Development of Oligo-GISH kits for efficient detection of chromosomal variants in peanut

Oligo probe staining is a low-cost and efficient chromosome identification technique.In this study,oligo genomic in situ hybridization(Oligo-GISH)technology was established in peanut.Peanut A and B subgenome-specific interspersed repeat(IR)oligo probe sets were developed based on clustering and electronic localization of tandem repeat sequences in the reference genome of Tifrunner.The OligoGISH kit was then used to perform staining of 15 Arachis species.The A-subgenome probe set stained the chromosomes of A-and E-genome Arachis species,the B-subgenome probe set stained those of B-,F-,K-,and E-genome species,and neither set stained those of H-genome species.These results indicate the relationships among the genomes of these Arachis species.The Oligo-GISH kit was also used for batch staining of the chromosomes of 389 seedlings from the irradiated M1generation,allowing 67 translocation and deletion lines to be identified.Subsequent Oligo-FISH karyotyping,FISH using single-copy probe libraries,and trait investigation identified seven homozygous chromosomal variants from the M3generation and suggested that there may be genes on chromosome 4B controlling seed number per pod.These findings demonstrate that the IR probe sets and method developed in this study can facilitate research on distant hybridization and genetic improvement in peanut.

Spatio-temporal variations of shallow seismic velocity changes in Salton Sea Geothermal Field,California in response to large regional earthquakes and long-term geothermal activities

We measure spatio-temporal variations of seismic velocity changes in Salton Sea Geothermal Field,California based on cross correlations of daily seismic traces recorded by a borehole seismic network from December 2007 to January 2014.We find clear co-seismic velocity reductions during the 2010 M 7.2 El Mayor–Cucapah,Mexico earthquake at~100 km further south,followed by long-term recoveries.The co-seismic reductions are larger with longer post-seismic recoveries in higher frequency bands,indicating that material damage and healing process mostly occurred in the shallow depth.In addition,the co-seismic velocity reductions are larger for ray paths outside the active fluid injection/extraction regions.The ray paths inside injection/extraction regions are associated with smaller co-seismic reductions,but subtle long-term velocity increases.We also build 3D transient water flow models based on monthly injection/extraction rates,and find correlations between several water flow parameters and co-seismic velocity reductions.We interpret the relative lack of co-seismic velocity changes within the geothermal region as unclogging of fracture network due to persistent fluid flows of geothermal production.The long-term velocity increase is likely associated with the ground water depletion and subsidence due to net production.

Knockdown of RCN1 contributes to the apoptosis of colorectal cancer via regulating IP3R1

Background:The incidence of colorectal cancer(CRC)has been increasing in recent years.Thus,the discovery of factors that can assist in alleviating CRC is urgently warranted.Methods:To identify a potential factor involved in the development of CRC,we screened the upregulated genes in tumor tissues through four datasets from an online database.The expression of reticulocalbin 1(RCN1),a Ca2+-binding protein,was upregulated in the four datasets.Based on loss-offunction experiments,the effect of RCN1 on cell viability was assessed by Cell Counting Kit-8(CCK-8)assay.The regulatory effect of RCN1 on apoptosis was evaluated through Annexin V-fluorescein 5-isothiocyanate(FITC)/propidium iodide(PI)staining assay and terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling(TUNEL)assay in RKO and SW480 cells.Activation of endoplasmic reticulum(ER)stress signaling pathways was confirmed by estimating the phosphorylation and expression of PRKR-like ER kinase(PERK),inositol-requiring kinase-1(IRE1),transcription factor 6(ACT6),and CCAAT/enhancer-binding protein-homologous protein(CHOP).The intracellular Ca2+homeostasis regulated by RCN1 was determined through the detection of Ca2+concentration and mitochondrial membrane potential(MMP)measurement.Moreover,whether inositol 1,4,5-trisphosphate receptor type 1(IP3R1)was involved in the regulation of RCN1 in CRC was verified through the depletion of IP3R1 in RKO cells.Results:Knockdown of RCN1 reduced cell viability and facilitated apoptosis in RKO and SW480 cells.Phosphorylation of PERK and IRE1,activation of ATF6,and upregulation of CHOP were induced by the absence of RCN1,suggesting that the unfolded protein response(UPR)was activated in CRC cells.The concentration of Ca2+in mitochondria was increased after RCN1 depletion,followed by reduction in the MMP and release of cytochrome c from mitochondria to the cytoplasm in RKO and SW480 cells.Moreover,it was demonstrated that IP3R1 mediates the effect of RCN1 on apoptosis induced by ER stress in CRC cells.The downregulation of IP3R1 restored the RCN1 loss-induced apoptosis and the increased Ca2+concentration.Conclusion:Taken together,our results confirmed that silencing of RCN1 disrupted intracellular Ca2+homeostasis and promoted cell apoptosis caused by TG-induced ER stress by regulating IP3R1 and activating the UPR signaling pathways.

