Causal genetic regulation of DNA replication on immune microenvironment in colorectal tumorigenesis: Evidenced by an integrated approach of trans-omics and GWAS

The interplay between DNA replication stress and immune microenvironment alterations is known to play a crucial role in colorectal tumorigenesis,but a comprehensive understanding of their association with and relevant biomarkers involved in colorectal tumorigenesis is lacking.To address this gap,we conducted a study aiming to investigate this association and identify relevant biomarkers.We analyzed transcriptomic and proteomic profiles of 904 colorectal tumor tissues and 342 normal tissues to examine pathway enrichment,biological activity,and the immune microenvironment.Additionally,we evaluated genetic effects of single variants and genes on colorectal cancer susceptibility using data from genome-wide association studies(GWASs)involving both East Asian(7062 cases and 195745 controls)and European(24476 cases and 23073 controls)populations.We employed mediation analysis to infer the causal pathway,and applied multiplex immunofluorescence to visualize colocalized biomarkers in colorectal tumors and immune cells.Our findings revealed that both DNA replication activity and the flap structure-specific endonuclease 1(FEN1)gene were significantly enriched in colorectal tumor tissues,compared with normal tissues.Moreover,a genetic variant rs4246215 G>T in FEN1 was associated with a decreased risk of colorectal cancer(odds ratio=0.94,95%confidence interval:0.90–0.97,P_(meta)=4.70×10^(-9)).Importantly,we identified basophils and eosinophils that both exhibited a significantly decreased infiltration in colorectal tumors,and were regulated by rs4246215 through causal pathways involving both FEN1 and DNA replication.In conclusion,this trans-omics incorporating GWAS data provides insights into a plausible pathway connecting DNA replication and immunity,expanding biological knowledge of colorectal tumorigenesis and therapeutic targets.

Statistical Method for Block in Replication Design and Its SAS Program

Large-scale genetic population used for genetic breeding researches covers a large area in the field experiment,and the effect of local control would be gradually weakened.The block in replication(BIR)design is suitable for large population,which is applied to the field experiment of genetic population.The statistical methods of analysis of variance(ANOVA)and heritability estimation in single and multiple environments were derived and implemented using the statistical analysis system(SAS)program for the analysis of BIR.As a work example,a comparison of statistical analysis between BIR design and the completely random block(CRB)design were conducted for the protein content from a panel containing 455 soybean germplasms.The results indicated the different estimates of average heritability in multiple environments.The research results provided technical support for the application of BIR design in genetics and breeding studies.

Transcriptional regulation of secondary metabolism and autophagy genes in response to DNA replication stress in Setosphaeria turcica

The fungal pathogen Setosphaeria turcica causes northern corn leaf blight(NCLB),which leads to considerable crop losses.Setosphaeria turcica elaborates a specialized infection structures called appressorium for maize infection.Previously,we demonstrated that the S.turcica triggers an S-phase checkpoint and ATR(Ataxia Telangiectasia and Rad3 related)-dependent self-protective response to DNA genotoxic insults during maize infection.However,how the regulatory mechanism works was still largely unknown.Here,we report a genome wide transcriptional profile analysis during appressorium formation in the present of DNA replication stress.We performed RNA-Seq analysis to identify S.tuicica genes responsive to DNA replication stress.In the current work,we found that appressorium-mediated maize infection by S.turcica is significantly blocked by S-phase checkpoint.A large serial of secondary metabolite and melanin biosynthesis genes were blocked in appressorium formation of S.turcica during the replication stress.The secondary metabolite biosynthesis genes including alcohol dehydrogenase GroES-like domain,multicopper oxidase,ABCtransporter families,cytochrome P450 and FAD-containing monooxygenase were related to plant pathogen infection.In addition,we demonstrated that autophagy in S.turcica is up-regulated by ATR as a defense response to stress.We identified StATG3,StATG4,StATG5,StATG7 and StATG16 genes for autophagy were induced by ATR-mediated S-phase checkpoint.We therefore propose that in response to genotoxic stress,S.turcica utilizes ATR-dependent pathway to turn off transcription of genes governing appressorium-mediated infection,and meanwhile inducing transcription of autophagy genes likely as a mechanism of self-protection,aside from the more conservative responses in eukaryotes.

