Serum/glucocorticoid regulated kinase 1 (SGK1) in neurological disorders: pain or gain.

Serum/Glucocorticoid Regulated Kinase 1 (SGK1), a serine/threonine kinase, is ubiquitous across a wide range of tissues, orchestrating numerous signaling pathways and associated with various human diseases. SGK1 has been extensively explored in diverse types of immune and inflammatory diseases, cardiovascular disorders, as well as cancer metastasis. These studies link SGK1 to cellular proliferation, survival, metabolism, membrane transport, and drug resistance. Recently, increasing research has focused on SGK1's role in neurological disorders, including a variety of neurodegenerative diseases (e.g., Alzheimer's disease, Huntington's disease and Parkinson's disease), brain injuries (e.g., cerebral ischemia and traumatic brain injury), psychiatric conditions (e.g., depression and drug addiction). SGK1 is emerging as an increasingly compelling therapeutic target across the spectrum of neurological disorders, supported by the availability of several effective agents. However, the conclusions of many studies observing the prevalence and function of SGK1 in neurological disorders are contradictory, necessitating a review of the SGK1 research within neurological disorders. Herein, we review recent literature on SGK1's primary functions within the nervous system and its impacts within different neurological disorders. We summarize significant findings, identify research gaps, and outline possible future research directions based on the current understanding of SGK1 to help further progress the understanding and treatment of neurological disorders.

Characteristics of soil microplastics and ecological risks in the Qilian Mountains region, Northeast Tibetan Plateau.

Microplastics (MPs) pollution has become a vital global environmental issue. However, comprehensive understanding of the ecological risks of MPs in soils of Northeast Tibetan Plateau still requires further study. In this study, we used laser diffuse reflectance infrared (LDIR) spectroscopy to analyze the characteristics of 10-1000 µm MPs in soils of different vegetation types throughout the Qilian Mountains basin, and to comprehensively explore the ecological risks of MPs in various ecological environments. The results indicate that MPs abundance is highest in soil of shrub areas (26,369 ± 32,147 items kg-1-dry weight (dw)), followed by woodland (22,215 ± 22,544 items kg-1-dw), desert (17,769 ± 9,040 items kg-1-dw), grassland (16,462 ± 12,872 items kg-1-dw), and forest (15,662 ± 13,857 items kg-1-dw). MPs in soils of different vegetation types show similar physical and chemical characteristics, with the shape dominated by fragments (93% - 96%), followed by fibers and a few beads, with dominant sizes of 10 - 30 µm (63% - 76%), and polymers dominated by polyamide and polyethylene terephthalate. Additionally, the environmental risks posed by the fundamental characteristics of MPs have been quantified through the Pollution Load Index (PLI), Pollution Hazard Index (PHI), and Potential Ecological Risk Index (PERI) models. According to the PLI assessment, the current levels of MPs in the environment have not yet imposed significant burdens on the ecosystem. However, the results of PHI and PERI indicate a higher risk of MPs pollution in the Qilian Mountains. This study offers vital information for MPs pollution in the whole Qilian Mountain regions and their potential environmental risks in remote areas' soil.

Microplastics in glaciers of Tibetan Plateau: Characteristics and potential sources.

Microplastics (MPs) in glaciers of remote areas are a hot topic linking the global transport of atmospheric MPs. The Tibetan Plateau (TP) holds large volume of glaciers, providing an effective way to trace MPs transport. Moreover, MPs in glaciers may have adverse effects on the local ecosystem and human health. In this study, we investigate MPs in snowpits collected from six glaciers across the different domain of the TP. The average abundance of MPs in six snowpits is 339.22 ± 51.85 items L-1 (with size ≥10 µm) measured by Agilent 8700 Laser Direct Infrared Chemical Imaging System (LDIR), represented by relatively high MPs abundance in the southern TP and low in the northern TP. The polymers with lower density, namely polyethylene (PE), polyamide (PA), and rubber, are the main MPs types, which are predominated by fragments with sizes smaller than 100 µm in each snowpit. Sources of MPs on glaciers include local tourism and vehicle traffic emissions of MPs. Meanwhile, long-range atmospheric transport of MPs from surrounded regions cannot be ignored. Backward trajectory analysis indicates cross-boundary transport of atmospheric MPs from South Asia play an important role on MPs deposited onto TP glaciers. Analysis further reveals that MPs in glaciers are associated with atmospheric mineral dust deposition. This study provides new data for the investigation of MPs in glaciers of remote areas, and a reference for studying MPs in the ice cores of TP glaciers.

