Distinguishing Rectal Cancer from Colon Cancer Based on the Support Vector Machine Method and RNA-sequencing Data

Colorectal cancer (CRC) is the third most commonly diagnosed cancer worldwide.Several studies have indicated that rectal cancer is significantly different from colon cancer interms of treatment, prognosis, and metastasis. Recently, the differential mRNA expression of coloncancer and rectal cancer has received a great deal of attention. The current study aimed to identifysignificant differences between colon cancer and rectal cancer based on RNA sequencing (RNA-seq)data via support vector machines (SVM). Here, 393 CRC samples from the The Cancer GenomeAtlas (TCGA) database were investigated, including 298 patients with colon cancer and 95 withrectal cancer. Following the random forest (RF) analysis of the mRNA expression data, 96 genessuch as HOXB13, PR4C, and BCLAFI were identified and utilized to build the SVM classificationmodel with the Leave-One-Out Cross-validation (LOOCV) algorithm. In the training (n= 196)and the validation cohorts (n=197), the accuracy (82. 1 % and 82.2 %, respectively) and the AUC(0.87 and 0.91, respectively) indicated that the established optimal SVM classification modeldistinguished colon cancer from rectal cancer reasonably. However, additional experiments arerequired to validate the predicted gene expression levels and functions.

Cloning of CRABS CLAW Gene from Brassica napus and Construction of Its RNA Interference Expression Vector

CRABS ClAW （CRC） is a member of the YABBYA transcription factor gene family that plays an important role in floral organ development of plants. This study aimed to further investigate the regulatory function of CRC transcription factor in the development of floral organs of rape （Brassica napus L. ）. A 580 bp fragment of CRC gene was cloned by RT-PCR from total RNA of buds of rape cultivar Ningyou No. 10 to construct an inverted repeated expression cassette of CRC gene using intermediate vector pHturieane. Firstly, CRC gene fragment was positively inserted into the 5＇ end of a spliceable intron and negatively inserted into the 3＇ end of the intron. Subsequently, CaMV35S promoter sequence and inverted repeated expression cassette of CRC gene were transferred into pUC18 multiple clone site of binary expression vector pCAMBIAI1390. The constructed interference expression vector was named pA6-CRCi, which was further confirmed by restriction enzyme digestion and sequencing.

Construction of RNAi Expression Vector Targeting Vernalizational Gene FaCONSTANS in Tall Fescue

[ Objective ] This study aimed to construct RNAi expression vector targeting vemalizational gene FaCONSTANS （GenBank accession number： GU214996） in tall rescue. [ Method] A 145 bp long Arabidopsis actin gene intron was inserted into the expression vector to construct an intermediate vector pBI121-M-INT. Two pairs of specific primers with restriction sites were designed to amplify a 351 bp long cDNA conserved sequence fragment of vemalizational gene FaCONSTANS for RT-PCR. After restriction enzyme digestion, the amplified fragment was inserted forwardly and reversely at two sides of the intron of intermediate vector to construct an RNAi expression vector with hairpin structure. [ Result ] Double digestion （HindIII ＋ BamHI） showed that the intron was successfully insert- ed into the vector pBI121. PCR amplification and double digestion indicated that target fragment FaCONSTANS was successfully inserted forwardly and reversely in- to the intermediate vector. [ Conclusion] This study laid foundation for breeding novel flowering-inhibited tall rescue cultivars.

Construction of RNAi Expression Vector against Riboflavin Synthase Gene

[Objective] This study aimed to construct RNAi expression vector against r/boflavin synthase （RS） gene. [Method] By using the primers designed based on RS gone coding sequence that was screened from Arabidopsis cDNA library, the 476 bp cDNA fragment of RS was amplified from pGADTT-RS recombinant plasmid, and then cloned into pUCm-T vector to obtain pUCm-RS. Two RS fragments （476 bp） were obtained through digesting pUCm-RS with restriction enzymes PstI/BamHI and PstI / Xhol, and then respectively connected into vector pBSSK-in to form pBSSK-RS-in-RS, in which the two RS fragments were inverted re- peats. Finally, the transform unit RS-intron-RS, got by digesting vector pBSSK-RS-in-RS with Sac I and Kpn I, was ligated into expression vector pCAMBIA1301 to obtain the RS gene silencing vector. [ Result] The restriction enzyme digestion sequencing analysis proved that the RS gene silencing vector was successfully con- structed. [ Conclusion] This study may provide a basic material for further studies on the bio-function of RS gene and the mechanism of signal transduction induced by HpaGxoo in plant.

