ASAPA: a bioinformatic pipeline based on Iso-Seq that identifies the links among alternative splicing, alternative transcription initiation and alternative polyadenylation.

BACKGROUND: Although the events associated with alternative splicing (AS), alternative polyadenylation (APA) and alternative transcription initiation (ATI) can be identified by many approaches based on isoform sequencing (Iso-Seq), these analyses are generally independent of each other and the links between these events are still rarely mentioned. However, an interdependency analysis can be achieved because the transcriptional start site, splice sites and polyA site could be simultaneously included in a long, full-length read from Iso-Seq. RESULTS: We create ASAPA pipeline that enables streamlined analysis for a robust detection of potential links among AS, ATI and APA using Iso-Seq data. We tested this pipeline using Arabidopsis data and found some interesting results: some adjacent introns tend to be simultaneously spliced or retained; coupling between AS and ATI or APA is limited to the initial or terminal intron; and ATI and APA are potentially linked in some special cases. CONCLUSION: Our pipeline enables streamlined analysis for a robust detection of potential links among AS, ATI and APA using Iso-Seq data, which is conducive to a better understanding of transcription landscape generation.

A three-dimensional composite film-modified electrode based on polyoxometalates and ionic liquid-decorated carbon nanotubes for the determination of L-tyrosine in food.

A stable and innovative composite film-modified electrode based on Dawson polyoxometalates H8P2Mo16V2O62 (P2Mo16V2) and ionic liquid (BMIMBr)-decorated carbon nanotubes, annotated as PEI/(P2Mo16V2/BMIMBr-CNTs)8, has been constructed by using the layer-by-layer self-assembly (LBL) method for the determination of L-tyrosine. The combination of three active components not only offers higher conductivity to facilitate rapid electron transfer, but also avoids the accumulation of P2Mo16V2 to expand the contact area and increase the reactive active sites. The modified electrode exhibits outstanding sensing performance for determination of Tyr with wide linear determination range of 5.8×10-7 M ~ 1.2×10-4 M, low determination limit of 1.7×10-7M (S/N=3), high selectivity for common interferences, and excellent stability at the potential of +0.78 V (vs. Ag/AgCl (3 M KCl)). The relative standard deviation (RSD) of 4.3% for five groups of parallel experiments shows the satisfactory repeatability of PEI/(P2Mo16V2/BMIMBr-CNTs)8. In addition, for determination of Tyr, the PEI/(P2Mo16V2/BMIMBr-CNTs)8 shows good recoveries of 98.8-99.8% in meat floss, which can be feasible in practical application.

Two Polyoxometalate-Encapsulated Two-Fold Interpenetrating dia Metal-Organic Frameworks for the Detection, Discrimination, and Degradation of Phenolic Pollutants.

Phenols are widely used for commercial production, while they pose a hazard to the environment and human health. Thus, investigation of convenient and efficient methods for the detection, discrimination, and degradation of phenols becomes particularly important. Herein, two new polyoxometalate (POM)-based compounds, [Co2(btap)4(H2O)4][SiW12O40] (Co-POM) and [Ni2(btap)4(H2O)4][SiW12O40] (Ni-POM) (btap = 3,5-bis(triazol-1-yl)pyridine), are prepared via a hydrothermal synthesis method. The compounds show a fascinating structural feature of a POM-encapsulated twofold interpenetrating dia metal-organic framework. More importantly, besides the novel structures, the compound Co-POM realizes three functions, namely, the simultaneous detection, discrimination, and degradation of phenols. Specifically, Co-POM shows an excellent colorimetric detection performance toward phenol with a detection limit (LOD) ca. 1.32 µM, which is lower than most reported colorimetric detectors for phenol. Also, a new colorimetric sensor system based on Co-POM can discriminate phenol, 4-chlorophenol, and o-cresol with ease. Further, Co-POM exhibits a photocatalytic degradation property for 4-chlorophenol under irradiation of visible light with the highest degradation rate at 62% after irradiation for 5 h. Therefore, this work provides the first example of a POMs-based multifunctional material for achieving the detection, discrimination, and degradation of phenolic pollutants.

Transcriptomic and phosphoproteomic profiling and metabolite analyses reveal the mechanism of NaHCO3-induced organic acid secretion in grapevine roots.