Preparation of Multistage Pore TS-1 with Enhanced Photocatalytic Activity, Including Process Studies and Artificial Neural Network Modeling for Synergy Assessment.

Antibiotic residues have been found in several aquatic ecosystems as a result of the widespread use of antibiotics in recent years, which poses a major risk to both human health and the environment. At present, photocatalytic degradation is the most effective and environmentally friendly method. Titanium silicon molecular sieve (TS-1) has been widely used as an industrial catalyst, but its photocatalytic application in wastewater treatment is limited due to its small pores and few active sites. In this paper, we report a method for preparing multistage porous TS-1 with a high specific surface area by alkali treatment. In the photocatalytic removal of CIP (ciprofloxacin) antibiotic wastewater experiments, the alkali-treated catalyst showed better performance in terms of interfacial charge transfer efficiency, which was 2.3 times higher than that of TS-1 synthesized by the conventional method, and it was found to maintain better catalytic performance in the actual water source. In addition, this research studied the effects of solution pH, contaminant concentration, and catalyst dosage on CIP degradation, while liquid chromatography-mass spectrometry (LC-MS) was used to identify intermediates in the degradation process and infer possible degradation pathways and the toxicity of CIP, and its degradation product was also analyzed using ECOSAR 2.2 software, and most of the intermediates were found to be nontoxic and nonharmful. Finally, a 3:5:1 artificial neural network model was established based on the experiments, and the relative importance of the influence of experimental conditions on the degradation rate was determined. The above results confirmed the feasibility and applicability of photocatalytic treatment of wastewater containing antibiotics using visible light excitation alkali post-treatment TS-1, which provided technical support and a theoretical basis for the photocatalytic treatment of wastewater containing antibiotics.

Biochar application regulates organic phosphorus fractions and the release of available phosphorus in farmland soil.

BACKGROUND: The relationship between phosphorus (P) related enzymatic activity and organic P turnover remains unclear, particularly in the context of biochar application. Field experiments were conducted on Phaeozem and Luvisol soil types to investigate the effects of biochar application rates - 0 t ha-1 (CK), 22.5 t ha-1 (D1), 67.5 t ha-1 (D2), and 112.5 t ha-1 (D3) - on soil organic fractions using 31P nuclear magnetic resonance (NMR) spectroscopy and relevant phosphatase activity. RESULTS: The application of biochar increased the soil organic carbon (SOC), pyrophosphate (pyro), and orthophosphate (ortho) content, as well as the acid phosphomonoesterase (AcP), alkaline phosphomonoesterase (AlP), inorganic pyrophosphatase (IPP), and phosphodiesterase (PD) activities. Biochar application also increased soil organic P (OPa), the sum of inorganic P forms (IP), ortho, monoesters, and myo-IHP contents, the pH value, AlP and PD activities in Phaeozem, but it significantly reduced diesters, polyphosphate (poly) contents, and IPP and AcP activities compared to those in Luvisol. Acid phosphomonoesterase and PD activities also showed an opposite trend in Luvisol. The structural equation model showed that the potential mechanism of organic P turnover in response to biochar application differed depending on the soil types, potentially influenced by P availability. CONCLUSION: Overall, the findings of this study enhance the comprehension of the variation of P fractions and their availability in the context of biochar application for agricultural production in northeastern China. © 2024 Society of Chemical Industry.

RVFV virulence factor NSs triggers the mitochondrial MCL-1-BAK axis to activate pathogenic NLRP3 pyroptosis.

