of life of patients with epilepsy.

BACKGROUND: Epilepsy is a nervous system disease characterized by recurrent attacks, a long disease course, and an unfavorable prognosis. It is associated with an enduring therapeutic process, and finding a cure has been difficult. Patients with epilepsy are predisposed to adverse moods, such as resistance, anxiety, nervousness, and anxiety, which compromise treatment compliance and overall efficacy. AIM: To explored the influence of intensive psychological intervention on treatment compliance, psychological status, and quality of life (QOL) of patients with epilepsy. METHODS: The clinical data of 105 patients with epilepsy admitted between December 2019 and July 2023 were retrospectively analyzed, including those of 50 patients who underwent routine intervention (control group) and 55 who underwent intensive psychological intervention (research group). Treatment compliance, psychological status based on the Self-Rating Anxiety Scale (SAS) and Depression Scale Self-Rating Depression Scale (SDS) scores, hope level assessed using the Herth Hope Scale (HHS), psychological resilience evaluated using the Psychological Resilience Scale, and QOL determined using the QOL in Epilepsy-31 Inventory (QOLIE-31) were comparatively analyzed. RESULTS: Treatment compliance in the research group was 85.5%, which is significantly better than the 68.0% of the control group. No notable intergroup differences in preinterventional SAS and SDS scores were identified (P > 0.05); however, after the intervention, the SAS and SDS scores decreased significantly in the two groups, especially in the research group (P < 0.05). The two groups also exhibited no significant differences in preinterventional HHS, Connor-Davidson Resilience Scale (CD-RISC), and QOLIE-31 scores (P > 0.05). After 6 months of intervention, the research group showed evidently higher HHS, CD-RISC, tenacity, optimism, strength, and QOLIE-31 scores (P < 0.05). CONCLUSION: Intensive psychological intervention enhances treatment compliance, psychological status, and QOL of patients with epilepsy.

Association between MTHFR C677T Gene Polymorphisms and the Efficacy of Vitamin Therapy in lowering Homocysteine Levels among Stroke Patients with Hyperhomocysteinemia.

BACKGROUND: The impact of the methylenetetrahydrofolate reductase (MTHFR) C677T mutation on the relationship between plasma homocysteine (Hcy) levels and stroke has been extensively studied and documented in previous study. However, it remains unclear whether the MTHFR C677T mutation can affect the response to Hcy lowering treatment in stroke patients with hyperhomocysteinemia (HHcy). Understanding the impact of genetic factors on treatment response can help optimize personalized treatment strategies for stroke patients with HHcy. We aimed to investigate the potential association between the MTHFR C677T gene polymorphisms and the effectiveness of Hcy lowering treatment using vitamin therapy in stroke patients with HHcy. METHODS: The MTHFR C677T genotype polymorphisms were identified using polymerase chain reaction-restriction fragment length polymorphism, and the distribution of three genotypes in the MTHFR C677T gene locus was compared. The treatment effects of Hcy lowering agents were compared among patients with different genotypes. RESULTS: Among the 320 stroke patients enrolled in the study, 258 (80.6%) were diagnosed with HHcy. Of these, 162 patients (Effective Group) responded well to the clinical Hcy lowering treatment, while 96 patients (Invalid Group) failed to achieve sufficient response even after taking combination supplements of folic acid, Vitamin B6, and methylcobalamin for one month. Significant differences were observed in terms of age (p < 0.001), hypertension (p = 0.034), dyslipidemia (p = 0.022), hyperuricemia (p = 0.013) and genotype distribution of MTHFR C677T gene polymorphism (p < 0.001) between the Invalid group and the Effective group. The multivariate regression analysis revealed that the T allele (odd rations [OR], 1.327; 95% confidence interval [CI], 1.114-1.580; p = 0.0015) was independently associated with an insufficient Hcy lowering treatment effect. Additionally, the TT genotype was independently associated with insufficient response in both the codominant model (OR, 1.645; 95% CI, 1.093-2.476; p = 0.017) and the recessive model (TT versus CC + CT; OR, 1.529; 95% CI, 1.145-2.042; p = 0.004). However, no relationship was observed between CT + TT genotypes and poor treatment effect in the dominate model. CONCLUSIONS: Our findings suggested that the TT genotype and T allele of MTHFR C677T polymorphism were independently associated with an insufficient Hcy lowering treatment effect in stroke patients with HHcy.