BACKGROUND: Organic acid secretion is a widespread physiological response of plants to alkalinity. However, the characteristics and underlying mechanism of the alkali-induced secretion of organic acids are poorly understood. RESULTS: Oxalate was the main organic acid synthesized and secreted in grapevine (a hybrid of Vitis amurensis, V. berlandieri and V. riparia) roots, while acetate synthesis and malate secretion were also promoted under NaHCO3 stress. NaHCO3 stress enhanced the H+ efflux rate of grapevine roots, which is related to the plasma membrane H+-ATPase activity. Transcriptomic profiling revealed that carbohydrate metabolism was the most significantly altered biological process under NaHCO3 stress; a total of seven genes related to organic acid metabolism were significantly altered, including two phosphoenolpyruvate carboxylases and phosphoenolpyruvate carboxylase kinases. Additionally, the expression levels of five ATP-binding cassette transporters, particularly ATP-binding cassette B19, and two Al-activated malate transporter 2 s were substantially upregulated by NaHCO3 stress. Phosphoproteomic profiling demonstrated that the altered phosphoproteins were primarily related to binding, catalytic activity and transporter activity in the context of their molecular functions. The phosphorylation levels of phosphoenolpyruvate carboxylase 3, two plasma membrane H+-ATPases 4 and ATP-binding cassette B19 and pleiotropic drug resistance 12 were significantly increased. Additionally, the inhibition of ethylene synthesis and perception completely blocked NaHCO3-induced organic acid secretion, while the inhibition of indoleacetic acid synthesis reduced NaHCO3-induced organic acid secretion. CONCLUSIONS: Our results demonstrated that oxalate was the main organic acid produced under alkali stress and revealed the necessity of ethylene in mediating organic acid secretion. Additionally, we further identified several candidate genes and phosphoproteins responsible for organic acid metabolism and secretion.

[Exploration and Minging of Large Medical Equipment Operation Data under Internet of Things].

With the technology development in Internet of Things (IoT) area, it is good to try to use IoT and cloud computing technologies to improve the efficiency of medical equipment management. This article described using CT as sample to do the data capture and data analysis with the IoT technology. The positive result got shows the benefit of the exploring.

The enhancement of tolerance to salt and cold stresses by modifying the redox state and salicylic acid content via the cytosolic malate dehydrogenase gene in transgenic apple plants.

In this study, we characterized the role of an apple cytosolic malate dehydrogenase gene (MdcyMDH) in the tolerance to salt and cold stresses and investigated its regulation mechanism in stress tolerance. The MdcyMDH transcript was induced by mild cold and salt treatments, and MdcyMDH-overexpressing apple plants possessed improved cold and salt tolerance compared to wild-type (WT) plants. A digital gene expression tag profiling analysis revealed that MdcyMDH overexpression largely altered some biological processes, including hormone signal transduction, photosynthesis, citrate cycle and oxidation-reduction. Further experiments verified that MdcyMDH overexpression modified the mitochondrial and chloroplast metabolisms and elevated the level of reducing power, primarily caused by increased ascorbate and glutathione, as well as the increased ratios of ascorbate/dehydroascorbate and glutathione/glutathione disulphide, under normal and especially stress conditions. Concurrently, the transgenic plants produced a high H2 O2 content, but a low O2·- production rate was observed compared to the WT plants. On the other hand, the transgenic plants accumulated more free and total salicylic acid (SA) than the WT plants under normal and stress conditions. Taken together, MdcyMDH conferred the transgenic apple plants a higher stress tolerance by producing more reductive redox states and increasing the SA level; MdcyMDH could serve as a target gene to genetically engineer salt- and cold-tolerant trees.

Nitrogen doped 1 T/2H mixed phase MoS2/CuS heterostructure nanosheets for enhanced peroxidase activity.

Heteroatom doping and phase engineering are effective ways to promote the catalytic activity of nanoenzymes. Nitrogen-doped 1 T/2H mixed phase MoS2/CuS heterostructure nanosheets N-1 T/2H-MoS2/CuS are prepared by a simple hydrothermal approach using polyoxometalate (POM)-based metal-organic frameworks (MOFs) (NENU-5) as a precursor and urea as nitrogen doping reagent. The XPS spectroscopy (XPS) and Raman spectrum of N-1 T/2H-MoS2/CuS prove the successful N-doping. NENU-5 was used as the template to prepare 1 T/2H-MoS2/CuS with high content of 1 T phase by optimizing the reaction time. The use of urea as nitrogen dopant added to 1 T/2H-MoS2/CuS, resulted in N-1 T/2H-MoS2/CuS with an increase in the content of the 1 T phase from 80 % to 84 % and higher number of defects. N-1 T/2H-MoS2/CuS shows higher peroxidase activity than 1 T/2H-MoS2/CuS and a catalytic efficiency (Kcat/Km) for H2O2 twice as high as that of 1 T/2H-MoS2/CuS. The enhanced catalytic activity has probably been attributed to several reasons: (i) the insertion of urea during the hydrothermal process in the S-Mo-S layer of MoS2, causing an increase in the interlayer spacing and in 1 T phase content, (ii) the replacement of S atoms in MoS2 by N atoms from the urea decomposition, resulting in more defects and more active sites. As far as we know, N-1 T/2H-MoS2/CuS nanosheets have the lowest detection limit (0.16 µm) for the colorimetric detection of hydroquinone among molybdenum disulfide-based catalysts. This study affords a new approach for the fabrication of high-performance nanoenzyme catalysts.

In situ coupling of a Co-Mo bimetallic sulfide derived from [CoMo12O40]6- clusters showing highly efficient electrocatalytic hydrogen evolution.

