Effects of the ammonium stress on photosynthesis and ammonium assimilation in submerged leaves of Ottelia cordata - an endangered aquatic plant.

Although ammonium (NH4+-N) is an important nutrient for plants, increases in soil nitrogen (N) input and atmospheric deposition have made ammonium toxicity a serious ecological problem. In this study, we explored the effects of NH4+-N stress on the ultrastructure, photosynthesis, and NH4+-N assimilation of Ottelia cordata (Wallich) Dandy, an endangered heteroblastic plant native to China. Results showed that 15 and 50 mg L-1 NH4+-N damaged leaf ultrastructure and decreased the values of maximal quantum yield (Fv/Fm), maximal fluorescence (Fm), and relative electron transport rate (rETR) in the submerged leaves of O. cordata. Furthermore, when NH4+-N was ≥ 2 mg L-1, phosphoenolpyruvate carboxylase activity (PEPC) and soluble sugar and starch contents decreased significantly. The content of dissolved oxygen in the culture water also decreased significantly. The activity of the NH4+-N assimilation enzyme glutamine synthetase (GS) significantly increased when NH4+-N was ≥ 10 mg L-1 and NADH-glutamate synthase (NADH-GOGAT) and Fd-glutamate synthase (Fd-GOGAT) increased when NH4+-N was at 50 mg L-1. However, the activity of nicotinamide adenine dinucleotide-dependent glutamate dehydrogenase (NADH-GDH) and nicotinamide adenine dinucleotide phosphate-dependent glutamate dehydrogenase (NADPH-GDH) did not change, indicating that GS/GOGAT cycle may play an important role in NH4+-N assimilation in the submerged leaves of O. cordata. These results show that short-term exposure to a high concentration of NH4+-N is toxic to O. cordata.

On-site Simultaneous Determination of Neonicotinoids, Carbamates, and Phenyl Pyrazole Insecticides in Vegetables by QuEChERS Extraction on Nitrogen and Sulfur co-doped Carbon Dots and Portable Mass Spectrometry.

In food safety monitoring, on-site and simultaneous detection of a variety of insecticides with different concentrations in the same matrix is necessary. However, the task remains challenging. In this study, a novel nitrogen and sulfur co-doped carbon dot (N, S-CD) was synthesized and used as a QuEChERS clean-up reagent to reduce matrix interferences in the determination of insecticides in vegetables. In addition, a portable mass spectrometer (µ-MS) was employed, without chromatography separation, to directly determine neonicotinoids, carbamates, and benzopyrazole insecticides (with acetamiprid, imidacloprid, thiamethoxam, fipronil, and carbofuran as models) in the pretreated samples. The N,S-CD µ-MS method exhibited effective clean-up performance with satisfactory matrix effects between -15.2% and 15.7%. The recoveries of spiked vegetable samples ranged from 82.2% to 109.7% for the five target insecticides, and the relative standard deviations (RSDs) ranged from 3.8% to 16.5%. The linear ranges were from 2.0 to 5.0 ng/g, with low detection limits (LOD) from 0.5 to 1.0 ng/g. Moreover, the total pretreatment and detection time was within 20 min. Thus, the incorporation of N,S-CD with QuEChERS extraction, together with the portable µ-MS system, could be a promising and feasible strategy for on-site, rapid, and simultaneous detection of various insecticides in vegetables.

Impacts of maize hybrids with different nitrogen use efficiency on root-associated microbiota based on distinct rhizosphere soil metabolites.

Plant genotypes shape root-associated microbiota that affect plant nutrient acquisition and productivity. It is unclear how maize hybrids modify root-associated microbiota and their functions and relationship with nitrogen use efficiency (NUE) by regulating rhizosphere soil metabolites. Here, two N-efficient (NE) (ZD958, DMY3) and two N-inefficient (NIE) maize hybrids (YD9953, LY99) were used to investigate this issue under low N (60 kg N ha-1 , LN) and high N (180 kg N ha-1 , HN) field conditions. NE hybrids had higher yield than NIE hybrids under LN but not HN. NE and NIE hybrids recruited only distinct root-associated bacterial microbiota in LN. The bacterial network stability was stronger in NE than NIE hybrids. Compared with NIE hybrids, NE hybrids recruited more bacterial taxa that have been described as plant growth-promoting rhizobacteria (PGPR), and less related to denitrification and N competition; this resulted in low N2 O emission and high rhizosphere NO3 - -N accumulation. NE and NIE hybrids had distinct rhizosphere soil metabolite patterns, and their specific metabolites were closely related to microbiota and specific genera under LN. Our findings reveal the relationships among plant NUE, rhizosphere soil metabolites, root-associated microbiota, and soil nutrient cycling, and this information is informative for breeding NE crops.