Variations of sediment organic phosphorus and organic carbon during the outbreak and decline of algal blooms in Lake Taihu, China.

In this study, sediment organic phosphorus (OP) and organic carbon (OC) in Lake Taihu, China, as well as their relationships, were analyzed during the outbreak and decline of algal blooms (ABs) over a five-month field study. The results showed synchronous temporal changes in the sediment OP and OC contents with the development of ABs. In addition, there was a significant positive correlation between the sediment OP and OC (p < 0.01), suggesting simultaneous deposition and consumption during the ABs outbreak. The sediment OP and OC contents decreased significantly at the early and last stages of the ABs outbreak and increased at the peak of the ABs outbreak and during the ABs decline. These temporal variation patterns suggest that the sediment OC and OP contents did not consistently increase during the ABs outbreak, even though algae are an important source of organic matter in sediments. The depletion or enrichment of OC and OP in sediments may also depend on the scale of the ABs outbreak. The obtained results revealed significant differences in the sediment OC and OP contents between the months (p < 0.05). In addition, OP in the sediments was dominated by orthophosphate diester (phospholipids and DNA-P) and orthophosphate monoester during the ABs outbreak and decline, respectively. The active OC contents and proportions in the sediments in the ABs outbreak were significantly lower than those observed in the ABs decline period, demonstrating the significant impacts of the ABs outbreak and decline on the sediment OC and OP in Lake Taihu.

Auxin homeostasis in plant responses to heavy metal stress.

Expeditious industrialization and anthropogenic activities have resulted in large amounts of heavy metals (HMs) being released into the environment. These HMs affect crop yields and directly threaten global food security. Therefore, significant efforts have been made to control the toxic effects of HMs on crops. When HMs are taken up by plants, various mechanisms are stimulated to alleviate HM stress, including the biosynthesis and transport of auxin in the plant. Interestingly, researchers have noted the significant potential of auxin in mediating resistance to HM stress, primarily by reducing uptake of metals, promoting chelation and sequestration in plant tissues, and mitigating oxidative damage. Both exogenous administration of auxin and manipulation of intrinsic auxin status are effective strategies to protect plants from the negative consequences of HMs stress. Regulation of genes and transcription factors related to auxin homeostasis has been shown to be related to varying degrees to the type and concentration of HMs. Therefore, to derive the maximum benefit from auxin-mediated mechanisms to attenuate HM toxicities, it is essential to gain a comprehensive understanding of signaling pathways involved in regulatory actions. This review primarily emphases on the auxin-mediated mechanisms participating in the injurious effects of HMs in plants. Thus, it will pave the way to understanding the mechanism of auxin homeostasis in regulating HM tolerance in plants and become a tool for developing sustainable strategies for agricultural growth in the future.

Arabidopsis seedlings respond differentially to nutrient efficacy of three rock meals by regulating root architecture and endogenous auxin homeostasis.

