The transcriptional regulator JAZ8 interacts with the C2 protein from geminiviruses and limits the geminiviral infection in Arabidopsis.

Jasmonates (JAs) are phytohormones that finely regulate critical biological processes, including plant development and defense. JASMONATE ZIM-DOMAIN (JAZ) proteins are crucial transcriptional regulators that keep JA-responsive genes in a repressed state. In the presence of JA-Ile, JAZ repressors are ubiquitinated and targeted for degradation by the ubiquitin/proteasome system, allowing the activation of downstream transcription factors and, consequently, the induction of JA-responsive genes. A growing body of evidence has shown that JA signaling is crucial in defending against plant viruses and their insect vectors. Here, we describe the interaction of C2 proteins from two tomato-infecting geminiviruses from the genus Begomovirus, tomato yellow leaf curl virus (TYLCV) and tomato yellow curl Sardinia virus (TYLCSaV), with the transcriptional repressor JAZ8 from Arabidopsis thaliana and its closest orthologue in tomato, SlJAZ9. Both JAZ and C2 proteins colocalize in the nucleus, forming discrete nuclear speckles. Overexpression of JAZ8 did not lead to altered responses to TYLCV infection in Arabidopsis; however, knock-down of JAZ8 favors geminiviral infection. Low levels of JAZ8 likely affect the viral infection specifically, since JAZ8-silenced plants neither display obvious developmental phenotypes nor present differences in their interaction with the viral insect vector. In summary, our results show that the geminivirus-encoded C2 interacts with JAZ8 in the nucleus, and suggest that this plant protein exerts an anti-geminiviral effect.

Combinatorial interactions between viral proteins expand the potential functional landscape of the tomato yellow leaf curl virus proteome.

Viruses manipulate the cells they infect in order to replicate and spread. Due to strict size restrictions, viral genomes have reduced genetic space; how the action of the limited number of viral proteins results in the cell reprogramming observed during the infection is a long-standing question. Here, we explore the hypothesis that combinatorial interactions may expand the functional landscape of the viral proteome. We show that the proteins encoded by a plant-infecting DNA virus, the geminivirus tomato yellow leaf curl virus (TYLCV), physically associate with one another in an intricate network, as detected by a number of protein-protein interaction techniques. Importantly, our results indicate that intra-viral protein-protein interactions can modify the subcellular localization of the proteins involved. Using one particular pairwise interaction, that between the virus-encoded C2 and CP proteins, as proof-of-concept, we demonstrate that the combination of viral proteins leads to novel transcriptional effects on the host cell. Taken together, our results underscore the importance of studying viral protein function in the context of the infection. We propose a model in which viral proteins might have evolved to extensively interact with other elements within the viral proteome, enlarging the potential functional landscape available to the pathogen.

Stress and Metabolomics for Prediction of Spontaneous Preterm Birth: A Prospective Nested Case-Control Study in a Tertiary Hospital.

Spontaneous preterm birth (sPTB) is the leading cause of infant morbidity and mortality worldwide. Deficiency of effective predict methods is an urgent problem that needs to be solved. Numbers of researchers spare no efforts to investigate differential indicators. To evaluate the value of the differential indicators, a prospective nested case-control study was carried out. Among an overall cohort of 1,050 pregnancies, 20 sPTB pregnancies, and 20 full-term pregnancies were enrolled in this study. Participants were followed-up until labor. The psychological profile was evaluated utilizing the Zung Self-Rating Depression Scale at 11-14 weeks. Stress-related biomarker-cortisol and metabolites were detected by Electrochemiluminescence Immunoassay (ECLIA) and Gas Chromatography-Mass Spectrometry (GC-MS) in serum samples during pregnancy, respectively. The expression level of cortisol was up-regulated in serum and the score of the Zung Self-Rating Depression Scale was significantly higher in the sPTB group when compared to the control group. Note that, 29 metabolomics were differentially expressed between the sPTB group and the control group. The scores of the Zung Self-Rating Depression Scale, the level of cortisol, Eicosane, methyltetradecanoate, and stearic acid in serum were selected to establish the model with lasso logistic regression. Validation of the model yielded an optimum corrected AUC value of 89.5%, 95% CI: 0.8006-0.9889 with a sensitivity of 100.0%, and specificity of 78.9%. In conclusion, this study establishes a prediction model of sPTB with five variables, which may predict sPTB more accurately and sensitively in the second trimester.

Exploration of Circular RNA Interactomes by RNA Pull-Down Method.