Scrutiny of NolA and NodD1 Regulatory Roles in Symbiotic Compatibility Unveils New Insights into Bradyrhizobium guangxiense CCBAU53363 Interacting with Peanut (Arachis hypogaea) and Mung Bean (Vigna radiata).

Bradyrhizobium guangxiense CCBAU53363 efficiently nodulates peanut but exhibits incompatible interaction with mung bean. By comparing the common nod region with those of other peanut bradyrhizobia efficiently nodulating these two hosts, distinctive characteristics with a single nodD isoform (nodD1) and a truncated nolA were identified. However, the regulatory roles of NodD1 and NolA and their coordination in legume-bradyrhizobial interactions remain largely unknown in terms of explaining the contrasting symbiotic compatibility. Here, we report that nolA was important for CCBAU53363 symbiosis with peanut but restricted nodulation on mung bean, while nodD1 was dispensable for CCBAU53363 symbiosis with peanut but essential for nodulation on mung bean. Moreover, nolA exerted a cumulative contribution with nodD1 to efficient symbiosis with peanut. Additionally, mutants lacking nolA delayed nodulation on peanut, and both nolA and nodD1 were required for competitive nodule colonization. It is noteworth that most of the nodulation genes and type III secretion system (T3SS)-related genes were significantly downregulated in a strain 53ΔnodD1nolA mutant compared to wild-type strain CCBAU53363, and the downregulated nodulation genes also had a greater impact than T3SS-related genes on the symbiotic defect of 53ΔnodD1nolA on peanut, which was supported by a more severe symbiotic defect induced by 53ΔnodC than that with the 53ΔnodD1nopP, 53ΔnodD1rhcJ, and 53ΔnodD1ttsI mutants. NolA did not regulate nod gene expression but did regulate the T3SS effector gene nopP in an indirect way. Meanwhile, nolA, nodW, and some T3SS-related genes besides nopP were also demonstrated as new "repressors" that seriously impaired CCBAU53363 symbiosis with mung bean. Taken together, the roles and essentiality of nolA and nodD1 in modulating symbiotic compatibility are sophisticated and host dependent. IMPORTANCE The main findings of this study were that we clarified that the roles and essentiality of nodD1 and nolA are host dependent. Importantly, for the first time, NolA was found to positively regulate T3SS effector gene nopP to mediate incompatibility on mung bean. Additionally, NolA does not regulate nod genes, which are activated by NodD1. nolA exerts a cumulative effect with nodD1 on CCBAU53363 symbiosis with peanut. These findings shed new light on our understanding of coordinated regulation of NodD1 and NolA in peanut bradyrhizobia with different hosts.

Coordinated regulation of symbiotic adaptation by NodD proteins and NolA in the type I peanut bradyrhizobial strain Bradyrhizobium zhanjiangense CCBAU51778.