BACKGROUND: Plants show developmental plasticity with variations in environmental nutrients. Considering low-cost rock dust has been identified as a potential alternative to artificial fertilizers for more sustainable agriculture, the growth responses of Arabidopsis seedlings on three rock meals (basalt, granite, and marlstone) were examined for the different foraging behavior, biomass accumulation, and root architecture. RESULTS: Compared to ½ MS medium, basalt and granite meal increased primary root length by 13% and 38%, respectively, but marlstone caused a 66% decrease, and they all drastically reduced initiation and elongation of lateral roots but lengthened root hairs. Simultaneous supply of organic nutrients and trace elements increased fresh weight due to the increased length of primary roots and root hairs. When nitrogen (N), phosphorus (P), and potassium (K) were supplied individually, N proved most effective in improving fresh weight of seedlings growing on basalt and granite, whereas K, followed by P, was most effective for those growing on marlstone. Unexpectedly, the addition of N to marlstone negatively affected seedling growth, which was associated with repressed auxin biosynthesis in roots. CONCLUSIONS: Our data indicate that plants can recognize and adapt to complex mineral deficiency by adjusting hormonal homeostasis to achieve environmental sensitivity and developmental plasticity, which provide a basis for ecologically sound and sustainable strategies to maximize the use of natural resources and reduce the production of artificial fertilizers.

Improved efficiency of Sedum lineare (Crassulaceae) in remediation of arsenic-contaminated soil by phosphate-dissolving strain P-1 in association with phosphate rock.

The selection of appropriate plants and growth strategies is a key factor in improving the efficiency and universal applicability of phytoremediation. Sedum lineare grows rapidly and tolerates multiple adversities. The effects of inoculation of Acinetobacter sp. phosphate solubilizing bacteria P-1 and application of phosphate rock (PR) as additives on the remediation efficiency of As-contaminated soil by S. lineare were investigated. Compared with the control, both the single treatment and the combination of inoculation with strain P-1 and application of PR improved the biomass by 30.7-395.5%, chlorophyll content by 48.1-134.8%, total protein content by 12.5-92.4% and total As accumulation by 45.1-177.5%, and reduced the As-induced oxidative damage. Inoculation with strain P-1 increased the activities of superoxide dismutases and catalases of S. lineare under As stress, decreased the accumulation of reactive oxygen species in plant tissues and promoted the accumulation of As in roots. In contrast, simultaneous application of PR decreased As concentration in S. lineare tissues, attenuated As-induced lipid peroxidation and improved As transport to shoots. In addition, the combined application showed the best performance in improving resistance and biomass, which significantly increased root length by 149.1%, shoot length by 33%, fresh weight by 395.5% and total arsenic accumulation by 159.2%, but decreased the malondialdehyde content by 89.1%. Our results indicate that the combined application of strain P-1 and PR with S. lineare is a promising bioremediation strategy to accelerate phytoremediation of As-contaminated soils.

Effects of heavy rain on the concentrations and forms of carbon, nitrogen and phosphorus in urban rivers of northern China.

Non-point source pollution caused by rainfall runoff is an important pollution source for river water. To explore the impact of heavy rain on urban river water environments, this paper studied the changes in carbon, nitrogen, and phosphorus levels, composition, and structure in the river water of Kaifeng, China, during the heavy rain in July 2021. The results showed that the concentrations of different forms of carbon, nitrogen, and phosphorus all increased under the effect of the heavy rain. The increase of phosphorus in the river was the largest, and that of carbon was the smallest. The most significant pollution from carbon, nitrogen, and phosphorus occurred in the HJ River. Colored dissolved organic matter (CDOM) was present in the form of macromolecules after the rain, and the degree of humification was deeper compared with before the rain. But heavy rain did not affect the CDOM composition in urban rivers. The spectral slope (SR) and the absorption coefficient at 240 nm to 420 nm (E2/E4) values showed that the CDOM was dominated by exogenous input after the rain, with endogenous pollution again becoming the main factor one week after the rain.

Mitochondrial Genome Sequence of Salvia officinalis (Lamiales: Lamiaceae) Suggests Diverse Genome Structures in Cogeneric Species and Finds the Stop Gain of Genes through RNA Editing Events.