Replication Strategy with Comprehensive Data Center Selection Method in Cloud Environments

As the amount of data continues to grow rapidly,the variety of data produced by applications is becoming more affluent than ever.Cloud computing is the best technology evolving today to provide multi-services for the mass and variety of data.The cloud computing features are capable of processing,managing,and storing all sorts of data.Although data is stored in many high-end nodes,either in the same data centers or across many data centers in cloud,performance issues are still inevitable.The cloud replication strategy is one of best solutions to address risk of performance degradation in the cloud environment.The real challenge here is developing the right data replication strategy with minimal data movement that guarantees efficient network usage,low fault tolerance,and minimal replication frequency.The key problem discussed in this research is inefficient network usage discovered during selecting a suitable data center to store replica copies induced by inadequate data center selection criteria.Hence,to mitigate the issue,we proposed Replication Strategy with a comprehensive Data Center Selection Method(RS-DCSM),which can determine the appropriate data center to place replicas by considering three key factors:Popularity,space availability,and centrality.The proposed RS-DCSM was simulated using CloudSim and the results proved that data movement between data centers is significantly reduced by 14%reduction in overall replication frequency and 20%decrement in network usage,which outperformed the current replication strategy,known as Dynamic Popularity aware Replication Strategy(DPRS)algorithm.

Comparison of the replication and neutralization of different SARS-CoV-2 Omicron subvariants in vitro

Background:New Omicron subvariants are emerging rapidly from BA.1 to BA.4 and BA.5.Their pathogenicity has changed from that of wild-type(WH-09)and Omicron variants have over time become globally dominant.The spike proteins of BA.4 and BA.5 that serve as the target for vaccine-induced neutralizing antibodies have also changed compared to the previous subvariants,which is likely to cause immune es-cape and the reduction of the protective effect of the vaccine.Our study addresses the above issues and provides a basis for formulating relevant prevention and control strategies.Methods:We collected cellular supernatant and cell lysates and measured the viral titers,viral RNA loads,and E subgenomic RNA(E sgRNA)loads in different Omicron subvariants grown in Vero E6 cells,using WH-09 and Delta variants as a reference.Additionally,we evaluated the in vitro neutralizing activity of different Omicron sub-variants and compared it to the WH-09 and Delta variants using macaque sera with different types of immunity.Results:As the SARS-CoV-2 evolved into Omicron BA.1,the replication ability in vitro began to decrease.Then with the emergence of new subvariants,the replication ability gradually recovered and became stable in the BA.4 and BA.5 subvariants.In WH-09-inactivated vaccine sera,geometric mean titers of neutralization antibodies against different Omicron subvariants declined by 3.7~15.4-fold compared to those against WH-09.In Delta-inactivated vaccine sera,geometric mean titers of neutrali-zation antibodies against Omicron subvariants declined by 3.1~7.4-fold compared to those against Delta.Conclusion:According to the findings of this research,the replication efficiency of all Omicron subvariants declined compared with WH-09 and Delta variants,and was lower in BA.1 than in other Omicron subvariants.After two doses of inactivated(WH-09 or Delta)vaccine,cross-neutralizing activities against various Omicron subvariants were seen despite a decline in neutralizing titers.

Graph-Based Replication and Two Factor Authentication in Cloud Computing

Many cutting-edge methods are now possible in real-time commercial settings and are growing in popularity on cloud platforms.By incorporating new,cutting-edge technologies to a larger extent without using more infrastructures,the information technology platform is anticipating a completely new level of devel-opment.The following concepts are proposed in this research paper:1)A reliable authentication method Data replication that is optimised;graph-based data encryp-tion and packing colouring in Redundant Array of Independent Disks(RAID)sto-rage.At the data centre,data is encrypted using crypto keys called Key Streams.These keys are produced using the packing colouring method in the web graph’s jump graph.In order to achieve space efficiency,the replication is carried out on optimised many servers employing packing colours.It would be thought that more connections would provide better authentication.This study provides an innovative architecture with robust security,enhanced authentication,and low cost.