Type I peanut bradyrhizobial strains can establish efficient symbiosis in contrast to symbiotic incompatibility induced by type II strains with mung bean. The notable distinction in the two kinds of key symbiosis-related regulators nolA and nodD close to the nodABCSUIJ operon region between these two types of peanut bradyrhizobia was found. Therefore, we determined whether NolA and NodD proteins regulate the symbiotic adaptations of type I strains to different hosts. We found that NodD1-NolA synergistically regulated the symbiosis between the type I strain Bradyrhizobium zhanjiangense CCBAU51778 and mung bean, and NodD1-NodD2 jointly regulated nodulation ability. In contrast, NodD1-NolA coordinately regulated nodulation ability in the CCBAU51778-peanut symbiosis. Meanwhile, NodD1 and NolA collectively contributes to competitive nodule colonization of CCBAU51778 on both hosts. The Fucosylated Nod factors and intact type 3 secretion system (T3SS), rather than extra nodD2 and full-length nolA, were critical for effective symbiosis with mung bean. Unexpectedly, T3SS-related genes were activated by NodD2 but not NodD1. Compared to NodD1 and NodD2, NolA predominantly inhibits exopolysaccharide production by promoting exoR expression. Importantly, this is the first report that NolA regulates rhizobial T3SS-related genes. The coordinated regulation and integration of different gene networks to fine-tune the expression of symbiosis-related genes and other accessory genes by NodD1-NolA might be required for CCBAU51778 to efficiently nodulate peanut. This study shed new light on our understanding of the regulatory roles of NolA and NodD proteins in symbiotic adaptation, highlighting the sophisticated gene networks dominated by NodD1-NolA.

[Detection of drugs in urine by ambient direct ionization mass spectrometry].

According to the Report of Drug Situation in China (2020), the growth rate of the number of drug abusers in China has decreased, but the number of drug abusers is still large. An efficient screening method is necessary for controlling drug abuse. As an important type of biological sample, urine is widely used for the rapid screening of drug addicts. However, because of the complex composition, low content, and strong interference from the body's metabolism, the detection of drugs in urine remains a challenge. Traditional rapid screening techniques such as immunocolloidal gold analysis have a high false positive rate and insufficient quantitative capability. In addition, laboratory mass spectrometry methods require complicated time-consuming sample pre-processing and strict environmental conditions, and hence, are unsuitable for on-site rapid analysis. In recent years, various direct ionization mass spectrometry techniques such as direct analysis in real time (DART), desorption electrospray ionization (DESI), and dielectric barrier discharge ionization (DBDI) have advanced rapidly. These techniques have been applied to public safety, food safety, environmental detection, etc. In contrast to traditional ionization mass spectrometry methods, these direct ionization techniques allow for the in situ analysis of samples with simple or no pretreatment; moreover, they have the advantages of high analytical efficiency and sensitivity. In particular, pulsed electrospray ionization has the characteristics of less sample demand, compact, lightweight equipment, and no carrier gas. This paper presents a rapid method based on pulsed electrospray ionization mass spectrometry for the detection of urine samples. A rapid detection platform comprising a probe electrospray ionization source, a portable linear ion trap mass spectrometer (MS), and their coupling interface is adopted. The probe electrospray ion source includes a conducting metal wire, plastic handle, and silica glass capillary, whose tip has an inner diameter of 50 µm. The guide rail at the coupling interface is used to align the probe with the sample inlet of the portable mass spectrometer and maintain a distance of 10 mm between the probe tip and the sample inlet of the MS. The spray voltage of the probe electrospray ion source and the temperature of the MS inlet capillary are optimized at 1.8 kV and 205 ℃, respectively. In addition, rapid and efficient pretreatment techniques for urine samples have been developed. Buffer salts used for pH regulation and liquid-liquid extraction based on ethyl acetate were adopted for the pretreatment process. The linearity of the detection ability and the linear ranges of various drug-spiked solutions were also investigated. The results showed that the correlation coefficients for the quantitative detection of methamphetamine, ketamine, methylenedioxymethamphetamine (MDMA), and cocaine were greater than 0.99 at concentrations ranging from 1 to 100 ng/mL. Moreover, the limits of detection (LODs) for the five conventional drug-spiked urine were 0.5-30 ng/mL. The spiked recoveries ranged from 56.1% to 103.7%, with relative standard deviations (RSDs) of 9.0%-27.8%, implying that the combination of the instruments and the pretreatment method can lead to good accuracy. To validate the performance of the rapid detection method, 40 positive and 110 negative urine samples were tested and analyzed. The overall accuracy was over 99%, and the five conventional drugs in urine samples could be detected within 20 s. The research findings of this work could promote the development of rapid detection technology, accelerate the popularization and application of ambient direct ionization mass spectrometry, and improve the services of on-site law enforcement.