Circular RNAs (circRNAs) are endogenous RNA molecules produced by back-splicing during the maturation process of mRNA precursors. Recent research revealed circRNAs as important regulators in a variety of physiological and pathological processes. However, the biological functions of circRNAs remains largely unknown. The RNA pull-down method can specifically and efficiently enrich circRNAs and their interacting partners. In order to further characterize the functions and working mechanism of circRNAs, here we provide a detailed RNA pull-down protocol for capturing and identifying the interactomes of circRNAs.

Long Noncoding RNAs: An Overview.

Recently an explosion in the discovery of long noncoding RNAs (lncRNAs) was obtained by high-throughput sequencing. Genome-wide transcriptome analyses, in conjugation with research for epigenetic modifications of chromatins, identified a novel type of non-protein coding transcripts longer than 200 nucleotides named lncRNAs . They are gradually emerging as functional and critical participants in many physiological processes. Here we gave an overview of the characteristics, biological functions, and working mechanism for this new class of noncoding RNA molecules.

Plant DNA polymerases α and δ mediate replication of geminiviruses.

Geminiviruses are causal agents of devastating diseases in crops. Geminiviruses have circular single-stranded (ss) DNA genomes that are replicated in the nucleus of the infected plant cell through double-stranded (ds) DNA intermediates by the plant DNA replication machinery. Which host DNA polymerase mediates geminiviral multiplication, however, has so far remained elusive. Here, we show that subunits of the nuclear replicative DNA polymerases α and δ physically interact with the geminivirus-encoded replication enhancer protein, C3, and that these polymerases are required for viral replication. Our results suggest that, while DNA polymerase α is essential to generate the viral dsDNA intermediate, DNA polymerase δ mediates the synthesis of new copies of the geminiviral ssDNA genome, and that the virus-encoded C3 may act selectively, recruiting DNA polymerase δ over ε to favour productive replication.

LncRNA DANCR represses Doxorubicin-induced apoptosis through stabilizing MALAT1 expression in colorectal cancer cells.

Long non-coding RNA (lncRNA) DANCR has been reported to participate in key processes such as stem cell differentiation and tumorigenesis. In a high throughput screening for lncRNAs involved in Doxorubicin-induced apoptosis, we found DANCR was suppressed by Doxorubicin and it acted as an important repressor of apoptosis in colorectal cancer. Further studies demonstrated that DANCR promoted the oncogenic lncRNA MALAT1 expression via enhancing the RNA stability of MALAT1 to suppress apoptosis. MALAT1 could efficiently mediate the suppressive function of DANCR on apoptosis. Mechanistic studies found the RNA-binding protein QK served as an interacting partner of both DANCR and MALAT1, and the protein level of QK was subjected to the regulation by DANCR. Furthermore, QK was able to modulate the RNA stability of MALAT1, and the interaction between QK and MALAT1 was controlled by DANCR. In addition, QK could mediate the function of DANCR in regulating the expression of MALAT1 and suppressing apoptosis. These results revealed DANCR played a critical role in Doxorubicin-induced apoptosis in colorectal cancer cells, which was achieved by the interaction between DANCR and QK to enhance the expression of MALAT1.

Birth and birth-related obstetrical characteristics in southwestern China associated with the current adjustment of family planning policy: a 7-year retrospective study.

In China, the adjustment of the family planning policy was expected to increase the number of births and trigger a change in the demographic and obstetrical background of pregnant women. The policy itself, and corresponding background variations of the pregnant mothers, might have various influences on certain birth-related characteristics. Moreover, the adaption of the medical system to the policy needs to be demonstrated. To address these issues, over 50,000 individual records from January 2012 to December 2018 were collected from a large tertiary care centre of southwest China as a representative. The monthly numbers of deliveries and births showed stabilized patterns after remarkable upward trends. Policy-sensitive women, among whom older age and multiparity were typical features, contributed considerably to the remarkable additional births. Indeed, multivariable logistic regression analysis identified the child policy and these two background characteristics as factors influencing CS (caesarean section) rate and certain pregnancy complications or adverse outcomes. After the implementation of the two-child policy, a care provider was faced with fewer but more difficult cases. Briefly speaking, more individual-based studies on family planning policy and more efforts to improve obstetrical service are needed to better guide clinical practice in the new era.

A Defense Pathway Linking Plasma Membrane and Chloroplasts and Co-opted by Pathogens.