Analysis of Malware Application Based on Massive Network Traffic

Security and privacy issues are magnified by velocity, volume, and variety of big data. User's privacy is an even more sensitive topic attracting most people's attention. While XcodeGhost, a malware of i OS emerging in late 2015, leads to the privacy-leakage of a large number of users, only a few studies have examined XcodeGhost based on its source code. In this paper we describe observations by monitoring the network activities for more than 2.59 million i Phone users in a provincial area across 232 days. Our analysis reveals a number of interesting points. For example, we propose a decay model for the prevalence rate of Xcode Ghost and we find that the ratio of the infected devices is more than 60%; that a lot of popular applications, such as Wechat, railway 12306, didi taxi, Youku video are also infected; and that the duration as well as the traffic volume of most Xcode Ghost-related HTTP-requests is similar with usual HTTP-request which makes it difficult to be found. Besides, we propose a heuristic model based on fingerprint and its web-knowledge to identify the infected applications. The identifying result shows the efficiency of this model.

Analysis and Prediction of Content Popularity for Online Video Service:A Youku Case Study

Understanding the characteristics and predicting the popularity of the newly published online videos can provide direct implications in various contexts such as service design, advertisement planning, network management and etc. In this paper, we collect a real-world large-scale dataset from a leading online video service provider in China, namely Youku. We first analyze the dynamics of content publication and content popularity for the online video service. Then, we propose a rich set of features and exploit various effective classification methods to estimate the future popularity level of an individual video in various scenarios. We show that the future popularity level of a video can be predicted even before the video's release, and by introducing the historical popularity information the prediction performance can be improved dramatically. In addition, we investigate the importance of each feature group and each feature in the popularity prediction, and further reveal the factors that may impact the video popularity. We also discuss how the early monitoring period influences the popularity level prediction. Our work provides an insight into the popularity of the newly published online videos, and demonstrates promising practical applications for content publishers,service providers, online advisers and network operators.

内侧前额叶皮质DNA甲基化调控大鼠酒精相关行为

酒精滥用不仅导致组织器官损伤,还易诱发神经精神疾病。研究表明,DNA甲基化在酒精诱导基因表达和行为改变中发挥重要作用,但具体的神经生物学机制尚未被阐明。为了探索DNA甲基化在酒精滥用中的作用机制,本研究选取健康成年雄性SD大鼠(Rattus norvegicus)32只,随机分为饮水对照组(n=16)和慢性酒精暴露组(n=16),运用双瓶选择实验(two bottle choice test,TBCT)评估大鼠酒精偏爱率(alcohol preference),通过旷场行为(open field test,OFT)评估活动状态并检测血酒精浓度。分离两组大鼠内侧前额叶皮质(medial prefrontal cortex,mPFC),提取总DNA,利用简化代表性重亚硫酸盐测序技术(reduced representation bisulfite sequencing,RRBS)构建mPFC甲基化谱,对差异基因进行功能富集和通路分析,筛选与酒精滥用密切相关的甲基化差异基因,运用qRT-PCR技术检测差异基因的表达,验证DNA甲基化对基因的表达调控;利用qRT-PCR和Western blot检测甲基转移酶(DNA methyltransferases,DNMTs)和甲基化CpG位点结合蛋白2(methyl CpG binding protein 2,MeCP2)的表达;同时,还检测了短期酒精暴露(7 d)对大鼠mPFC内DNMTs和MeCP2的影响(n=8/组)。结果表明,慢性酒精暴露大鼠mPFC内基因启动子区甲基化水平显著升高。与酒精滥用密切相关的差异基因中,慢性酒精暴露组Ntf3和Ppm1G启动子区甲基化水平升高,mRNA表达降低;Hap1和DUSP1启动子区甲基化水平降低,mRNA表达升高。慢性酒精暴露使DNMT3B和MeCP2 mRNA和蛋白表达升高,而短期内酒精暴露不影响它们的表达。本研究初步证实DNA甲基化与酒精滥用的发展相关,可能受DNMT3B和MeCP2分子的调控,并发现了与酒精滥用相关的靶基因Ntf3、Ppm1G、Hap1和DUSP1,为研究酒精滥用的神经生物学机制提供了新见解,同时为酒精滥用治疗提供了可能的药理学靶点。