Single Cell Mass Spectrometry With a Robotic Micromanipulation System for Cell Metabolite Analysis.

OBJECTIVE: The increasing demand for unraveling cellular heterogeneity has boosted single cell metabolomics studies. However, current analytical methods are usually labor-intensive and hampered by lack of accuracy and efficiency. METHODS: we developed a first-ever automated single cell mass spectrometry system (named SCMS) that facilitated the metabolic profiling of single cells. In particular, extremely small droplets of sub nano-liter were generated to extract the single cells, and the underlying mechanism was verified theoretically and experimentally. This was crucial to minimize the dilution of the trace cellular contents and enhance the analytical sensitivity. Based on the precise 3D positioning of the pipette tip, we established a visual servoing robotic micromanipulation platform on which single cells were sequentially extracted, aspirated, and ionized, followed by the mass spectrometry analyses. RESULTS: With the SCMS system, inter-operator variability was eliminated and working efficiency was improved. The performance of the SCMS system was validated by the experiments on bladder cancer cells. MS and MS2 analyses of single cells enable us to identify several cellular metabolites and the underlying inter-cell heterogeneity. CONCLUSION: In contrast to traditional methods, the SCMS system functions without human intervention and realizes a robust single cell metabolic analysis. SIGNIFICANCE: the SCMS system upgrades the way how single cell metabolites were analyzed, and has the potential to be a powerful tool for single cell metabolomics studies.

Hypermethylation of secreted frizzled related protein 2 gene promoter serves as a noninvasive biomarker for HBV-associated hepatocellular carcinoma.

For patients with hepatocellular carcinoma (HCC), early detection is critical to improve survival. Secreted frizzled-related protein 2 (SFRP2) is a candidate tumor suppressor as Wnt antagonist and SFRP2 promoter has been found hypermethylated in various malignancies. This study aimed to investigate the methylation status of SFRP2 promoter in hepatitis B virus (HBV) associated HCC and estimate its diagnostic value as a non-invasive biomarker. A total of 293 patients, including 132 patients with HBV-associated HCC, 121 with chronic hepatitis B (CHB) and 40 healthy controls (HCs) were enrolled. SFRP2 methylation level in peripheral mononuclear cells (PBMCs) was quantitatively detected by MethyLight. SFRP2 methylation level was significantly higher in patients with HBV-associated HCC than in those with CHB (p < 0.001) and HCs (p < 0.001) while mRNA level of SFRP2 was significantly lower in HCC group than the other two groups (p < 0.05). In HCC subgroup, SFRP2 methylation level markedly increased in patients >50 years old, female, with negative HBeAg, negative HBV-DNA and poor differentiation compared with the remaining groups (P < 0.05). Furthermore, SFRP2 methylation level showed a significantly better diagnostic value than alpha-fetoprotein (AFP) and the combination of AFP and methylation levels of SFRP2 markedly improved the area under the receiver operating characteristic curve (p < 0.05). In conclusion, hypermethylation of SFRP2 promoter exists in HBV-associated HCC. The combination of SFRP2 methylation level in PBMCs and AFP could significantly improve the diagnostic ability of AFP in discriminating HBV-associated HCC from CHB and SFRP2 methylation level had the potential to serve as a non-invasive biomarker for HCC diagnosis.

5-Aza-2'-deoxycytidine may enhance the frequency of T regulatory cells from CD4+ naïve T cells isolated from the peripheral blood of patients with chronic HBV infection.

OBJECTIVES: Methylation pattern of gene modification is essential for the differentiation of T regulatory cells (Tregs) and 5-Aza-2'-deoxycytidine is a common inhibitor of methylation. This study aimed to investigate the potential effects of Treg polarizing conditions and 5-Aza-2'-deoxycytidine treatment in the differentiation of naïve T cells during chronic hepatitis B virus (HBV) infection. METHODS: The frequency of Tregs in peripheral blood was determined by flow cytometry from patients with chronic hepatitis B (CHB) (n = 51), liver cirrhosis (LC) (n = 47), hepatocellular carcinoma (HCC) (n = 40) and healthy controls (HCs) (n = 17). Gene expression were detected by qRT-PCR and DNA methyltransferases (DNMT) Activity was also determined. RESULTS: The frequency of Tregs and Foxp3 expression in peripheral blood from 5-Aza-2'-deoxycytidine-treated groups were higher than that with acetic acid treatment as a control. Foxp3 mRNA and the frequency of Tregs derived from naïve CD4+T cells from peripheral blood of patients with HCC or LC were more pronounced compared with HCs. 5-Aza-2'-deoxycytidine may have induced a more pronounced upward trend of PD-1 expression in HBV patients. CONCLUSIONS: 5-Aza-2'-deoxycytidine mediated demethylation has potential effects on enhancing the differentiation of naïve T cells to Tregs in chronic HBV infection.