Chloroplasts are crucial players in the activation of defensive hormonal responses during plant-pathogen interactions. Here, we show that a plant virus-encoded protein re-localizes from the plasma membrane to chloroplasts upon activation of plant defense, interfering with the chloroplast-dependent anti-viral salicylic acid (SA) biosynthesis. Strikingly, we have found that plant pathogens from different kingdoms seem to have convergently evolved to target chloroplasts and impair SA-dependent defenses following an association with membranes, which relies on the co-existence of two subcellular targeting signals, an N-myristoylation site and a chloroplast transit peptide. This pattern is also present in plant proteins, at least one of which conversely activates SA defenses from the chloroplast. Taken together, our results suggest that a pathway linking plasma membrane to chloroplasts and activating defense exists in plants and that such pathway has been co-opted by plant pathogens during host-pathogen co-evolution to promote virulence through suppression of SA responses.

Large-scale multiplexed weak reflector array fabricated with a femtosecond laser for a fiber-optic quasi-distributed acoustic sensing system.

In this Letter, we propose a large-scale multiplexed weak reflector array fabrication method by using a femtosecond laser with relatively high reflectivity and low transmission loss. This kind of weak reflector array can be used in a quasi-distributed acoustic sensing system as sensing fiber instead of single-mode fiber (SMF) to achieve an ultrahigh signal-to-noise ratio (SNR). An automated fabrication system is designed, and a reflector geometric structure with high reflectivity and low scattering loss is designed based on this system. As a prototype to demonstrate the performance, one thousand weak reflectors are written on the SMF with an interval of 10 m, a reflectivity around -42dB, and a transmission loss of 0.34 dB/km. In comparison to the method of using SMF as the sensing fiber, at least 15.8 dB enhancement to the SNR can be achieved by using the reflector array as the sensing fiber.

Transcriptional reprogramming caused by the geminivirus Tomato yellow leaf curl virus in local or systemic infections in Nicotiana benthamiana.

BACKGROUND: Viruses have evolved to create a cellular environment permissive for viral replication in susceptible hosts. Possibly both enabling and resulting from these virus-triggered changes, infected hosts undergo a dramatic transcriptional reprogramming, the analysis of which can shed light on the molecular processes underlying the outcome of virus-host interactions. The study of the transcriptional changes triggered by the plant DNA viruses geminiviruses is potentially hampered by the low representation of infected cells in the total population, a situation that becomes extreme in those cases, like that of Tomato yellow leaf curl virus (TYLCV), in which the virus is restricted to phloem companion cells. RESULTS: In order to gain insight into how different the transcriptional landscapes of TYLCV-infected cells or whole tissues of TYLCV-infected plants might be, here we compare the transcriptional changes in leaf patches infected with TYLCV by agroinfiltration or in systemic leaves of TYLCV-infected plants in Nicotiana benthamiana. Our results show that, in agreement with previous works, infection by TYLCV induces a dramatic transcriptional reprogramming; the detected changes, however, are not equivalent in local and systemic infections, with a much larger number of genes differentially expressed locally, and some genes responding in an opposite manner. Interestingly, a transcriptional repression of the auxin signalling pathway and a transcriptional activation of the ethylene signalling pathway were detected in both local and systemically infected samples. A transcriptional activation of defence was also detectable in both cases. Comparison with the transcriptional changes induced by systemic infection by the geminivirus Tobacco curly shoot virus (TbSV) shows common subsets of up- and down-regulated genes similarly affected by both viral species, unveiling a common transcriptional repression of terpenoid biosynthesis, a process also suppressed by the geminivirus Tomato yellow leaf curl China virus. CONCLUSIONS: Taken together, the results presented here not only offer insight into the transcriptional changes derived from the infection by TYLCV in N. benthamiana, but also demonstrate that the resolution provided by local and systemic infection approaches largely differs, highlighting the urge to come up with a better system to gain an accurate view of the molecular and physiological changes caused by the viral invasion.

Quasi-distributed fiber-optic acoustic sensing system based on pulse compression technique and phase-noise compensation.

In this Letter, an ultra-low noise level is achieved for a quasi-distributed acoustic sensing system. This system is based on a pulse compression technique and phase-noise compensation configuration. In this system, a prototype of a weak reflector array is designed and fabricated to have ∼-40dB reflectivity with a 20 m interval, and is used for improving the system's signal-to-noise ratio. The two techniques reduce the noise level by 18 dB, among which 11.56 dB is obtained with the assistance of the phase-noise compensation configuration. In the experiment to simulate the scenario with a link loss of 20 km and 20 m array interval, the system noise level is demonstrated to be -93.16dBrerad/√Hz at 500-2500 Hz, which equals a strain resolution of 92.84fε/√Hz at 500-2500 Hz.

Highly sensitive quasi-distributed fiber-optic acoustic sensing system by interrogating a weak reflector array.