A HEVC Video Steganalysis Method Using the Optimality of Motion Vector Prediction

Among steganalysis techniques,detection against MV(motion vector)domain-based video steganography in the HEVC(High Efficiency Video Coding)standard remains a challenging issue.For the purpose of improving the detection performance,this paper proposes a steganalysis method that can perfectly detectMV-based steganography in HEVC.Firstly,we define the local optimality of MVP(Motion Vector Prediction)based on the technology of AMVP(Advanced Motion Vector Prediction).Secondly,we analyze that in HEVC video,message embedding either usingMVP index orMVD(Motion Vector Difference)may destroy the above optimality of MVP.And then,we define the optimal rate of MVP as a steganalysis feature.Finally,we conduct steganalysis detection experiments on two general datasets for three popular steganographymethods and compare the performance with four state-ofthe-art steganalysis methods.The experimental results demonstrate the effectiveness of the proposed feature set.Furthermore,our method stands out for its practical applicability,requiring no model training and exhibiting low computational complexity,making it a viable solution for real-world scenarios.

Construction of Short Hairpin RNA Vector with σNS & σC Genes of Avian Reovirus and Determination of Interference Effect

[ Objective] The aim was to explore novel method for treatment of Avian Reovirus. [ Method] According to the design principle of siRNA target sequences, siRNA templates were designed and synthesized and then cloned into the shRNA expression vector, namely, pSilencer-CMV 4.1 neo. Short hairpin RNA vector C1, C2, C3, which contain σC gene, and shRNA vector NS1, NS2, NS3, which contain aNS gene, were constructed separately. The constructed shRNA vectors and negative control were co-transfected into DF-1 cells with the eukaryotic expression vector pEG- FP-σC and pEGFP-σNS, respectively. [ Result] Observation through fluorescence microscope indicated that the constructed 6 shRNA could inhibit the expression of fusion protein to different degrees. In addition, results of Real-time PCR suggested that C3 and NS1 have the best interference effect to the viral duplication in vitro. [ Conclusionl Construction and selection of specific shRNA expression vectors inhibiting Avian Reovirus are significant for researching effects of σC and oNS proteins in infection and duplication of ARV, providing new idea for ARV antiviral therapy.

Non-coding RNAs in acute ischemic stroke:from brain to periphery

Acute ischemic stroke is a clinical emergency and a condition with high morbidity,mortality,and disability.Accurate predictive,diagnostic,and prognostic biomarkers and effective therapeutic targets for acute ischemic stroke remain undetermined.With innovations in high-throughput gene sequencing analysis,many aberrantly expressed non-coding RNAs(ncRNAs)in the brain and peripheral blood after acute ischemic stroke have been found in clinical samples and experimental models.Differentially expressed ncRNAs in the post-stroke brain were demonstrated to play vital roles in pathological processes,leading to neuroprotection or deterioration,thus ncRNAs can serve as therapeutic targets in acute ischemic stroke.Moreover,distinctly expressed ncRNAs in the peripheral blood can be used as biomarkers for acute ischemic stroke prediction,diagnosis,and prognosis.In particular,ncRNAs in peripheral immune cells were recently shown to be involved in the peripheral and brain immune response after acute ischemic stroke.In this review,we consolidate the latest progress of research into the roles of ncRNAs(microRNAs,long ncRNAs,and circular RNAs)in the pathological processes of acute ischemic stroke–induced brain damage,as well as the potential of these ncRNAs to act as biomarkers for acute ischemic stroke prediction,diagnosis,and prognosis.Findings from this review will provide novel ideas for the clinical application of ncRNAs in acute ischemic stroke.

Whole Perfect Vectors and Fermat’s Last Theorem

A naïve discussion of Fermat’s last theorem conundrum is described. The present theorem’s proof is grounded on the well-known properties of sums of powers of the sine and cosine functions, the Minkowski norm definition, and some vector-specific structures.