A Broker-Based Task-Scheduling Mechanism Using Replication Approach for Cloud Systems

The reliability and availability of cloud systems have become major concerns of service providers,brokers,and end-users.Therefore,studying fault-tolerance mechanisms in cloud computing attracts intense attention in industry and academia.The task-scheduling mechanisms can improve the fault-tolerance level of cloud systems.A task-scheduling mechanism distributes tasks to a group of instances to be executed.Much work has been undertaken in this direction to improve the overall outcome of cloud computing,such as improving service qual-ity and reducing power consumption.However,little work on task scheduling has studied the problem of lost tasks from the broker’s perspective.Task loss can hap-pen due to virtual machine failures,server crashes,connection interruption,etc.The broker-based concept means that the backup task can be allocated by the bro-ker on the same cloud service provider(CSP)or a different CSP to reduce costs,for example.This paper proposes a novel fault-tolerant mechanism that employs the primary backup(PB)model of task scheduling to address this issue.The pro-posed mechanism minimizes the impact of failure events by reducing the number of lost tasks.The mechanism is further improved to shorten the makespan time of submitted tasks in cloud systems.The experiments demonstrated that the pro-posed mechanism decreased the number of lost tasks by about 13%–15%com-pared with other mechanisms in the literature.

Efficient Heuristic Replication Techniques for High Data Availability in Cloud

Most social networks allow connections amongst many people based on shared interests.Social networks have to offer shared data like videos,photos with minimum latency to the group,which could be challenging as the storage cost has to be minimized and hence entire data replication is not a solution.The replication of data across a network of read-intensive can potentially lead to increased savings in cost and energy and reduce the end-user’s response time.Though simple and adaptive replication strategies exist,the solution is non-deter-ministic;the replicas of the data need to be optimized to the data usability,perfor-mance,and stability of the application systems.To resolve the non-deterministic issue of replication,metaheuristics are applied.In this work,Harmony Search and Tabu Search algorithms are used optimizing the replication process.A novel Har-mony-Tabu search is proposed for effective placement and replication of data.Experiments on large datasets show the effectiveness of the proposed technique.It is seen that the bandwidth saving for proposed harmony-Tabu replication per-forms better in the range of 3.57%to 18.18%for varying number of cloud data-centers when compared to simple replication,Tabu replication and Harmony replication algorithm.

基于Oracle GoldenGate和Cloud Data Replication的灾备解决方案研究

一、引言随着信息时代的到来,企业信息化发展越来越快,导致积累的数据越来越多,这些数据对于企业来说是非常宝贵的资源,尤其对数据信息依赖程度很高的行业更是如此。要保障业务系统稳定而且持续的运行,就要保证数据的安全性、完整性和可用性。数据备份是数据安全最基础的保障,它几乎是任何信息化系统中必需的组成部分,意外断电、系统崩溃.

教育定量研究范式:价值、困境与创新路径

教育定量研究范式是以实证主义为基础,运用数学工具或统计分析等手段对教育现象或教育过程进行测量,依据数据资料检验理论假设,揭示教育现象中各种因素相关关系的研究范式。它是提升教育研究科学化的关键,是引领教育高质量发展的工具,也是适应教育数字化转型需要的必然趋势。但是,当前教育定量研究在推动教育学走向科学化与实证化的过程中面临着多重困境,表现为方法的“内生性”问题、量化的“前提性”问题和研究的“规范性”问题。我国教育研究向实证研究范式的转型、信息技术的迅猛发展、数据共享与公开机制的形成,为定量研究范式创新提供了现实可能。未来,教育定量研究范式应在多种维度上进行变革和创新,推行复制性研究,发展计算教育学,加强教育预测研究。

具NK细胞的溶瘤病毒疗法的模型分析

本文建立了一类包含自然杀伤细胞(NK细胞)免疫反应的肿瘤病毒相互作用模型。首先分析了系统的边界性态,将系统的平衡点进行完整的分类,讨论了边界平衡点的局部稳定性,并从数值上验证了周期解的存在性,最后讨论了NK细胞在病毒治疗中所起到的作用。数值结果表明:a)整体肿瘤大小与病毒感染率成反比,与肿瘤生长速率成正比;b)对于NK细胞相关参数,NK细胞从淋巴结的流入速率越大,最终肿瘤越小;若产生NK细胞增殖,当增殖速率比较小时,相较于无NK增殖时,最终肿瘤变大,即较小的NK细胞增殖对治疗产生负面的影响,但当NK细胞的增殖速率过高时,将会导致肿瘤和病毒的完全清除。