Our previous study was the first to confirm that the predominant conformation of mitochondrial genome (mitogenome) sequence of Salvia species contains two circular chromosomes. To further understand the organization, variation, and evolution of Salvia mitogenomes, we characterized the mitogenome of Salvia officinalis. The mitogenome of S. officinalis was sequenced using Illumina short reads and Nanopore long reads and assembled using a hybrid assembly strategy. We found that the predominant conformation of the S. officinalis mitogenome also had two circular chromosomes that were 268,341 bp (MC1) and 39,827 bp (MC2) in length. The S. officinalis mitogenome encoded an angiosperm-typical set of 24 core genes, 9 variable genes, 3 rRNA genes, and 16 tRNA genes. We found many rearrangements of the Salvia mitogenome through inter- and intra-specific comparisons. A phylogenetic analysis of the coding sequences (CDs) of 26 common protein-coding genes (PCGs) of 11 Lamiales species and 2 outgroup taxa strongly indicated that the S. officinalis was a sister taxon to S. miltiorrhiza, consistent with the results obtained using concatenated CDs of common plastid genes. The mapping of RNA-seq data to the CDs of PCGs led to the identification of 451 C-to-U RNA editing sites from 31 PCGs of the S. officinalis mitogenome. Using PCR amplification and Sanger sequencing methods, we successfully validated 113 of the 126 RNA editing sites from 11 PCGs. The results of this study suggest that the predominant conformation of the S. officinalis mitogenome are two circular chromosomes, and the stop gain of rpl5 was found through RNA editing events of the Salvia mitogenome.

Phytotoxicity of zinc oxide nanoparticles and multi-walled carbon nanotubes, alone or in combination, on Arabidopsis thaliana and their mutual effects on oxidative homeostasis.

The extensive use of engineered nanoparticles (ENPs) has raised concerns about their potentially harmful effects on the ecosystem. Despite previous reports of a variety of individual ENPs, the mutual effects of ENPs when used in combination were not well understood. In this study, we first investigated the effects of different sizes and concentrations of ZnO nanoparticles (ZnO NPs) or multi-walled carbon nanotubes (MWCNTs) on the growth performance of Arabidopsis thaliana seedlings. Then, two concentrations of ZnO NP (40 and 50 mg/L) with a diameter of 90 nm and MWCNTs (100 and 500 mg/L) with an outer diameter of 40-60 nm were used to evaluate their respective or simultaneous phytotoxicity to Arabidopsis. The results showed that seedlings exposed to either ZnO NPs or MWCNTs exhibited significant phytotoxic symptoms. ZnO NPs caused stronger inhibitory effects than MWCNTs on several plant growth indices, including reduced root length, chlorophyll content, and increased ROS concentration. When applied together, the concurrent effects of ZnO NPs and MWCNTs on Arabidopsis seedlings appeared to be more negative, as evidenced not only by the further deterioration of several growth indices but also by their synergistic or additive regulation of the activities of several antioxidant enzymes such as superoxide dismutase (SOD), catalase (CAT) and glutathione reductase (GR). Moreover, qRT-PCR analysis revealed that in the presence of ZnO NPs and MWCNTs, the expression of genes important for maintaining cellular ROS homeostasis was differentially regulated in shoots and roots of Arabidopsis seedlings. Overall, our data may provide new insights into how plants respond to more than one type of nanomaterial and help us better understand the associated environmental risks.

De Novo Hybrid Assembly of the Salvia miltiorrhiza Mitochondrial Genome Provides the First Evidence of the Multi-Chromosomal Mitochondrial DNA Structure of Salvia Species.