MicroRNA-regulated viral vectors for gene therapy

Safe and effective gene therapy approaches require targeted tissue-specific transfer of a therapeutic transgene.Besides traditional approaches, such as transcriptional and transductional targeting, micro RNA-dependent posttranscriptional suppression of transgene expression has been emerging as powerful new technology to increase the specificity of vector-mediated transgene expression. Micro RNAs are small non-coding RNAs and often expressed in a tissue-, lineage-, activation- or differentiation-specific pattern. They typically regulate gene expression by binding to imperfectly complementary sequences in the 3' untranslated region(UTR) of the m RNA. To control exogenous transgene expression, tandem repeats of artificial micro RNA target sites are usually incorporated into the 3' UTR of the transgene expression cassette, leading to subsequent degradation of transgene m RNA in cel s expressing the corresponding micro RNA. This targeting strategy, first shown for lentiviral vectors in antigen presenting cells, has now been used for tissue-specific expression of vector-encoded therapeutic transgenes, to reduce immune response against the transgene, to control virus tropism for oncolytic virotherapy, to increase safety of live attenuated virus vaccines and to identify and select cell subsets for pluripotent stem cell therapies, respectively. This review provides an introduction into the technical mechanism underlying micro RNA-regulation, highlights new developments in this field and gives an overview of applications of micro RNA-regulated viral vectors for cardiac, suicide gene cancer and hematopoietic stem cell therapy, as well as for treatment of neurological and eye diseases.

Construction of a lentiviral vector for RNA interference of human VIM gene and its silencing effect in pancreatic cancer cells

目的将为人的活力基因的 RNA 干扰(RNAi ) 构造 lentiviral 表示向量；并且在胰腺的癌症房间线 Panc-1 估计它的基因 silencing 效果。短发卡 RNA (shRNA ) 定序的三人的活力基因用联机的可得到的一个软件和一对被设计的方法来自文件。在合成以后并且退火，四双 stranded oligonucleotides (dsOligo ) 被克隆进 pGCL-GFP/U6 原生质标志，它被聚合酶链反应(PCR ) 和 DNA 定序分析随后证实。实时 PCR 并且西方弄污被用来在 293T 房间屏蔽有效 pGCL-GFP-shRNA 原生质标志，然后，最有效的被挤进有包装材料 pHelper 的 lentiviral 的 recombinant lentivirus Lv-VIM-shRNA 1.0 并且 pHelper 2.0 在 293T 房间。lentivirus 的 titer 被 hole-by-dilution titer 试金决定。在 Panc-1 房间的 Lv-VIM-shRNA 的 silencing 效果被即时 PCR 验证并且西方弄污。结果有效 Lv-VIM-shRNA 成功地被构造。lentivirus 的 titer 在 2 ×上被决定 10 9 TU/mL。活力 mRNA 和 vimentin 的表情是在感染 Lv-VIM-shRNA 的 Panc-1 房间的 down-regluated。有效 Lv-VIM-shRNA 能在 vitro 在 Panc-1 房间禁止活力基因的表示的结论，它为在发信号的小径调查活力基因的角色提供一个工具在胰腺的癌症和寻找的新治疗学的目标的 tumorigenesis 和前进包含了。

Down-regulation of STAT3 expression by vector-based small interfering RNA inhibits pancreatic cancer growth

AIM:To evaluate the effect of RNA interference (RNAi) mediated silence of signal transduction and activation of transcription (STAT)3 on the growth of human pancreatic cancer cells both in vitro and in vivo.METHODS:STAT3 specific shRNA was used to silence the expression of STAT3 in pancreatic cancer cell line SW1990.The anti-growth effects of RNAi against STAT3 were studied in vitro and in experimental cancer xenografts in nude mice.The potential pathways involved in STAT3 signaling were detected using reverse transcription polymerase chain reaction and western blotting.RESULTS:The expression of the STAT3 was inhibited using RNAi in SW1990 cells.RNAi against STAT3 inhibited cell proliferation,induced cell apoptosis and significantly reduced the levels of CyclinD1 and Bcl-xL when compared with parental and control vector-transfected cells.In vivo experiments showed that RNAi against STAT3 inhibited the tumorigenicity of SW1990 cells and significantly suppressed tumor growth when it was directly injected into tumors.CONCLUSION:STAT3 signaling pathway plays an important role in the progression of pancreatic cancer,and silence of STAT3 gene using RNAi technique may be a novel therapeutic option for treatment of pancreatic cancer.