中学历史教育研究2023年度报告——基于2023年《复印报刊资料·中学历史、地理教与学》转载历史教育论文的分析

2023年度《复印报刊资料·中学历史、地理教与学》转载发表的中学历史教育类成果,集中反映了年度研究基本概况:历史课程功能研究具体化、历史教学理论研究实践化、历史教学改革研究综合化、历史教科书及其运用研究融通化、历史学科试题及命制研究素养化、历史课程核心素养研究过程化、历史教育国际比较研究价值化、历史教师职业素养研究需要强化。面对未来挑战,历史教育理论、课程改革、历史学习、教师教育研究需要深化。

猪圆环病毒2型ORF1部分位点突变对病毒复制能力的影响

猪圆环病毒2型(PCV2)可引起断奶仔猪多系统衰竭综合征,导致仔猪逐渐消瘦。PCV2 ORF1表达的Rep蛋白及其剪切体Rep′是PCV2复制所需的重要蛋白。为了研究PCV2 ORF1部分位点对PCV2复制能力的影响,本试验通过构建PCV2 ORF1区域点突变双拷贝感染性克隆质粒,在无PCV2污染的PK-15细胞中进行病毒拯救,使用荧光定量PCR检测不同位点突变病毒培养不同代次上清液的Ct值。结果:将PCV2 Rep的17 aa、19 aa、20 aa和21 aa突变为丙氨酸后病毒无法成功拯救,2 aa突变后严重影响病毒的复制能力,3 aa、5 aa和18 aa突变后病毒的复制能力增强且细胞病毒载量高于PCV2原毒株,推测17 aa、19 aa、20 aa和21 aa是影响PCV2复制的关键作用位点。本研究结果为未来PCV2复制相关研究提供了试验依据。

C8orf4基因编码蛋白对猪流行性腹泻病毒体外复制的抑制效应

C8orf4,也称为甲状腺癌1(thyroid carcinoma 1,TC1),最初是从甲状腺癌及其周围正常甲状腺组织克隆而来,在脊椎动物中普遍表达,具有跨物种的序列保守性。研究表明,C8orf4在肿瘤中高表达,参与各种癌细胞间信息通讯,是一种与癌症和炎症有关的新型调节因子,并通过调节NF-κB的转录增强炎症反应,但对病毒的影响知之甚少。为研究C8orf4编码蛋白对猪流行性腹泻病毒(porcine epidemic diarrhea virus, PEDV)复制的影响,将PEDV接种于Vero细胞,通过qRT-PCR和Western blot检测不同时间点PEDV对C8orf4表达的影响;设计并合成表达C8orf4基因的真核表达载体pcDNA3.1-C8orf44-His和特异性siRNA,通过过表达和抑制C8orf4表达,利用qRT-PCR和Western blot检测C8orf4对PEDV复制的影响;进一步,通过过表达C8orf4编码蛋白,明确C8orf4编码蛋白对PEDV复制周期各阶段的增殖变化。随着PEDV感染时间的增长,细胞中C8orf4表达呈上升趋势;过表达C8orf4显著抑制PEDV复制,而干扰C8orf4表达促进PEDV复制,并且C8orf4编码蛋白主要作用于PEDV复制周期的生物合成阶段。本研究表明C8orf4编码蛋白具有抑制PEDV复制的作用,为C8orf4的功能研究提供参考,为抗PEDV复制机制研究提供基础。

SQL Server CE中RDA与Replication的研究

介绍移动数据库SQL Server CE及其特点,详细分析RDA(远程数据访问)和Replica-tion(合并复制)数据同步技术,探讨两种技术的各自特点和应用环境,描述两种数据同步技术的实现过程,比较这两种技术适合的环境。