Salvia miltiorrhiza has been an economically important medicinal plant. Previously, an S. miltiorrhiza mitochondrial genome (mitogenome) assembled from Illumina short reads, appearing to be a single circular molecule, has been published. Based on the recent reports on the plant mitogenome structure, we suspected that this conformation does not accurately represent the complexity of the S. miltiorrhiza mitogenome. In the current study, we assembled the mitogenome of S. miltiorrhiza using the PacBio and Illumina sequencing technologies. The primary structure of the mitogenome contained two mitochondrial chromosomes (MC1 and MC2), which corresponded to two major conformations, namely, Mac1 and Mac2, respectively. Using two approaches, including (1) long reads mapping and (2) polymerase chain reaction amplification followed by Sanger sequencing, we observed nine repeats that can mediate recombination. We predicted 55 genes, including 33 mitochondrial protein-coding genes (PCGs), 3 rRNA genes, and 19 tRNA genes. Repeat analysis identified 112 microsatellite repeats and 3 long-tandem repeats. Phylogenetic analysis using the 26 shared PCGs resulted in a tree that was congruent with the phylogeny of Lamiales species in the APG IV system. The analysis of mitochondrial plastid DNA (MTPT) identified 16 MTPTs in the mitogenome. Moreover, the analysis of nucleotide substitution rates in Lamiales showed that the genes atp4, ccmB, ccmFc, and mttB might have been positively selected. The results lay the foundation for future studies on the evolution of the Salvia mitogenome and the molecular breeding of S. miltiorrhiza.

Functional Characterization and Phenotyping of Protoplasts on a Microfluidics-Based Flow Cytometry.

A better understanding of the phenotypic heterogeneity of protoplasts requires a comprehensive analysis of the morphological and metabolic characteristics of many individual cells. In this study, we developed a microfluidic flow cytometry with fluorescence sensor for functional characterization and phenotyping of protoplasts to allow an unbiased assessment of the influence of environmental factors at the single cell level. First, based on the measurement of intracellular homeostasis of reactive oxygen species (ROS) with a DCFH-DA dye, the effects of various external stress factors such as H2O2, temperature, ultraviolet (UV) light, and cadmium ions on intracellular ROS accumulation in Arabidopsis mesophyll protoplasts were quantitatively investigated. Second, a faster and stronger oxidative burst was observed in Petunia protoplasts isolated from white petals than in those isolated from purple petals, demonstrating the photoprotective role of anthocyanins. Third, using mutants with different endogenous auxin, we demonstrated the beneficial effect of auxin during the process of primary cell wall regeneration. Moreover, UV-B irradiation has a similar accelerating effect by increasing the intracellular auxin level, as shown by double fluorescence channels. In summary, our work has revealed previously underappreciated phenotypic variability within a protoplast population and demonstrated the advantages of a microfluidic flow cytometry for assessing the in vivo dynamics of plant metabolic and physiological indices at the single-cell level.

Overexpression of a SHORT-ROOT transcriptional factor enhances the auxin mediated formation of adventitious roots and lateral roots in poplar trees.

SHORT-ROOT (SHR) defines root stem cells and maintains radial patterning, but its involvement in adventitious root (AR) formation has not been reported. In this study, we showed that PtSHR2 was transcriptionally upregulated by excision before the formation of AR and responded dynamically to auxin. PtSHR2 overexpression (SHR2BOE) in hybrid poplars resulted in an increased number of ARs with an initial delay. Despite a lower endogenous content in the stems than in wild-type plants, indole-3-acetic acid (IAA) content at the SHR2BOE basal stem increased rapidly after cutting and reached a higher maximum than in wild-type plants, which was accompanied by a more sustained and stronger induction of AR formation marker genes. In addition, the higher auxin content in SHR2BOE ARs resulted in more and longer lateral roots (LRs). Application of auxin abolished the early delay in the formation of AR and largely other AR phenotypes of SHR2BOE plants, whereas the polar auxin transport inhibitor N-1-naphthylphthalamic acid completely inhibited both AR and LR abnormalities. Since the enhanced rooting ability of SHR2BOE stem cuttings in hydroponics was clearly confirmed, our results suggest a novel role of poplar SHR2 as a positive regulator during the organogenesis of AR and LR by affecting local auxin homeostasis.

Control strategies for biofilm control in reclaimed water distribution systems from the perspective of microbial antagonism and electrochemistry.