Infection of Rift Valley fever virus (RVFV), a highly pathogenic mosquito-borne zoonotic virus, triggers severe inflammatory pathogenesis but the underlying mechanism of inflammation activation is currently unclear. Here, we report that the non-structural protein NSs of RVFV triggers mitochondrial damage to activate the NLRP3 inflammasome leading to viral pathogenesis in vivo. It is found that the host transcription inhibition effect of NSs causes rapid down-regulation of myeloid cell leukemia-1(MCL-1), a pro-survival member of the Bcl-2 (B-cell lymphoma protein 2) protein family. MCL-1 down-regulation led to BAK activation in the mitochondria, which triggered mtROS production and release of oxidized mitochondrial DNA (ox-mtDNA) into the cytosol. Cytosolic ox-mtDNA binds and activates the NLRP3 inflammasome triggering NLRP3-GSDMD pyroptosis in RVFV infected cells. A NSs mutant virus (RVFV-NSsRM) that is compromised in inducing transcription inhibition did not trigger MCL-1 down-regulation nor NLRP3-GSDMD pyroptosis. RVFV infection of the Nlrp3-/- mouse model demonstrated that the RVFV-triggered NLRP3 pyroptosis contributed to RVFV inflammatory pathogenesis and fatal infection in vivo. Infection with the RVFV-NSsRM mutant virus similarly showed alleviated inflammatory pathogenesis and reduced fatality rate. Taken together, these results revealed a mechanism by which a virulence factor activates the mitochondrial MCL-1-BAK axis through inducing host transcription inhibition to trigger NLRP3-dependent inflammatory pathogenesis.

Visual analysis of abdominal aortitis treatment using the CiteSpace bibliometric method.

BACKGROUND: Abdominal aortitis can induce aneurysms, and tumor rupture can lead to organ ischemia or even sudden death. At present, there is a lack of extensive understanding and identification of key problems in the treatment of abdominal aortitis, which needs to be further analyzed using bibliometric analysis. AIM: To discuss the research hotspot and development trend of abdominal aortitis treatment. METHODS: We searched the English literature (published from January 1, 2000 to March 12, 2024) on the treatment of abdominal aortitis in the Web of Science database. Then, we identified and screened duplicate literature using CiteSpace 6.1R2 software. We conducted an analysis of the number of papers, a co-occurrence analysis of the authors and institutions, and co-occurrence and cluster analyses of the keywords. Then, we drew the author, institution, and keywords of the studies into graphs for visualization. Finally, we expounded on the author, institutional network interactions, and hot keywords of the studies on the treatment of abdominal aortitis. RESULTS: We included 210 English literature articles involving 190 authors; the author cooperation team was mainly represented by Caradu Caroline, Berard Xavier, Lu Guanyi, Harada Kenichi, and Sharma Ashish K. In the keyword analysis, high-frequency keywords include abdominal aortic aneurysm (38), abdominal aorta (24), Takayasu arteritis (22), etc. The three most central keywords were disease (0.69), classification (0.68), and abdominal aortic aneurysm (0.55). The first nine clusters of keywords are case report, abdominal aortic aneurysm, Takayasu arteritis, dyspnea hematuria, aortic elastic, IgG4-related disease, report, mid aortic dysplastic syndrome, and statin. In the keyword emergent analysis, 14 emergent words were obtained. Among them, seven keywords with strong abruptness were Takayasu arteritis, abdominal aortic aneurysm, disease, retroperitoneal fibrosis, expression, management, and large vessel vasculitis. In the past 3 years, the incidences of abdominal aortic aneurysm (intensity: 4.62) and inflammation (intensity: 1.99) were higher. CONCLUSION: The number of published papers is on the increase, but the cooperation among authors is scattered. The research focus is mainly on the pathogenesis and treatment of abdominal aortitis-related diseases.

Characteristics of microplastics and their abundance impacts on microbial structure and function in agricultural soils of remote areas in west China.

As an emergent pollutant, microplastics (MPs) are becoming prevalent in the soil environment. However, the characteristics of MPs and the response of microbial communities to the abundance of MPs in agricultural soils in West China still need to be elucidated in detail. This study utilized the Agilent 8700 Laser Direct Infrared (LDIR) to analyze the characteristics of small-sized MPs (20-1000 µm) in soils from un-mulched and mulched agricultural fields in West China, and illustrated their correlation with microbial diversity. The results revealed a higher abundance of MPs in mulched soil ((4.12 ± 2.13) × 105 items kg-1) than that in un-mulched soil ((1.04 ± 0.26) × 105 items kg-1). The detected MPs were dominated by fragments, 20-50 µm and Polyamide (PA). High-throughput sequencing analysis indicated that alpha diversity (Chao1 and Shannon indices) in the plastisphere was lower compared to that in soil, and varied significantly with MPs abundance in soil. As the abundance of MPs increased, the proportion of soil about the degradation of organic matte and photoautotrophic taxa increased, which showed enrichment in the plastisphere. Functional predictions further indicated that MPs abundance affected potential soil functions, such as metabolic pathways associated with the C and N cycling. The plastisphere showed higher functional abundance associated with organic matter degradation, indicating higher potential health risks compared to soil environments. Based on the RDA analyses, it was determined that environmental physicochemical properties and MPs abundance had a greater impact on fungal communities than on bacterial communities. In general, the abundance of MPs affected the microbial diversity composition and potentially influenced the overall performance of soil ecosystems. This study offers empirical data on the abundance of MPs in long-term mulched agricultural fields and new insights for exploring the ecological risk issues associated with MPs.