Effectsof growth-promoting rhizobacteria on maize growth and rhizosphere microbial community under conservation tillage in Northeast China.

Conservation tillage in conjunction with straw mulching is a sustainable agricultural approach. However, straw mulching reduces the soil temperature, inhibits early maize growth and reduces grain yield in cold regions. To address this problem, we investigated the effects of inoculation of plant growth-promoting rhizobacteria (PGPR) on maize growth and rhizosphere microbial communities under conservation tillage in Northeast China. The PGPR strains Sinorhizobium sp. A15, Bacillus sp. A28, Sphingomonas sp. A55 and Enterobacter sp. P24 were isolated from the maize rhizosphere in the same area and inoculated separately. Inoculation of these strains significantly enhanced maize growth, and the strains A15, A28 and A55 significantly increased grain yield by as much as 22%-29%. Real-time quantitative PCR and high-throughput sequencing showed that separate inoculation with the four strains increased the abundance and species richness of bacteria in the maize rhizosphere. Notably, the relative abundance of Acidobacteria_Subgroup_6, Chloroflexi_KD4-96, and Verrucomicrobiae at the class level and Mucilaginibacter at the genus level were positively correlated with maize biomass and yield. Inoculation with PGPR shows potential for improvement of maize production under conservation tillage in cold regions by regulating the rhizosphere bacterial community structure and by direct stimulation of plant growth.

Ultra-trace level detection of nonvolatile compounds studied by ultrasonic cutter blade coupled with dielectric barrier discharge ionization-mass spectrometry.

In analytical mass spectrometry, an efficient desorption is needed for nonvolatile compounds at ultra-trace level detection. In this paper, an ultrasonic cutter-assisted non-thermal desorption method for ultra-trace level detection of different types of nonvolatile compounds such as drugs of abuse, explosives, pharmaceuticals, spinosad, cholesterol, rhodamine B, glucose and amino acids has been described. The relevant compounds were deposited on the ultrasonic blade except pharmaceutical tablets that were used directly, and gently touched on perfluoroalkoxy (PFA) made substrate with oscillation frequency about 40 kHz in order to desorb the solid molecules. The desorbed gaseous molecules were ionized using a home-made helium dielectric barrier discharge ionization (DBDI) source and then detected by an ion trap mass spectrometer. The synergistic effect caused by gaining the oscillation and frictional/mechanical energy enhanced desorption of the solid molecules into gaseous phase, thereby, resulting in detection at ultra-trace level. PFA made substrate showed better limits of detection (LODs) compared to that of wood made substrate. The LOD values for most of the target analytes were ranging from 20.00 ± 0.91 to 200.25 ± 9.04 pg with RSD values ≤ 5% except for pharmaceutical tablets where only depletion amounts were estimated. The LOD value of cocaine in urine was 39.88 ± 1.65 pg with RDS ≤4.56% showed to be a very promising analytical tool for analysis of drugs of abuse in biological samples under ambient conditions. Drugs of abuse, pharmaceuticals, spinosad, cholesterol, rhodamine B, glucose and amino acids were detected mostly as their protonated molecular ions while RDX and HMX were detected as their molecular cluster/adduct ions as [M + NO2]- and [M + NO3]-, and AN was detected as a cluster ion of HNO3 with NO3-, [HNO3 + NO3]-, without suffering from fragmentation. An effective mechanism of the enhanced sensitivity of the tribodesorption-DBDI-MS system in analyzing the nonvolatile compounds has been discussed.