The hydrogen evolution reaction (HER) is important for "green" hydrogen production from water electrolysis. Nowadays, there is an urgent need to construct highly efficient electrocatalysts to boost the HER and achieve hydrogen production. Herein, we present the preparation of a new composite Co-Mo bimetallic sulfide supported on carbon cloth (MoS2/CoS2/CC) via a one-pot hydrothermal sulfurization strategy using (C3H5N2)6[CoMo12O40]·10H2O (CoMo12) as a metal source and thiourea as a sulfur source. The obtained MoS2/CoS2/CC catalyst exhibited outstanding HER ability, with an overpotential of 69 mV when the current density is 10 mA cm-2 in KOH solution, showing comparable performance with those of the advanced Pt/C electrodes tested under the same conditions. Additionally, the results of XRD after the catalytic reaction showed that the electrode had excellent stability in the electrolyte of 1.0 M KOH.

Fe Foam-Supported FeS2-MoS2 Electrocatalyst for N2 Reduction under Ambient Conditions.

Highly efficient catalysts with enough selectivity and stability are essential for electrochemical nitrogen reduction reaction (e-NRR) that has been considered as a green and sustainable route for synthesis of NH3. In this work, a series of three-dimensional (3D) porous iron foam (abbreviated as IF) self-supported FeS2-MoS2 bimetallic hybrid materials, denoted as FeS2-MoS2@IFx, x = 100, 200, 300, and 400, were designed and synthesized and then directly used as the electrode for the NRR. Interestingly, the IF serving as a slow-releasing iron source together with polyoxomolybdates (NH4)6Mo7O24·4H2O as a Mo source were sulfurized in the presence of thiourea to form self-supported FeS2-MoS2 on IF (abbreviated as FeS2-MoS2@IF200) as an efficient electrocatalyst. Further material characterizations of FeS2-MoS2@IF200 show that flower cluster-like FeS2-MoS2 grows on the 3D skeleton of IF, consisting of interconnected and staggered nanosheets with mesoporous structures. The unique 3D porous structure of FeS2-MoS2@IF together with synergy and interface interactions of bimetallic sulfides would make FeS2-MoS2@IF possess favorable electron transfer tunnels and expose abundant intrinsic active sites in the e-NRR. It is confirmed that synthesized FeS2-MoS2@IF200 shows a remarkable NH3 production rate of 7.1 ×10-10 mol s-1 cm-2 at -0.5 V versus the reversible hydrogen electrode (vs RHE) and an optimal faradaic efficiency of 4.6% at -0.3 V (vs RHE) with outstanding electrochemical and structural stability.

Melatonin enhances salt tolerance by promoting MYB108A-mediated ethylene biosynthesis in grapevines.

The signal molecules melatonin and ethylene play key roles in abiotic stress tolerance. The interplay between melatonin and ethylene in regulating salt tolerance and the underlying molecular mechanism of this interplay remain unclear. Here, we found that both melatonin and 1-aminocyclopropane-1-carboxylic acid (ACC, a precursor of ethylene) enhanced the tolerance of grapevine to NaCl; additionally, ethylene participated in melatonin-induced salt tolerance. Further experiments indicated that exogenous treatment and endogenous induction of melatonin increased the ACC content and ethylene production in grapevine and tobacco plants, respectively. The expression of MYB108A and ACS1, which function as a transcription factor and a key gene involved in ethylene production, respectively, was strongly induced by melatonin treatment. Additionally, MYB108A directly bound to the promoter of ACS1 and activated its transcription. MYB108A expression promoted ACC synthesis and ethylene production by activating ACS1 expression in response to melatonin treatment. The suppression of MYB108A expression partially limited the effect of melatonin on the induction of ethylene production and reduced melatonin-induced salt tolerance. Collectively, melatonin promotes ethylene biosynthesis and salt tolerance through the regulation of ACS1 by MYB108A.

Modifications of 'Gold Finger' Grape Berry Quality as Affected by the Different Rootstocks.

Berry qualities of the grafted 'Gold Finger' grapevines were determined to evaluate the impacts of the resistant rootstocks on fruit quality. Compared to the own-rooted vines, berry and cluster weights and skin color were altered by the rootstocks to varying extents. The rootstock of 101-14M maintained TSS/TA and the contents of fructose, glucose, and sucrose, and SO4 decreased these parameters. 101-14M and 3309C increased and reduced the resveratrol content, respectively. SO4, 5BB, and 3309C decreased the total free amino acid content, along with the changes in amino acid composition. The amounts of aroma components were widely altered by the rootstocks. Additionally, a digital gene expression tag profiling revealed that the biological processes were largely altered by 3309C and 101-14M, including sugar, amino acid, and aroma metabolisms. In summary, the rootstock of 101-14M generally maintained berry quality, and SO4, 5BB, and 3309C imparted varying influences on different quality parameters.