A dual-signal optical sensing platform of CDs-MnO2 NS composites for facile detection of ascorbic acid based on a combination of Tyndall effect scattering and fluorescence.

A dual-signal optical sensing platform was successfully developed for the determination of ascorbic acid (AA) based on blue fluorescent carbon dots (CDs) and manganese dioxide nanosheets (MnO2 NSs) with strong Tyndall effect (TE) scattering and fluorescence quenching capabilities. In this nanosystem, CDs-MnO2 NS composites were employed as probes to evaluate the AA concentration. Owing to the strong reduction, the presence of the target AA could reduce the MnO2 NSs to Mn2+ and induce the degradation of the MnO2 NSs, resulting in a significant decrease in the TE scattering intensity of the MnO2 NSs and the fluorescence recovery of the CDs. Therefore, a novel optical sensor based on TE scattering and fluorescence dual detectors was developed for the sensitive determination of AA. Under optimized conditions, the limits of detection (LODs) of the two modes were 113 and 3 nM, respectively. Furthermore, the dual-signal optical sensing platform was successfully applied for the detection of AA in human serum.

Gibberellins regulate masculinization through the SpGAI-SpSTM module in dioecious spinach.

The sex of dioecious plants is mainly determined by genetic factors, but it can also be converted by environmental cues such as exogenous phytohormones. Gibberellic acids (GAs) are well-known inducers of flowering and sexual development, yet the pathway of gibberellin-induced sex conversion in dioecious spinach (Spinacia oleracea L.) remains elusive. Based on sex detection before and after GA3 application using T11A and SSR19 molecular markers, we confirmed and elevated the masculinization effect of GA on a single female plant through exogenous applications of GA3, showing complete conversion and functional stamens. Silencing of GIBBERELLIC ACID INSENSITIVE (SpGAI), a single DELLA family protein that is a central GA signaling repressor, results in similar masculinization. We also show that SpGAI can physically interact with the spinach KNOX transcription factor SHOOT MERISTEMLESS (SpSTM), which is a homolog of the flower meristem identity regulator STM in Arabidopsis. The silencing of SpSTM also masculinized female flowers in spinach. Furthermore, SpSTM could directly bind the intron of SpPI to repress SpPI expression in developing female flowers. Overall, our results suggest that GA induces a female masculinization process through the SpGAI-SpSTM-SpPI regulatory module in spinach. These insights may help to clarify the molecular mechanism underlying the sex conversion system in dioecious plants while also elucidating the physiological basis for the generation of unisexual flowers so as to establish dioecy in plants.

Enhancing axonal myelination: Clemastine attenuates cognitive impairment in a rat model of diffuse traumatic brain injury.

Traumatic brain injury (TBI) has a significant impact on cognitive function, affecting millions of people worldwide. Myelin loss is a prominent pathological feature of TBI, while well-functioning myelin is crucial for memory and cognition. Utilizing drug repurposing to identify effective drug candidates for TBI treatment has gained attention. Notably, recent research has highlighted the potential of clemastine, an FDA-approved allergy medication, as a promising pro-myelinating drug. Therefore, in this study, we aim to investigate whether clemastine can enhance myelination and alleviate cognitive impairment following mild TBI using a clinically relevant rat model of TBI. Mild diffuse TBI was induced using the Closed-Head Impact Model of Engineered Rotational Acceleration (CHIMERA). Animals were treated with either clemastine or an equivalent volume of the vehicle from day 1 to day 14 post-injury. Following treatment, memory-related behavioral tests were conducted, and myelin pathology in the cortex and hippocampus was assessed through immunofluorescence staining and ProteinSimple® capillary-based immunoassay. Our results showed that TBI leads to significant myelin loss, axonal damage, glial activation, and a decrease in mature oligodendrocytes in both the cortex and hippocampus. The TBI animals also exhibited notable deficits in memory-related tests. In contrast, animals treated with clemastine showed an increase in mature oligodendrocytes, enhanced myelination, and improved performance in the behavioral tests. These preliminary findings support the therapeutic value of clemastine in alleviating TBI-induced cognitive impairment, with substantial clinical translational potential. Our findings also underscore the potential of remyelinating therapies for TBI.