Diagnostic Value of the Hypomethylation of the WISP1 Promoter in Patients with Hepatocellular Carcinoma Associated with Hepatitis B Virus.

Wnt1-inducible signaling pathway protein 1 (WISP1) regulates cell proliferation, differentiation, adhesion, migration and survival. Abnormal WISP1 expression is associated with the carcinogenesis of hepatocellular carcinoma (HCC). Aberrant DNA methylation is one of the major epigenetic alterations in HCC. However, the methylation status of the WISP1 promoter is still unclear. We therefore aimed to determine the methylation status of the WISP1 promoter and evaluate its clinical value in HCC. The study enrolled 251 participants, including 123 participants with HCC, 90 participants with chronic hepatitis B (CHB) and 38 healthy controls (HCs). WISP1 methylation status, mRNA levels and plasma soluble WISP1 were detected by methylation-specific polymerase chain reaction (MSP), quantitative real-time PCR (RT-qPCR) and enzyme-linked immunosorbent assay (ELISA), respectively. We found that the methylation frequency of WISP1 in patients with HCC was significantly lower than that in patients with CHB and HCs, while the relative expression levels of WISP1 mRNA were markedly higher in patients with HCC than in patients with CHB and HCs. Furthermore, the plasma soluble WISP1 in patients with HCC was obviously lower than in that in patients with CHB and HCs. Alpha-fetoprotein (AFP) is a widely recognized biomarker to diagnose HCC which lacks enough sensitivity and specificity. WISP1 promoter methylation status combined with AFP significantly improved the diagnostic ability in discriminating HCC from CHB compared with AFP or WISP1 methylation status alone. In conclusion, hypomethylation of the WISP1 gene promoter may serve as a noninvasive biomarker for detecting HBV-associated HCC.

Multiple Genes of Symbiotic Plasmid and Chromosome in Type II Peanut Bradyrhizobium Strains Corresponding to the Incompatible Symbiosis With Vigna radiata.

Rhizobia are capable of establishing compatible symbiosis with their hosts of origin and plants in the cross-nodulation group that the hosts of origin belonged to. However, different from the normal peanut Bradyrhizobium (Type I strains), the Type II strains showed incompatible symbiosis with Vigna radiata. Here, we employed transposon mutagenesis to identify the genetic loci related to this incompatibility in Type II strain CCBAU 53363. As results, seven Tn5 transposon insertion mutants resulted in an increase in nodule number on V. radiata. By sequencing analysis of the sequence flanking Tn5 insertion, six mutants were located in the chromosome of CCBAU 53363, respectively encoding acyltransferase (L265) and hypothetical protein (L615)-unique to CCBAU 53363, two hypothetical proteins (L4 and L82), tripartite tricarboxylate transporter substrate binding protein (L373), and sulfur oxidation c-type cytochrome SoxA (L646), while one mutant was in symbiotic plasmid encoding alanine dehydrogenase (L147). Significant differences were observed in L147 gene sequences and the deduced protein 3D structures between the Type II (in symbiotic plasmid) and Type I strains (in chromosome). Conversely, strains in both types shared high homologies in the chromosome genes L373 and L646 and in their protein 3D structures. These data indicated that the symbiotic plasmid gene in Type II strains might have directly affected their symbiosis incompatibility, whereas the chromosome genes might be indirectly involved in this process by regulating the plasmid symbiosis genes. The seven genes may initially explain the complication associated with symbiotic incompatibility.

MIR-520f Regulated Itch Expression and Promoted Cell Proliferation in Human Melanoma Cells.

Accumulating evidence suggests that abnormal expression and dysfunction of microRNA is involved in development of cancers. However, the function of miR-520f especially in human melanoma remains elusive. In the current study, the underlying function of miR-520f in human melanoma was investigated. Our study demonstrated that the miR-520f level in human melanoma cell lines and clinical tissues was increased. Overexpression of miR-520f promoted cell proliferation by using the 3-(4,5-dimethylthiazole-2-yl)-2,5-diphenyltetrazolium bromide assay, colony formation, anchorage-independent growth assay, and 5-bromo-2-deoxyuridine assays. Furthermore, we revealed that miR-520f could interact with circular RNA Itchy E3 ubiquitin protein ligase (ITCH) 3'-untranslated region and suppress ITCH expression in human melanoma cells. The inhibitory effect of miR-520f-in could be partially restored by knockdown of ITCH in human melanoma cells. In summary, this study provides novel insights into miR-520f act as a crucial role in the regulation of human melanoma cell growth via regulating ITCH, which might be a potential biomarker and therapeutic target of human melanoma.