In this Letter, we demonstrate a highly sensitive quasi-distributed fiber-optic acoustic sensing system. This system interrogates a weak reflector array by using phase-sensitive optical time domain reflectometry with coherent detection. A phase-noise-compensated configuration is proposed to reduce the influence of 1/f noise, which is the main limitation when coherent detection is used in this high-sensitivity system. In the experiment to simulate the scenario with a link loss of 20 km fiber and 10 m array interval, the noise level shows an acoustic signal sensitivity of 3.84 pϵ/√Hz at 10-2500 Hz.

Characterization of Climacteric and Non-Climacteric Fruit Ripening.

Senescence is the terminal stage of plant development. It is a strategic and tactical response to seasonal and unpredictable stresses. As an important part of plant senescence, fruit ripening is normally viewed distinctly as climacteric or non-climacteric. In this chapter we describe protocols for the determination of a number of parameters that have been used in characterizing the ripening behavior of fruits. These include changes in respiratory rate, ethylene, flesh firmness, sugar, acidity, starch, pectin, enzymes, aroma volatiles, and expression of ripening-related genes during fruit ripening and senescence.

Dynamic Virus-Dependent Subnuclear Localization of the Capsid Protein from a Geminivirus.

Viruses are intracellular parasites with a nucleic acid genome and a proteinaceous capsid. Viral capsids are formed of at least one virus-encoded capsid protein (CP), which is often multifunctional, playing additional non-structural roles during the infection cycle. In animal viruses, there are examples of differential localization of CPs associated to the progression of the infection and/or enabled by other viral proteins; these changes in the distribution of CPs may ultimately regulate the involvement of these proteins in different viral functions. In this work, we analyze the subcellular localization of a GFP- or RFP-fused CP from the plant virus Tomato yellow leaf curl virus (TYLCV; Fam. Geminiviridae) in the presence or absence of the virus upon transient expression in the host plants Nicotiana benthamiana and tomato. Our findings show that, in agreement with previous reports, when the CP is expressed alone it localizes mainly in the nucleolus and weakly in the nucleoplasm. Interestingly, the presence of the virus causes the sequential re-localization of the CP outside of the nucleolus and into discrete nuclear foci and, eventually, into an uneven distribution in the nucleoplasm. Expression of the viral replication-associated protein, Rep, is sufficient to exclude the CP from the nucleolus, but the localization of the CP in the characteristic patterns induced by the virus cannot be recapitulated by co-expression with any individual viral protein. Our results demonstrate that the subcellular distribution of the CP is a dynamic process, temporally regulated throughout the progression of the infection. The regulation of the localization of the CP is determined by the presence of other viral components or changes in the cellular environment induced by the virus, and is likely to contribute to the multifunctionality of this protein. Bearing in mind these observations, we suggest that viral proteins should be studied in the context of the infection and considering the temporal dimension in order to comprehensively understand their roles and effects in the interaction between virus and host.

[Preparation of OMC-Au/L-Lysine/Au modified glassy carbon electrode and the study on its detection response to hydroquinone and catechol].

Ordered mesoporous carbon-Au nanoparticles (OMC-Au) nanocomposites were synthesized by a one-step chemical reduction route, and an OMC-Au/L-Lysine/Au composite film-modified glassy carbon electrode (GCE) was constructed. The microstructure of OMC and OMC-Au/L-Lysine/Au composite films were characterized by SEM, and the preparation process of OMC-Au/L-Lysine/Au modified glassy carbon electrode was investigated using cyclic voltammetry and electrochemical impedance spectroscopy. The electrocatalytic oxidation of hydroquinone and catechol on the modified electrode was discussed by differential pulse voltammetry in this study, and a sensor for separate determination of hydroquinone and catechol based on OMC-Au/L-Lysine/Au modified glassy carbon electrode was developed. Under the optimal conditions, the cathodic peak current was linearly related to hydroquinone concentration over ranges from 1.0 x 10(-6) mol x L(-1) to 8.0 x 10(-4) mol x L(-1) with a detection limit of 3.0 x 10(-7) mol x L(-1), and linearly related to catechol concentration from 1.0 x 10(-7) mol x L(-1) to 8.0 x 10(-5) mol x L(-1) with a detection limit of 8.0 x 10(-7) mol x L(-1).

A tyrosinase biosensor based on ordered mesoporous carbon-Au/L-lysine/Au nanoparticles for simultaneous determination of hydroquinone and catechol.