猪急性腹泻综合征冠状病毒诱导细胞自噬并增强病毒复制的研究

为研究猪急性腹泻综合征冠状病毒(SADS-CoV)感染细胞是否诱导自噬及自噬对病毒复制的影响,本研究将SADS-CoV(MOI 0.1)接种Vero E6细胞培养36 h后,经透射电子显微镜观察可见,SADS-CoV感染的细胞中出现了包裹胞浆的自噬体样双层膜结构,证实SADS-CoV可以诱导Vero E6细胞发生自噬。构建pEGFP-LC3的真核表达质粒并经双酶切及测序鉴定正确后转染Vero E6细胞,24 h后以SADS-CoV感染,24 h后经激光共聚焦显微镜观察可见,与阴性对照组细胞相比,感染SADS-CoV的细胞出现绿色荧光的点状聚集。进一步将SADS-CoV(MOI 0.1)感染Vero E6细胞不同时间后通过western blot检测自噬相关蛋白LC3-Ⅱ和p62表达水平的变化,结果显示,与阴性对照组相比,SADS-CoV感染组LC3-Ⅱ的表达水平升高,LC3-Ⅱ/GAPDH比值呈上升趋势,而p62蛋白表达水平则显著降低(P<0.05),表明SADS-CoV感染能够诱导Vero E6细胞产生完整的自噬应答。为了探究自噬对病毒复制的影响,本研究分别采用自噬抑制剂3-MA和自噬诱导剂Rapamycin处理Vero E6细胞后以SADS-CoV感染,于感染后不同时间收获细胞,通过western blot和病毒滴度(TCID_(50))测定检测SADS-CoV N蛋白表达水平的变化。结果显示,与仅感染病毒的对照组相比,采用3-MA处理Vero E6细胞后SADS-CoV N蛋白的表达水平及TCID_(50)均显著降低(P<0.05),而采用Rapamycin处理后SADS-CoV N蛋白的表达水平及TCID_(50)则均显著升高(P<0.05)。针对ATG5基因设计3条特异性的ATG5 si RNA(siATG5-1/2/3),将干扰效率较好的siATG5-1转染Vero E6细胞后再以SADS-CoV感染,24 h后检测病毒滴度并利用western blot检测SADS-CoV N蛋白表达水平的变化。结果显示,与未转染siATG5的3组阴性细胞相比,转染细胞中SADS-CoV N蛋白的表达水平及病毒滴度均显著降低(P<0.05)。本研究首次表明SADS-CoV感染可以诱导宿主细胞自噬并促进病毒的复制,该结果为深入研究SADS-CoV感染与其致病机理以及防控该病毒的感染奠定了基础。

细胞糖酵解对猪流行性腹泻病毒复制的影响

为研究猪流行性腹泻病毒(PEDV)感染细胞后,细胞糖酵解的变化及其对PEDV复制的影响,本试验通过实时荧光定量PCR和Western blot检测PEDV感染猪小肠上皮细胞IPEC-J2后36 h糖酵解相关酶己糖激酶2(HK2)的表达水平,然后通过添加糖酵解抑制剂2-脱氧-D-葡萄糖(2-DG)来进一步验证细胞糖酵解对PEDV复制的影响,最后检测了正常浓度葡萄糖(5.5 mmol/L)和高浓度葡萄糖(11.1 mmol/L和22.2 mmol/L)培养条件下PEDV复制情况来探究葡萄糖浓度对PEDV复制的影响。结果表明,PEDV感染显著增加糖酵解限速酶HK2的表达,PEDV感染可增强IPEC-J2细胞的糖酵解,细胞糖酵解水平增强有利于PEDV的复制。在一定范围内提高葡萄糖浓度可促进PEDV复制。研究结果为初步阐明PEDV感染机制以及冠状病毒病的综合防控提供了理论依据。