The role of serum/glucocorticoid-regulated kinase 1 in brain function following cerebral ischemia.

Cardiopulmonary arrest (CA) is a major cause of death/disability in the U.S. with poor prognosis and survival rates. Current therapeutic challenges are physiologically complex because they involve hypoperfusion (decreased cerebral blood flow), neuroinflammation, and mitochondrial dysfunction. We previously discovered novel serum/glucocorticoid-regulated kinase 1 (SGK1) is highly expressed in brain of neurons that are susceptible to ischemia (hippocampus and cortex). We inhibited SGK1 and utilized pharmacological (specific inhibitor, GSK650394) and neuron-specific genetic approaches (shRNA) in rodent models of CA to determine if SGK1 is responsible for hypoperfusion, neuroinflammation, mitochondrial dysfunctional, and neurological deficits after CA. Inhibition of SGK1 alleviated cortical hypoperfusion and neuroinflammation (via Iba1, GFAP, and cytokine array). Treatment with GSK650394 enhanced mitochondrial function (via Seahorse respirometry) in the hippocampus 3 and 7 days after CA. Neuronal injury (via MAP2, dMBP, and Golgi staining) in the hippocampus and cortex was observed 7 days after CA but ameliorated with SGK1-shRNA. Moreover, SGK1 mediated neuronal injury by regulating the Ndrg1-SOX10 axis. Finally, animals subjected to CA exhibited learning/memory, motor, and anxiety deficits after CA, whereas SGK1 inhibition via SGK1-shRNA improved neurocognitive function. The present study suggests the fundamental roles of SGK1 in brain circulation and neuronal survival/death in cerebral ischemia-related diseases.

Clinical and molecular epidemiology of enterovirus D68 from 2013 to 2020 in Shanghai.

Enterovirus D68 (EV-D68) is an emerging pathogen that has caused outbreaks of severe respiratory disease worldwide, especially in children. We aim to investigate the prevalence and genetic characteristics of EV-D68 in children from Shanghai. Nasopharyngeal swab or bronchoalveolar lavage fluid samples collected from children hospitalized with community-acquired pneumonia were screened for EV-D68. Nine of 3997 samples were EV-D68-positive. Seven of nine positive samples were sequenced and submitted to GenBank. Based on partial polyprotein gene (3D) or complete sequence analysis, we found the seven strains belong to different clades and subclades, including three D1 (detected in 2013 and 2014), one D2 (2013), one D3 (2019), and two B3 (2014 and 2018). Overall, we show different clades and subclades of EV-D68 spread with low positive rates (0.2%) among children in Shanghai between 2013 and 2020. Amino acid mutations were found in the epitopes of the VP1 BC and DE loops and C-terminus; similarity analysis provided evidence for recombination as an important mechanism of genomic diversification. Both single nucleotide mutations and recombination play a role in evolution of EV-D68. Genetic instability within these clinical strains may indicate large outbreaks could occur following cumulative mutations.

Black carbon: a general review of its sources, analytical methods, and environmental effects in snow and ice in the Tibetan Plateau.

Tibetan Plateau (TP) is known as the water tower of Asia, and glaciers are solid reservoirs that can regulate the amount of water. Black carbon (BC), as one of the important factors accelerating glacier melting, is causing evident environmental effects in snow and ice. However, a systematical summary of the potential sources, analytical methods, distributions, and environmental effects of BC in snow and ice on the TP's glaciers is scarce. Therefore, this study drew upon existing research on snow and ice BC on glaciers of the TP to describe the detection methods and uncertainties associated with them to clarify the concentrations of BC in snow and ice and their climatic effects. The primary detection methods are the optical method, the thermal-optical method, the thermochemical method, and the single-particle soot photometer method. However, few studies have systematically compared the results of BC and this study found that concentrations of BC in different types of snow and ice varied by 1-3 orders of magnitude, which drastically affected the regional hydrologic process by potentially accelerating the ablation of glaciers by approximately 15% and reducing the duration of snow accumulation by 3-4 days. In general, results obtained from the various testing methods differ drastically, which limited the systematical discussion. Accordingly, a universal standard for the sampling and measurement should be considered in the future work, which will be beneficial to facilitate the comparison of the spatiotemporal features and to provide scientific data for the model-simulated climatic effects of BC.