Using machine learning algorithms to estimate stand volume growth of Larix and Quercus forests based on national-scale Forest Inventory data in China

Estimating the volume growth of forest ecosystems accurately is important for understanding carbon sequestration and achieving carbon neutrality goals.However,the key environmental factors affecting volume growth differ across various scales and plant functional types.This study was,therefore,conducted to estimate the volume growth of Larix and Quercus forests based on national-scale forestry inventory data in China and its influencing factors using random forest algorithms.The results showed that the model performances of volume growth in natural forests(R^(2)=0.65 for Larix and 0.66 for Quercus,respectively)were better than those in planted forests(R^(2)=0.44 for Larix and 0.40 for Quercus,respectively).In both natural and planted forests,the stand age showed a strong relative importance for volume growth(8.6%–66.2%),while the edaphic and climatic variables had a limited relative importance(<6.0%).The relationship between stand age and volume growth was unimodal in natural forests and linear increase in planted Quercus forests.And the specific locations(i.e.,altitude and aspect)of sampling plots exhibited high relative importance for volume growth in planted forests(4.1%–18.2%).Altitude positively affected volume growth in planted Larix forests but controlled volume growth negatively in planted Quercus forests.Similarly,the effects of other environmental factors on volume growth also differed in both stand origins(planted versus natural)and plant functional types(Larix versus Quercus).These results highlighted that the stand age was the most important predictor for volume growth and there were diverse effects of environmental factors on volume growth among stand origins and plant functional types.Our findings will provide a good framework for site-specific recommendations regarding the management practices necessary to maintain the volume growth in China's forest ecosystems.

Identification of a stable major QTL for fresh-seed germination on chromosome Arahy.04 in cultivated peanut(Arachis hypogaea L.)

Fresh-seed germination(FSG)impairs peanut production,especially in areas where the peanut harvest season coincides with rainy weather.Developing FSG-resistant cultivars by molecular breeding is expected to mitigate yield loss and quality impairment caused by FSG.However,the genetic control of FSG awaits elucidation.In this study,FSG at 1,3,5,7,and 9 days post-imbibition in three environments were tested,and quantitative-trait loci(QTL)associated with FSG were mapped in a peanut recombinant inbred line population by leveraging existing high-density peanut genetic maps.Of 24 QTL identified in 13 linkage groups,qFSGA04 was a stable major QTL on linkage group 04(LG04).It was consistently detected in five germination stages and three environments.By designing and validating DNA markers in the confidence interval of qFSGA04,we identified one single-nucleotide polymorphism and one In Del closely associated with FSG that could be used as linked markers for FSG resistance in peanut breeding.

Holder Regularity for Abstract Fractional Cauchy Problems with Order in(0,1)

In this paper, we study the regularity of mild solution for the following fractional abstract Cauchy problem Dt αu(t)=Au(t)+f(t), t ∈ (0,T] u(0)= x0 on a Banach space X with order α ∈ (0,1), where the fractional derivative is understood in the sense of Caputo fractional derivatives. We show that if A generates an analytic α-times resolvent family on X and f ∈ Lp ([0,T];X) for some p > 1/α, then the mild solution to the above equation is in Cα-1/p[ò,T] for every ò > 0. Moreover, if f is H?lder continuous, then so are the Dt αu(t) and Au(t).