Rho A-Rock 1信号通路对传染性脾肾坏死病毒感染的调控及作用

【目的】探究传染性脾肾坏死病毒(ISKNV)复制增殖与Rho A-Rock 1通路的关系。【方法】采用实时荧光定量PCR(RT-qPCR)检测ISKNV感染CPB细胞12,24,48,72和96 h后病毒DNA拷贝数的变化;同时采用RT-qPCR和蛋白免疫印迹方法检测病毒感染CPB细胞12,24,48和72 h后Rho A与Rock 1转录及蛋白表达水平的变化;通过Rho A抑制剂(CCG-1423和Rhosin)、Rock 1抑制剂(Thiazovivin和Y-27632)及siRNA抑制Rho A-Rock 1通路,研究Rho A-Rock 1通路抑制对ISKNV复制增殖的影响。【结果】ISKNV感染12~48 h,病毒的DNA拷贝数无显著变化,感染72 h病毒DNA拷贝数显著上升,感染96 h病毒的拷贝数上升变缓,说明ISKNV感染72 h时病毒正处于复制增殖的高峰期。RT-qPCR及蛋白免疫印迹结果表明,ISKNV感染72 h时,Rho A和Rock 1 mRNA转录水平和蛋白水平均显著上调。Rho A抑制剂Rhosin和CCG-1423及Rock 1抑制剂Y-27632和Thiazovivin均可使ISKNV基因组拷贝数和病变的CPB细胞数显著下调;利用siRNA敲降Rho A和Rock 1时,ISKNV的基因组拷贝数也显著下调。【结论】Rho A-Rock 1信号通路可正调控ISKNV的感染,抑制Rho A-Rock 1通路可显著抑制ISKNV复制增殖。

盐霉素体外对猪流行性腹泻病毒的抑制效果

猪流行性腹泻(porcine epidemic diarrhea, PED)是由猪流行性腹泻病毒(porcine epidemic diarrhea virus, PEDV)引起的一种以水样腹泻、呕吐和脱水为主要特征的猪肠道传染病,给全球养猪业造成巨大的经济损失,但目前仍无有效的疫苗和治疗药物。盐霉素(salinomycin, SLM)是一种常用的抗生素,具有不易产生耐药性、排泄迅速、残留量极低的优点。为明确SLM对PEDV的抑制作用,首先通过TCID_(50)(tissue culture infective dose)检测PEDV在Vero细胞上的增殖规律,进一步经CCK-8试验和细胞病变效应(cytopathic effect, CPE)测定SLM的半数细胞毒性浓度(half-cytotoxic concentration, CC_(50))和其对PEDV的半数抑制浓度(median inhibition concentration, IC_(50)),最后建立SLM、PEDV和Vero细胞的作用模型,利用RT-qPCR、免疫印迹(Western blot)和间接免疫荧光(indirect immunofluorescent assay, IFA)技术检测SLM对PEDV复制周期的影响。结果表明PEDV感染Vero细胞后24 h病毒滴度最高(10^(7.7)·0.1 mL^(-1));SLM对Vero细胞的CC_(50)为7.698μmol·L^(-1),对PEDV的IC_(50)为1.617μmol·L^(-1);随着SLM浓度的增加,PEDV滴度、N蛋白和N基因mRNA的表达量逐渐下降;SLM抑制PEDV的复制阶段,对病毒的吸附、入侵和释放阶段无明显影响。该研究结果可以为进一步挖掘PEDV抑制药物提供新思路。

Characterization of the infectivity of an Indonesian Zika virus strain in mammalian cell lines

Objective:To characterize the infection patterns and growth characteristics of the Zika virus(ZIKV)strain JMB-185 from Indonesia in various mammalian cell lines.Methods:ZIKV was grown in human(A549,HEK293,HepG2,Huh7,Jurkat,and THP-1)and non-human mammalian(RAW264.7,Vero,and Vero76)cell lines.Viral replication kinetics were measured using plaque assay,while intra-and extracellular viral RNA concentrations were assessed using RT-PCR.Flow cytometry was used to quantify the infected cells and cell viability was measured using an MTT assay.The ability of ZIKV to infect cell lines was visualized using a fluorescence immunostaining assay.Results:This ZIKV strain preferentially infected the lung,kidney,and liver cell lines A549,HEK293,Huh7,Vero,and Vero76,but not the immune cells Jurkat,RAW264.7,and THP-1.By contrast,the ZIKV showed no sign of infection in HepG2 cells,while maintaining viral titer over 3 days post-infection,with no infection recorded in immunostaining,no increase in viral RNA,and no indication of cell deterioration.Conclusions:The Indonesian ZIKV strain has a similar infection profile as other strains,except for its poor infectivity on HepG2 cells.Information on the growth characteristics of Indonesia ZIKV will help expand our understanding of the biology of ZIKV which will be useful for various applications including antiviral discovery.