Biofilm formation in reclaimed water (RW) distribution systems presents significant technical challenges to RW utilization. Two main technologies to control biofilm formation, microbial antagonism (MA) and electrochemical oxidation (EO), are not yet widely used in drip irrigation systems (DIS) and their mechanisms of action need further clarification. In this study, we first showed that the MA and EO treatments reduced biofilm formation by about 62% and 68%, respectively, and extracellular polymeric substance (EPS) content by 14% and 49%, respectively, in biofilms compared with raw RW type 1 (R-RW1) in unused pipes, thus effectively improving the performance of DIS. When MA-RW and EO-RW were applied to already clogged systems, the degree of clogging alleviation varied depending on the severity of the original clogging. We recommend adding the antagonist, Bacillus subtilis, to RW at 25% clogging for the maximum effect and to slow the microbial adaptation process. Compared to MA, the recovery effect of EO was slower initially but lasted longer and had a significantly better alleviating effect on severely clogged pipelines. Illumina Mi-SEQ high-throughput sequencing data showed that both MA and EO resulted in a significant decrease in microbial diversity, dynamic changes in bacterial community structure, and disruption of network interaction and network modularity. Meanwhile, both treatments promoted the growth of specific microorganisms, enhanced the interaction between certain microbial components, and improved the efficiency of information, matter, and energy exchange within the modules. In summary, we verified the dredging effect of two strategies on DIS under different water conditions, revealed the differences in their mechanisms of action, and proposed their application scenarios. Our results will help improve the efficiency of RW in agricultural drip irrigation systems and effectively reduce maintenance costs.

Overexpression of SHORT-ROOT2 transcription factor enhances the outgrowth of mature axillary buds in poplar trees.

SHORT-ROOT (SHR) transcription factors play important roles in asymmetric cell division and radial patterning of Arabidopsis roots. In hybrid poplar (P. tremula × P. alba clone INRA 717-1B4), PtaSHR2 was preferentially expressed in axillary buds (AXBs) and transcriptionally up-regulated during AXB maturation and activation. Overexpression of SHR2 (PtSHR2OE) induced an enhanced outgrowth of AXBs below the bud maturation point, with a simultaneous transition of an active shoot apex into an arrested terminal bud. The larger and more mature AXBs of PtSHR2OE trees revealed altered expression of genes involved in axillary meristem initiation and bud activation, as well as a higher ratio of cytokinin to auxin. To elucidate the underlying mechanism of PtSHR2OE-induced high branching, subsequent molecular and biochemical studies showed that compared with wild-type trees, decapitation induced a quicker bud outburst in PtSHR2OE trees, which could be fully inhibited by exogenous application of auxin or cytokinin biosynthesis inhibitor, but not by N-1-naphthylphthalamic acid. Our results indicated that overexpression of PtSHR2B disturbed the internal hormonal balance in AXBs by interfering with the basipetal transport of auxin, rather than causing auxin biosynthesis deficiency or auxin insensitivity, thereby releasing mature AXBs from apical dominance and promoting their outgrowth.

Effect of algal blooms outbreak and decline on phosphorus migration in Lake Taihu, China.

Algal blooms (ABs) can affect the migration of phosphorus (P) among sediments, interstitial water and overlying water. It is important to analyze the characteristics of P and their interactions in the three media during ABs. A 5-month field study (June to October in 2016) was conducted in Zhushan Bay of Lake Taihu. P fractions, P adsorption characteristics and P diffusion fluxes at the sediment-water interface (SWI) were investigated. During the outbreak period of ABs from June to August, labile P concentrations in the sediment measured by diffusive gradients in thin films (DGT-labile P) and its diffusion fluxes across the SWI increased significantly. The equilibrium P concentration (EPC0) of the sediment was higher than the PO43--P concentration in the overlying water. During the period of decline of ABs from September to October, the concentrations and diffusion fluxes of DGT-labile P sharply decreased. However, the sediment total P (TP), overlying water TP, total dissolved P (TDP) and PO43--P concentrations increased. These results show that the ability of sediment solids to supplement interstitial water labile P was significantly enhanced by the outbreak of ABs. Labile P was then intensively released into the overlying water by interstitial water. Degraded algae became a crucial P source during the period of decline of ABs. P from the degraded algae was re-released to the sediment and overlying water. The observed DGT-labile P and DGT-labile Fe coupling in June, September and October confirmed the Fe redox-driven P release mechanism in sediment during these periods. The decoupling of DGT-labile P and DGT-labile Fe was observed in July and August and was probably caused by algal decomposition, labile organic P degradation and/or sulfate reduction in sediment stimulated by the ABs outbreak.