Knockdown of SIRT2 Rescues YARS-induced Charcot-Marie-Tooth Neuropathy in Drosophila

Dear Editor,Charcot-Marie-Tooth disease,the most common inherited peripheral neuropathology,is highly heterogeneous among patients and associated with mutations in~100 different genes at an incidence of at least 1:2,500[1].Over 30 mutated genes have been identified in CMT2,which is characterized by peripheral axon degeneration and distal deficits in motor function[2].The aminoacyl-tRNA synthetase is the largest family in CMT2 and includes tyrosyl-tRNA synthetase(YARS,tyrosyl-tRNA synthetase).

A Malvaceae-specific miRNA targeting the newly duplicated GaZIP1L to regulate Zn^(2+)ion transporter capacity in cotton ovules

MicroRNAs(miRNAs)play critical roles in regulating gene expression in plants,yet their functions underlying cultivated diploid Gossypium arboreum cotton ovule development are largely unknown.Here,we acquired small RNA profiles from G.arboreum ovules and fibers collected at different growth stages,and identified 46 novel miRNAs that accounted for 23.7%of all miRNAs in G.arboreum reported in the latest plant sRNA database.Through analysis of 84(including 38 conserved)differentially expressed G.arboreum miRNAs,we detected 215 putative protein-coding genes in 26 biological processes as their potential targets.A Malvaceae-specific novel miRNA named gar-miRN44 was found to likely regulate cotton ovule growth by targeting to a newly duplicated Zn^(2+)ion transporter gene GaZIP1L.During cotton ovule development,gar-miRN44 transcript level decreased sharply after 10 to 15 days post-anthesis(DPA),while that of the GaZIP1L increased significantly,with a concomitant increase of Zn^(2+)ion concentration in late ovule developmental stages.Molecular dynamics simulation and ion absorption analysis showed that GaZIP1L has stronger Zn2+ion binding ability than the original GaZIP1,indicating that the newly evolved GaZIP1L may be more suitable for maintaining high Zn2+ion transport capacity that is likely required for cotton ovule growth via enhanced cellulose synthase activities.Our systematic miRNA profiling in G.arboreum and characterization of gar-miRN44 not only contribute to the understanding of miRNA function in cotton,but also provide potential targets for plant breeding.

Free-standing hybrid films comprising of ultra-dispersed titania nanocrystals and hierarchical conductive network for excellent high rate performance of lithium storage

The construction of advanced electrode materials is key to the field of energy storage.Herein,a free-standing anatase titania(TiO_(2))nanocrystal/carbon nanotube(CNT)film is reported using a simple and scalable sol-gel method,followed by calcination.This unique free-standing film comprises ultra-small TiO_(2) nanocrystals(~5.9 nm)and super-aligned CNTs,with ultra-dispersed TiO_(2) nanocrystals on the surfaces of the CNTs.On the one hand,these TiO_(2) nanocrystals can significantly decrease the diffusion distance of the charges and on the other hand,the cross-linked CNTs can act as a three-dimensional(3D)conductive network,allowing the fast transport of electrons.In addition,the film is free-standing,without requiring electrode fabrication and additional conductive agents and binders.Owing to these above synergistic effects,the film is directly used as an anode in Li-ion batteries,and delivers a high discharge capacity of~105 mAh·g^(−1) at high rate of 60 C(1 C=170 mA·g^(−1))and excellent cycling performance over 2,500 cycles at 30 C.These results indicate that the free-standing anatase TiO_(2) nanocrystal/CNT film affords a superior performance among the various TiO_(2) materials and can be a promising anode material for fast-charging Li-ion batteries.Moreover,the TiO_(2)/CNT film exhibits an areal capacity of up to 2.4 mAh·cm^(−2),confirming the possibility of its practical use.

Fabrication of Regular Hierarchical Structures with Superhydrophobic and High Adhesion Performances on a 304 Stainless Steel Surface via Picosecond Laser

Hierarchical structures significantly influence the development of metal surface wettability.In this study,three kinds of hierarchical structures fbimed by the superimposition of different nanoscale(quasi-)periodic structures on micro-column arrays were fabricated on 304 stainless steel surfaces via picosecond laser irradiation.Scanning Electron Microscope(SEM)and Confocal Laser Scanning Microscope(CLSM)were used to characterize the created hierarchical structures.An optical contact angle meter was used to analyse the wetting performances.The results show that the surfaces of these fabricated samples have superhydrophobic properties and strong adhesion per formances,which can be attributed to the formation of hierarchical structure that causes a reduction in the liquid-solid contact area and the change in the direction of surfece tension.By controlling the dimensionof the nanotextures on the micro-column arrays,the hydrophobic property of 304 stainless steel surfaces can be greatly improved.