TNFRSF12A and a new prognostic model identified from methylation combined with expression profiles to predict overall survival in hepatocellular carcinoma.

BACKGROUND: It has been proved that DNA methylation, as an epigenetic regulatory mode, plays a crucial role in the initiation, progression and invasion of hepatocellular carcinoma (HCC). However, there still are some pathways and factors that regulates the carcinogenesis of HCC remains unclear. METHODS: The original datasets comparing DNA methylation, clinical information and transcriptome profiling between HCC and normal controls were downloaded from The Cancer Genome Atlas (TCGA) database. R software was used to screen for methylation-differential genes (MDGs) and methylation-driven genes. Gene-functional enrichment analysis, ConsensusPathDB pathway analysis, protein-protein interaction (PPI) network construction and survival analysis were performed; methylation-specific polymerase chain reaction (MSP) and real-time quantitative polymerase chain reaction (RT-qPCR) were used for validation. RESULTS: One hundred and sixty-seven MDGs and 285 methylation-driven genes were identified. Function and pathway enrichment analysis revealed that they are associated with sequence-specific DNA binding, nuclear nucleosome, regulation of insulin-like growth factor transport, etc. An eight-gene (HIST1H1D, RP11-476B1.1, OR2AK2, TNFRSF12A, CTD-2313N18.8, AC133644.2, RP11-467L13.4 and LINC00989) prognostic model was identified from the MDGs; its methylation degree can strongly predict the overall survival of HCC. Among them, TNFRSF12A being the only one belongs to both MDGs and methylation-driver genes, shows a significant independent correlation with the prognosis of HCC. That was validated in further details. CONCLUSIONS: Our research has identified a registry of novel genes and pathways that's important for regulating the carcinogenesis of HCC. In addition, we identified a strong molecular model for prognostic prediction. These findings will not only provide guidance for clinical individualized treatment, but also to set us targets for further research on the molecular mechanism of HCC.

[Effects of multifunctional plant rhizosphere promoting bacteria on maize growth in black soil areas in Northeast China]. / å¤šåŠŸèƒ½æ¤ç‰©æ ¹é™ ä¿ƒç”ŸèŒå¯¹ä¸œåŒ—é»‘åœŸåŒºçŽ‰ç±³çš„ä¿ƒç”Ÿæ•ˆæžœ.

The application of microbial fertilizer plays an important role in improving soil restoration and fertilizer utilization. The effects of microbial fertilizer are greatly affected by crop genotypes and ecological conditions. Little is known about the effects of microbial fertilizers on maize production in Northeast China. To develop microbial fertilizer specific to the black soil and the climate characteristics of Northeast China, we isolated five plant rhizosphere-promoting bacteria (PGPR), named as MZ1, MZ2, MZ3, MZ4 and MZ5, with different degrees of biological functions such as IAA synthesis, phosphate-solubilizing, potassium-solubilizing and siderophore-releasing, from the rhizosphere of maize field. The analysis of ecological adaptability showed that those five strains differed in salt resistance, drought tolerance, acid and alkali resistance, pesticide resistance. The 16S rRNA gene sequences analysis showed that the strains MZ1, MZ2, MZ3, MZ4 and MZ5 belonged to the genus of Sphingomonas, Enterobacter, Pseudomonas, Bacillus and Rhizobium, respectively. In maize field experiment with 50% nitrogen fertilizer reduction, the inoculation with MZ1, MZ3 and MZ5 increased grain yield by 19.9%-25.0%. MZ1, MZ3, and MZ5 could be used as microbial fertilizers for maize in Northeast China.

Statistical study of biomechanics of living brain cells during growth and maturation on artificial substrates.