ROS Homeostasis Involved in Dose-Dependent Responses of Arabidopsis Seedlings to Copper Toxicity.

As an essential element in plant nutrition, copper (Cu) can promote or inhibit plant growth depending on its concentration. However, the dose-dependent effects of copper, particularly on DNA damage associated with reactive oxygen species (ROS) homeostasis, are much less understood. In this work, we analyzed the dual effect of Cu (5, 20, and 60 µM) on the reproductive performance of Arabidopsis plants. Whereas Cu5 promoted inflorescence initiation and increased kilo seed weight, two higher concentrations, Cu20 and Cu60, delayed inflorescence initiation and negatively affected silique size. Excess Cu also induced changes in cellular redox homeostasis, which was examined by in situ visualization and measurements of ROS, including superoxide (O2•-), hydrogen peroxide (H2O2), malonyldialdehyde (MDA), and plasma membrane damage. The most dramatic increases in the production of O2•- and H2O2 along with increased activity of superoxide dismutase (SOD) and glutathione peroxidase (GPX) and decreased activity of catalase (CAT) and ascorbate peroxidase (APX) were observed in roots with Cu60. Oxidative stress also modulated the expression levels of a number of genes involved in the DNA damage response (DDR), particularly those related to DNA repair. The Cu-induced chlorosis of Arabidopsis seedlings could be alleviated by exogenous addition of glutathione (GSH) and ascorbate (Asc), as the chlorophyll content was significantly increased. Overall, internal homeostasis ROS and the associated DDR pathway and the corresponding scavenging mechanisms play a central role in the response of Arabidopsis to oxidative stress induced by inhibitory Cu concentrations. Our results have shown, for the first time, that the biphasic responses of Arabidopsis seedlings to increasing Cu concentrations involve different DNA damage responses and oxidative reactions. They provide the basis for elucidating the network of Cu-induced DDR-related genes and the regulatory mechanism of the complex ROS production and scavenging system.

Phylogenetic analysis and development of molecular markers for five medicinal Alpinia species based on complete plastome sequences.

BACKGROUND: Alpinia species are widely used as medicinal herbs. To understand the taxonomic classification and plastome evolution of the medicinal Alpinia species and correctly identify medicinal products derived from Alpinia species, we systematically analyzed the plastome sequences from five Alpinia species. Four of the Alpinia species: Alpinia galanga (L.) Willd., Alpinia hainanensis K.Schum., Alpinia officinarum Hance, and Alpinia oxyphylla Miq., are listed in the Chinese pharmacopeia. The other one, Alpinia nigra (Gaertn.) Burtt, is well known for its medicinal values. RESULTS: The four Alpinia species: A. galanga, A. nigra, A. officinarum, and A. oxyphylla, were sequenced using the Next-generation sequencing technology. The plastomes were assembled using Novoplasty and annotated using CPGAVAS2. The sizes of the four plastomes range from 160,590 bp for A. galanga to 164,294 bp for A. nigra, and display a conserved quadripartite structure. Each of the plastomes encodes a total of 111 unique genes, including 79 protein-coding, 28 tRNA, and four rRNA genes. In addition, 293-296 SSRs were detected in the four plastomes, of which the majority are mononucleotides Adenine/Thymine and are found in the noncoding regions. The long repeat analysis shows all types of repeats are contained in the plastomes, of which palindromic repeats occur most frequently. The comparative genomic analyses revealed that the pair of the inverted repeats were less divergent than the single-copy region. Analysis of sequence divergence on protein-coding genes showed that two genes (accD and ycf1) had undergone positive selection. Phylogenetic analysis based on coding sequence of 77 shared plastome genes resolves the molecular phylogeny of 20 species from Zingiberaceae. In particular, molecular phylogeny of four sequenced Alpinia species (A. galanga, A. nigra, A. officinarum, and A. oxyphylla) based on the plastome and nuclear sequences showed congruency. Furthermore, a comparison of the four newly sequenced Alpinia plastomes and one previously reported Alpinia plastomes (accession number: NC_048461) reveals 59 highly divergent intergenic spacer regions. We developed and validated two molecular markers Alpp and Alpr, based on two regions: petN-psbM and psaJ-rpl33, respectively. The discrimination success rate was 100 % in validation experiments. CONCLUSIONS: The results from this study will be invaluable for ensuring the effective and safe uses of Alpinia medicinal products and for the exploration of novel Alpinia species to improve human health.