Virulence, antimicrobial resistance, and molecular characteristics of carbapenem-resistant Klebsiella pneumoniae in a hospital in Shijiazhuang City from China / Virulencia, resistencia a los antimicrobianos y características moleculares de Klebsiella pneumoniae resistente a carbapenémicos en un hospital de la ciudad de Shijiazhuang de China

Carbapenem-resistant Klebsiella pneumoniae (CRKP), as one of the most common drug-resistant bacteria threatening human health, is hyper-resistant to multiple antimicrobial drugs and carbapenems, which can be dealt with only limited clinical treatment options. This study described the epidemiological characteristics of CRKP in this tertiary care hospital from 2016 to 2020. Specimen sources included blood, sputum, alveolar lavage fluid, puncture fluid, secretions from a burn wound, and urine. Among the 87 carbapenem-resistant strains, ST11 was the predominant isolate, followed by ST15, ST273, ST340, and ST626. These STs were in broad agreement with the STs defined by pulsed-field gel electrophoresis clustering analysis in discriminating clusters of related strains. Most CRKP isolates contained the blaKPC-2 gene, some isolates carried the blaOXA-1, blaNDM-1, and blaNDM-5 genes, and the isolates carrying carbapenem resistance genes were more resistant to the antimicrobials of β-lactams, carbapenems, macrolides, and fluoroquinolone. The OmpK35 and OmpK37 genes were detected in all CRKP strains, and the Ompk36 gene was detected in some CRKP strains. All detected OmpK37 had 4 mutant sites, and OmpK36 had 11 mutant sites, while no mutant sites were found in OmpK35. More than half of the CRKP strains contained the OqxA and OqxB efflux pump genes. The virulence genes were most commonly combined with urea-wabG-fimH-entB-ybtS-uge-ycf. Only one CRKP isolate was detected with the K54 podoconjugate serotype. This study elucidated the clinical epidemiological features and molecular typing of CRKP, and grasped the distribution of drug-resistant genotypes, podocyte serotypes, and virulence genes of CRKP, providing some guidance for the subsequent treatment of CRKP infection.(AU)

A Multitask Network for People Counting, Motion Recognition, and Localization Using Through-Wall Radar.

Due to the outstanding penetrating detection performance of low-frequency electromagnetic waves, through-wall radar (TWR) has gained widespread applications in various fields, including public safety, counterterrorism operations, and disaster rescue. TWR is required to accomplish various tasks, such as people detection, people counting, and positioning in practical applications. However, most current research primarily focuses on one or two tasks. In this paper, we propose a multitask network that can simultaneously realize people counting, action recognition, and localization. We take the range-time-Doppler (RTD) spectra obtained from one-dimensional (1D) radar signals as datasets and convert the information related to the number, motion, and location of people into confidence matrices as labels. The convolutional layers and novel attention modules automatically extract deep features from the data and output the number, motion category, and localization results of people. We define the total loss function as the sum of individual task loss functions. Through the loss function, we transform the positioning problem into a multilabel classification problem, where a certain position in the distance confidence matrix represents a certain label. On the test set consisting of 10,032 samples from through-wall scenarios with a 24 cm thick brick wall, the accuracy of people counting can reach 96.94%, and the accuracy of motion recognition is 96.03%, with an average distance error of 0.12 m.

A rapid method for assembly of single chromosome and identification of sex determination region based on single-chromosome sequencing.

The sex-determining-region (SDR) may offer the best prospects for studying sex-determining gene, recombination suppression, and chromosome heteromorphism. However, current progress of SDR identification and cloning showed following shortcomings: large near-isogenic lines need to be constructed, and a relatively large population is needed; the cost of whole-genome sequencing and assembly is high. Herein, the X/Y chromosomes of Spinacia oleracea L. subsp. turkestanica were successfully microdissected and assembled using single-chromosome sequencing. The assembly length of X and Y chromosome is c. 192.1 and 195.2 Mb, respectively. Three large inversions existed between X and Y chromosome. The SDR size of X and Y chromosome is c. 13.2 and 24.1 Mb, respectively. MSY region and six male-biased genes were identified. A Y-chromosome-specific marker in SDR was constructed and used to verify the chromosome assembly quality at cytological level via fluorescence in situ hybridization. Meanwhile, it was observed that the SDR located on long arm of Y chromosome and near the centromere. Overall, a technical system was successfully established for rapid cloning the SDR and it is also applicable to rapid assembly of specific chromosome in other plants. Furthermore, this study laid a foundation for studying the molecular mechanism of sex chromosome evolution in spinach.