There is increasing evidence that mechanical issues play a vital role in neuron growth and brain development. The importance of this grows as novel devices, whose material properties differ from cells, are increasingly implanted in the body. In this work, we studied the mechanical properties of rat brain cells over time and on different materials by using a high throughput magnetic tweezers system. It was found that the elastic moduli of both neurite and soma in networked neurons increased with growth. However, neurites at DIV4 exhibited a relatively high stiffness, which could be ascribed to the high outgrowth tension. The power-law exponents (viscoelasticity) of both neurites and somas of neurons decreased with culture time. On the other hand, the stiffness of glial cells also increased with maturity. Furthermore, both neurites and glia become softer when cultured on compliant substrates. Especially, the glial cells cultured on a soft substrate obviously showed a less dense and more porous actin and GFAP mesh. In addition, the viscoelasticity of both neurites and glia did not show a significant dependence on the substrates' stiffness.

Implementation and application of a novel 2D magnetic twisting cytometry based on multi-pole electromagnet.

We implemented a novel 2D magnetic twisting cytometry (MTC) based on a previously reported multi-pole high permeability electromagnet, in which both the strength and direction of the twisting field can be controlled. Thanks to the high performance twisting electromagnet and the heterodyning technology, the measurement frequency has been extended to the 1 kHz range. In order to obtain high remanence of the ferromagnetic beads, a separate electromagnet with feedback control was adopted for the high magnetic field polarization. Our setup constitutes the first instrument which can be operated both in MTC mode and in magnetic tweezers (MT) mode. In this work, the mechanical properties of HL-1 cardiomyocytes were characterized in MTC mode. Both anisotropy and log-normal distribution of cell stiffness were observed, which agree with our previous results measured in MT mode. The response from these living cells at different frequencies can be fitted very well by the soft glassy rheology model.

Magnetic tweezers with high permeability electromagnets for fast actuation of magnetic beads.

As a powerful and versatile scientific instrument, magnetic tweezers have been widely used in biophysical research areas, such as mechanical cell properties and single molecule manipulation. If one wants to steer bead position, the nonlinearity of magnetic properties and the strong position dependence of the magnetic field in most magnetic tweezers lead to quite a challenge in their control. In this article, we report multi-pole electromagnetic tweezers with high permeability cores yielding high force output, good maneuverability, and flexible design. For modeling, we adopted a piece-wise linear dependence of magnetization on field to characterize the magnetic beads. We implemented a bi-linear interpolation of magnetic field in the work space, based on a lookup table obtained from finite element simulation. The electronics and software were custom-made to achieve high performance. In addition, the effects of dimension and defect on structure of magnetic tips also were inspected. In a workspace with size of 0.1 × 0.1 mm(2), a force of up to 400 pN can be applied on a 2.8 µm superparamagnetic bead in any direction within the plane. Because the magnetic particle is always pulled towards a tip, the pulling forces from the pole tips have to be well balanced in order to achieve control of the particle's position. Active video tracking based feedback control is implemented, which is able to work at a speed of up to 1 kHz, yielding good maneuverability of the magnetic beads.

[New paradigm for soil and water conservation: a method based on watershed process modeling and scenario analysis].

With the increase of severe soil erosion problem, soil and water conservation has become an urgent concern for sustainable development. Small watershed experimental observation is the traditional paradigm for soil and water control. However, the establishment of experimental watershed usually takes long time, and has the limitations of poor repeatability and high cost. Moreover, the popularization of the results from the experimental watershed is limited for other areas due to the differences in watershed conditions. Therefore, it is not sufficient to completely rely on this old paradigm for soil and water loss control. Recently, scenario analysis based on watershed modeling has been introduced into watershed management, which can provide information about the effectiveness of different management practices based on the quantitative simulation of watershed processes. Because of its merits such as low cost, short period, and high repeatability, scenario analysis shows great potential in aiding the development of watershed management strategy. This paper elaborated a new paradigm using watershed modeling and scenario analysis for soil and water conservation, illustrated this new paradigm through two cases for practical watershed management, and explored the future development of this new soil and water conservation paradigm.