A novel biosensor was developed based on tyrosinase immobilization with ordered mesoporous carbon-Au (OMC-Au), L-lysine membrane and Au nanoparticles on a glassy carbon electrode (GCE). It was applied for the simultaneous determination of dihydroxybenzene isomers using differential pulse voltammetry (DPV). The tyrosinase/OMC-Au/L-lysine/Au film was characterized by scanning electron microscopy (SEM) and impedance spectra. Under optimized conditions, the DPV study results for two isomers, hydroquinone (HQ, 1,4-dihydroxybenzene) and catechol (CC, 1,2-dihydroxybenzene) showed low peak potentials, and the peak-to-peak difference was about 135.85 mV, which ensured the anti-interference ability of the biosensor and made simultaneous detection of dihydroxybenzene isomers possible in real samples. DPV peak currents increased linearly with concentration over the range of 4.0 × 10(-7) to 8.0 × 10(-5) M, and the detection limits of hydroquinone and catechol were 5 × 10(-8) M and 2.5 × 10(-8) M (S/N = 3), respectively. The tyrosinase biosensor exhibited good repeatability and stability. In addition, the response mechanism of enzyme catalysed redox on the OMC-Au/L-lysine/Au film modified electrode based on electrochemical study was discussed. The proposed method could be extended for the development of other enzyme-based biosensors.

Optical detection of NADH based on biocatalytic growth of Au-Ag core-shell nanoparticles.

We have developed an optical assay for NADH (Dihydronicotinamide adenine dinucleotide) based on the catalytic growth of gold-silver core-shell nanoparticles (Au-Ag-CSNPs). The nanoparticles were immobilized on pretreated glass slide and are shown to catalyze the NADH-mediated reduction of Ag(I) ions in the presence of 1,4-benzoquinone and cetyltrimethyl ammonium ion. This leads to the formation of Au-Ag-CSNPs on the glass. The absorption peak of the Au-Ag-CSNPs at 415 nm increases with the concentration of NADH in the solution used, and this can be measured by UV-vis photometry. High-resolution scanning electron microscopy analysis of the morphology of the surface of the Au-Ag-CSNPs before and after the catalytic reaction revealed a growth of their diameter. Under optimal conditions, NADH can be determined in the concentration range from 0.2 to 3.2mM, and the detection limit is 15.6 µM. The sensor has good precision and good storage stability, simple in operation, and can be fabricated at low costs, which made it suitable for the determination of NADH in complex biological systems and in related degradation processes of contaminants.

Immobilization of laccase on magnetic bimodal mesoporous carbon and the application in the removal of phenolic compounds.

A novel magnetically separable laccase immobilized system was constructed by adsorbing laccase into bimodal carbon-based mesoporous magnetic composites (CMMC). A large adsorption capacity (491.7 mg g(-1)), excellent activity recovery (91.0%) and broader pH and temperature profiles than free laccase have been exhibited by the immobilized laccase. Thermal stability was enhanced to a great extent and operational stability was increased to a certain extent. The shift of kinetic parameters indicated affinity change between enzyme and substrate. Application of the immobilized system in phenol and p-chlorophenol removal was investigated in a batch system. Adsorption effects of the support were responsible for the quick removal rate in the first hour, and up to 78% and 84% of phenol and p-chlorophenol were removed in the end of the reaction, respectively, indicating that the magnetic bimodal mesoporous carbon is a promising carrier for both immobilization of laccase and further application in phenol removal.

Electrochemical detection of Pseudomonas aeruginosa 16S rRNA using a biosensor based on immobilized stem-loop structured probe.

We have designed an electrochemical DNA biosensor based on stem-loop structured probes for enzymatic detection of Pseudomonas aeruginosa 16S ribosomal RNA (rRNA) in composting degradation. The probe modified with a thiol at its 5' end and a biotin at its 3' end was immobilized on a gold electrode through self-assembly. The stem-loop structured probes were "closed" when target was absent, then the hybridization of the target induced the conformational changes to "open", along with the biotin at its 3' end binding with streptavidin-horseradish peroxidase (HRP), and subsequent quantification of the target was detected via electrochemical detecting the enzymatic product in the presence of substrate. Under the optimum experiment conditions, the amperometric current response to HRP-catalyzed reaction was linearly related to the logarithm of the target nucleic acid concentration, ranging from 0.3 and 600 pg/µL, with the detection limit of 0.012 pg/µL. A correlation coefficient of 0.9960 was identified. The 16S rRNA extracted from P. aeruginosa was analyzed by this proposed sensor. The results were in agreement with the reference values deduced from UV spectrometric data. The biosensor was indicative of good precision, stability, sensitivity, and selectivity.