一种新的基于A-I RNA编辑预测乳腺癌预后模型的建立和验证

目的:开发一种基于腺苷到肌苷的脱氨基(A-to-I RNA编辑,ATIRE)的预后模型用于改善乳腺癌的个体化治疗。方法:首先使用单变量Cox回归分析来获得训练集中与总生存(OS)相关的ATIRE位点,然后进行最小绝对收缩和选择算子(LASSO)回归算法来确定最佳预后ATIRE位点,进行多因素Cox比例风险回归分析建立风险模型,纳入ATIRE风险评分和临床病理学特征变量构建预后列线图,绘制校准曲线并计算一致性指数以评价模型的预测概率与实际的一致性,通过决策曲线分析(DCA)评价该模型的临床收益价值。结果:确定18个预后位点用来构建预后模型,并生成ATIRE风险评分。高风险评分患者的中位生存时间显著缩短,列线图在预测乳腺癌的OS概率方面表现良好。校准曲线表现出优异的一致性,决策曲线显示其具有更高的净收益。结论:分析ATIRE事件在预测乳腺癌生存中的作用,基于AITRE的预后模型可以帮助临床医师更好进行临床决策。

Lentivector-mediated RNAi Efficiently Downregulates Expression of Murine TNF-α Gene in vitro and in vivo

In order to explore the role of TNF-α in Niemann-Pick type C （NPC） disease, lentiviral-delivered RNA interference （RNAi） was used to silence the expression of murine TNF-α gene in vitro and in npc mice. Interference efficiency of the lentivirus expressing TNF-α-siRNA, previously constructed with the concentration of 2 x 108 ifu/mL, was determined by RT-PCR and ELISA in BV-2 cells and astrocytes. At the same time, the constructed Lenti-TNF-α-siRNA was intracerebroventricularly infused into 4-week old npc mice for a 4-week period, and the mice were divided into 3 groups： Lenti-TNF-α-siRNA （n=6）, control lentivirus （n=6）, and NPC mice without any intervention （n=4）. By using immunohistochemistry and real-time PCR, the down-regulation of the target genes was detected. The Lenti-TNF-α-siRNA downregulated the expression of murine TNF-α gene efficiently in vitro and the interference efficiency was 66.7%. Lentivirus could be expressed stably for long-term in the npc mice brain. Immunohistochemistry and real-time PCR revealed that, as compared with non-intervention group and Lenti-control group, Lenti-TNF-α-siRNA efficiently down-regulated the expression of murine TNF-α gene with the interference efficiency being 66.9%. TNF-α-siRNA downregulated the expression of TNF-α gene in vitro and in vivo, which provided a potential tool for studying and treating neurodegenerative diseases and TNF-α-related diseases.

Construction and Identification of a Vector Expressing RNA Interference Aimed at the Human CyclinD1 Gene and its Expression in Vitro

OBJECTIVE To construct a eukaryotic expression vector for RNA interference of the human cyclinD1 gene,and to detect its interference effect in human ovarian cancer cells(HO-8910). METHODS Four target gene segments were synthesized and cloned into the pSUPER vector respectively to construct four recombinant eukaryotic expression vectors,pSUPER-C1~4.The four recombinant vectors were identified by enzyme digestion analysis and DNAsequencing.Then HO-8910 cells were transfected with the pSUPER-C1~4 vectors and subjected to G418 selection.In G418-resistant cells,the interference effect was detected by RT-PCR. RESULTS Enzyme digestion analysis and DNA sequencing showed that the target segments were cloned into the pSUPER vector.The four recombinant vectors inhibited transcription of the cyclinD1 gene.The pSUPER-C2 vector had a better interference effect. CONCLUSION The sequence-specific siRNA effectively interfered with expression of the cyclinD1 gene that was selected.The transcription and expression of the cyclinD1 gene were inhibited effectively by the constructed RNAi eukaryotic expression vectors in the ovarian cancer cel s.These results indicate that it is possible to search for a new tumor gene therapy method.

Using Engineered microRNAs as Vectors for Animal RNA Interference: Promises and Challenges

microRNAs are post-transcriptional regulators of gene expression that recruit RNA silencing complexes to target transcripts to prevent translation and promote their degradation. Experimental studies suggest that microRNA binding to target transcripts can result in as much as a 90% decrease in gene expression. Because of this feature, the microRNA pathway has been utilized as a vehicle for potent RNA interference (RNAi). In recent years, significant advances have been made in engineering artificial microRNA vectors for RNAi in a number of biological systems, with the most progress in plants but also some success in mouse and human cell lines. In this mini-review, we provide a brief discussion of the potential of this technology in comparison with other RNAi strategies, and the current challenges in the design of microRNA-based RNAi vectors, particularly for animal systems.