Bioinformatics analysis and identification of genes and molecular pathways involved in Parkinson's disease in patients with mutations in the glucocerebrosidase gene.

Glucocerebrosidase (GBA) mutations occur frequently in Parkinson's disease (PD) patients. This study aims to identify potential crucial genes and pathways associated with GBA mutations in patients with PD and to further analyze new molecular mechanisms related to the occurrence of gene mutations from the perspective of bioinformatics. Gene expression profiles of datasets GSE53424 and GSE99142 were acquired from the Gene Expression Ominibus database. Differentially expressed genes (DEGs) were detected, using the 'limma' package in R, comparing IDI-PD 1 (idiopathic PD patients) and GBA-PD 1 [PD patients with heterozygous GBA mutations (GBA N370S)] group samples. The functions of top modules were assessed using the DAVID, whereas gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed. Protein-protein interaction networks were assembled with Cytoscape software and separated into subnetworks using the Molecular Complex Detection Algorithm. Data from GSE53424 and GSE99142 were also extracted to verify our findings. There were 283 DEGs identified in PD patients heterozygous for GBA mutations. Module analysis revealed that GBA mutations in PD patients were associated with significant pathways, including Calcium signaling pathway, Rap1 signaling pathway and Cytokine-cytokine receptor interaction. Hub genes of the two modules were corticotropin-releasing hormone (CRH) and Melatonin receptor 1B (MTNR1B). The expression of CRH was downregulated, whereas that of MTNR1B was upregulated in PD patients with GBA mutations. The expression of CRH and MTNR1B has diagnostic value for PD patients with heterozygous GBA mutations. Novel DEGs and pathways identified herein might provide new insights into the underlying molecular mechanisms of heterozygous GBA mutations in PD patients.

Response of organic phosphorus in lake water to environmental factors: A simulative study.

Transformation of organic phosphorus (P) is directly related to a range of environmental factors, therefore exploring their relationships is vital to understanding the biogeochemical cycling of P and its significance in eutrophication of lake waters. In this study, a series of experiments were conducted to simulate the organic P transformation in the water under the influence of dissolved oxygen (DO), temperature and phytoplankton growth. Results showed that the transformation rate of total organic P increased with temperature, ranging from 0.02 to 0.25 mg L-1 day-1 at 5 °C, and from 0.04 to 0.72 mg L-1 day-1at 30 °C. The transformation rate of total organic P was significantly higher under anaerobic conditions than that under aerobic conditions at 20 °C and 30 °C, indicating that DO is a more important factor for the transformation of total organic P at the high temperature. However, different compounds of organic P responded differently to environmental factors. The change of orthophosphate monoester (Mono-P) content was consistent with that of total organic P when the temperature and DO were the same, but the transformation rates of phosphonate and DNA in the water were less affected by changes of temperature and DO. Additionally, the transformation rate of Mono-P was increased by the growth of phytoplankton when it was used as a P source. Although the relationships between alkaline phosphatase (ALP) activity and organic P are complex, ALP may be the main factor affecting the transformation of organic P at lower temperatures.