Molecular Defensive Mechanism of Echinacea purpurea (L.) Moench against PAH Contaminations.

The understanding of the molecular defensive mechanism of Echinacea purpurea (L.) Moench against polycyclic aromatic hydrocarbon (PAH) contamination plays a key role in the further improvement of phytoremediation efficiency. Here, the responses of E. purpurea to a defined mixture of phenanthrene (PHE) and pyrene (PYR) at different concentrations or a natural mixture from an oilfield site with a history of several decades were studied based on transcriptomics sequencing and widely targeted metabolomics approaches. The results showed that upon 60-day PAH exposure, the growth of E. purpurea in terms of biomass (p < 0.01) and leaf area per plant (p < 0.05) was negatively correlated with total PAH concentration and significantly reduced at high PAH level. The majority of genes were switched on and metabolites were accumulated after exposure to PHE + PYR, but a larger set of genes (3964) or metabolites (208) showed a response to a natural PAH mixture in E. purpurea. The expression of genes involved in the pathways, such as chlorophyll cycle and degradation, circadian rhythm, jasmonic acid signaling, and starch and sucrose metabolism, was remarkably regulated, enhancing the ability of E. purpurea to adapt to PAH exposure. Tightly associated with transcriptional regulation, metabolites mainly including sugars and secondary metabolites, especially those produced via the phenylpropanoid pathway, such as coumarins, flavonoids, and their derivatives, were increased to fortify the adaptation of E. purpurea to PAH contamination. These results suggest that E. purpurea has a positive defense mechanism against PAHs, which opens new avenues for the research of phytoremediation mechanism and improvement of phytoremediation efficiency via a mechanism-based strategy.

Lineage-specific amplification and epigenetic regulation of LTR-retrotransposons contribute to the structure, evolution, and function of Fabaceae species.

BACKGROUND: Long terminal repeat (LTR)-retrotransposons (LTR-RTs) are ubiquitous and make up the majority of nearly all sequenced plant genomes, whereas their pivotal roles in genome evolution, gene expression regulation as well as their epigenetic regulation are still not well understood, especially in a large number of closely related species. RESULTS: Here, we analyzed the abundance and dynamic evolution of LTR-RTs in 54 species from an economically and agronomically important family, Fabaceae, and also selected two representative species for further analysis in expression of associated genes, transcriptional activity and DNA methylation patterns of LTR-RTs. Annotation results revealed highly varied proportions of LTR-RTs in these genomes (5.1%~68.4%) and their correlation with genome size was highly positive, and they were significantly contributed to the variance in genome size through species-specific unique amplifications. Almost all of the intact LTR-RTs were inserted into the genomes 4 Mya (million years ago), and more than 50% of them were inserted in the last 0.5 million years, suggesting that recent amplifications of LTR-RTs were an important force driving genome evolution. In addition, expression levels of genes with intronic, promoter, and downstream LTR-RT insertions of Glycine max and Vigna radiata, two agronomically important crops in Fabaceae, showed that the LTR-RTs located in promoter or downstream regions suppressed associated gene expression. However, the LTR-RTs within introns promoted gene expression or had no contribution to gene expression. Additionally, shorter and younger LTR-RTs maintained higher mobility and transpositional potential. Compared with the transcriptionally silent LTR-RTs, the active elements showed significantly lower DNA methylation levels in all three contexts. The distributions of transcriptionally active and silent LTR-RT methylation varied across different lineages due to the position of LTR-RTs located or potentially epigenetic regulation. CONCLUSION: Lineage-specific amplification patterns were observed and higher methylation level may repress the activity of LTR-RTs, further influence evolution in Fabaceae species. This study offers valuable clues into the evolution, function, transcriptional activity and epigenetic regulation of LTR-RTs in Fabaceae genomes.