虾青素通过CCN1调节肾间质纤维化的潜在分子作用机制

目的探讨虾青素(AST)对肾间质纤维化的潜在分子作用机制,为临床防治肾脏纤维化提供数据。方法动物实验采用单侧输尿管结扎(UUO)法建立肾间质纤维化模型。60只雄性C57BL/6小鼠随机分为6组(10只/组):假手术组、假手术+AST(200 mg/kg)组、UUO模型组、UUO+AST(50 mg/kg)组、UUO+AST(100 mg/kg)组、UUO+AST(200 mg/kg)组。细胞实验采用TGF-β1诱导HK-2细胞株上皮间充质转化(EMT)模型。质粒转染实验将HK-2细胞分为7组:对照组、空白组、CCN1过表达组、CCN1敲低组、TGF-β1诱导组、TGF-β1+CCN1过表达组、TGF-β1+CCN1敲低组。AST处理实验将HK-2细胞分为5组:对照组、TGF-β1诱导组、TGF-β1+AST组、TGF-β1+CCN1敲低组、TGF-β1+CCN1敲低+AST组。实时定量荧光PCR法检测肾组织肾损伤生物标志物中性粒细胞明胶酶相关脂质运载蛋白(NGAL)、肾损伤分子-1(KIM-1)、血清胱抑素-C(Cys-C)和白介素-18(IL-18)。Western印迹检测肾组织和细胞的纤维化标志物Ⅰ型胶原蛋白(Col-Ⅰ)、纤连蛋白(FN)、α-平滑肌肌动蛋白(α-SMA)、波形蛋白和E-钙粘蛋白(E-cad),以及TGF-β1/Smad和Notch信号通路分子:pSmad3、Notch1、Notch3、Jagged-1的表达。结果与假手术组相比,UUO组小鼠肾损伤生物标志物NGAL、KIM-1、Cys-C和IL-18的水平显著升高;肾脏纤维化标志物蛋白表达水平显著升高,E-cad表达水平显著下降;pSmad3、Notch1、Notch3、Jagged-1的蛋白表达水平显著增加,Smad7表达显著减少。AST处理使肾损伤生物标志物(NGAL、KIM-1、Cys-C和IL-18)、纤维化标志物蛋白表达水平显著下降,E-cad蛋白表达显著上升且呈剂量依赖性。细胞实验结果显示:CCN1过表达可以抑制TGF-β1/Smad和Notch信号通路的激活,而敲低CCN1不仅增强了TGF-β1/Smad和Notch信号通路的激活,还减弱了AST在TGF-β1诱导的EMT模型中的保护作用。结论AST可能通过CCN1调节TGF-β1/Smad和Notch信号通路,从而可能具有减轻肾间质纤维化、保护肾脏的作用。

Characterizing PM2.5 in Beijing and Shanxi Province using terahertz radiation

Particles of aerodynamic diameter〈2.5 pm （PM/.5） caused extremely severe and persistent haze pollution is of concern in many cities. In this study, samples of PM2.5 were collected from atmosphere environment of Beijing and Shanxi Province, and analyzed using terahertz （THz） radiation. The transmission spectrum of PM2.5 in Shanxi Province had two distinct absorption peaks at 6.0 and 6.7 THz, and the curve was increasing on the whole. However, the transmission spectrum of PMa.5 in Beijing had obviously different variation tendency and the absorption peak was studied by monitoring PM2.5 masses in conjunction with two-dimensional correlation spectro- scopy （2DCOS）. By comparing the pollutant species and concentrations of Shanxi Province and Beijing over the time of collecting samples, the concentrations of sulfate and ammonium were similar, which contributed to emerge absorption bands in the same position. While the concentrations of organic matter （OM）, nitrate, chloride and elemental carbon （EC） were different. Furthermore, dust and some other inorganic ion are unique to Shanxi province, which lead to different variation tendency of the transmission spectrum of PM2.5. These results will be of importance for environmental monitoring and for control- ling PM emissions. According to this research, optical techniques, and especially spectral methods, should be considered for PM2.5 monitoring.