基于自动化提取HCV RNA荧光定量检测系统的性能验证

目的 基于Stream SP96全自动核酸提取仪、ABI7500实时荧光定量PCR仪对丙型肝炎病毒(HCV)RNA定量检测系统的性能指标进行验证。方法 依据《临床实验室对商品定量试剂盒分析性能的验证》WS/T 420-2013性能验证方案,采用Stream SP96全自动核酸提取平台及ABI7500荧光定量PCR仪检测HCV RNA,对其准确度、精密度、线性区间、检测限、定量限和抗干扰能力等进行方法学性能验证。结果 低、高浓度标准物质的均值与靶值的误差分别为0.20和0.25,均小于靶值对数值±0.4 log;低浓度样本的批内、批间不精密度变异系数值分别为0.79%、1.01%,高浓度样本的批内、批间不精密度变异系数值分别为0.52%、1.22%,均<5%;线性相关系数r>0.980,线性区间可达20~1.0×10^(8),呈良好线性(R^(2)=0.997 3);检出限为20 IU/mL,最低定量限为50 IU/mL;含胆红素(300 mg/L)、血红蛋白(300 g/L)、甘油三酯(3 000 mg/L)的干扰物质对样本检测结果无影响。结论 HCV RNA实时荧光PCR定量法检测系统准确度、精密度、线性范围、检出限、定量限、抗干扰能力均符合厂家声明,能够满足临床对HCV RNA定量检测的需求。

A Novel Vector for Abundant Expression of Antisense RNA, Triplex forming RNA and Ribozyme in vivo

For abundant expression of antisense RNA, triplex forming RNA and Ribozyme in vivo, a novel vector pBSKneo rU6’ was constructed by PCR cloning. This vector contains the intact human snRNA U6 gene expression unit, yet replacing the 61 nt sequence in the middle of U6 snRNA coding region with three restriction enzyme sites. Hela nuclear extract in vitro transcription experiments demonstrated that this vector can effectively express U6 mutant RNA. Containing neo r at the same time, stably transfected pBSKneo rU6’ can be selected easily.

A semantic vector map-based approach for aircraft positioning in GNSS/GPS denied large-scale environment

Accurate positioning is one of the essential requirements for numerous applications of remote sensing data,especially in the event of a noisy or unreliable satellite signal.Toward this end,we present a novel framework for aircraft geo-localization in a large range that only requires a downward-facing monocular camera,an altimeter,a compass,and an open-source Vector Map(VMAP).The algorithm combines the matching and particle filter methods.Shape vector and correlation between two building contour vectors are defined,and a coarse-to-fine building vector matching(CFBVM)method is proposed in the matching stage,for which the original matching results are described by the Gaussian mixture model(GMM).Subsequently,an improved resampling strategy is designed to reduce computing expenses with a huge number of initial particles,and a credibility indicator is designed to avoid location mistakes in the particle filter stage.An experimental evaluation of the approach based on flight data is provided.On a flight at a height of 0.2 km over a flight distance of 2 km,the aircraft is geo-localized in a reference map of 11,025 km~2using 0.09 km~2aerial images without any prior information.The absolute localization error is less than 10 m.

Lentivirual vector-mediated doxycycline-inducible iASPP gene targeted RNA interference in hepatocellular carcinoma

Background and Objective:iASPP, an inhibitory member of the apoptosis-stimulating proteins of p53 (ASPP) family, has been found to be up-regulated in various human tumor types.This study was to construct an efficient doxycycline-regulated, lentiviral vector-mediated knockdown system for iASPP that will allow for inducible down-regulation of iASPP gene expression and preliminary functional analysis.Methods:A pair of complementary oligos with hairpin structures targeting the iASPP gene and a negative control were synthesized, then ligated with pLVTHM vector and sequenced.The fragment containing the shRNA cassette was cloned to pLVCT-tTR-KRAB plasmid.The recombinant vectors were co-transfected with viral packaging mix into 293T cells, and viral supernatant was harvested to determine the titer.After treatment with or without doxycycline, HepG2 cells infected with virus were harvested and the expression of iASPP was detected by reverse transcription-polymerase chain reaction (RT-PCR) and Western blot analysis.Its effects on tumor growth were characterized using MTS assay, soft agar colony formation, and flow cytometry analysis.Results:The lentiviral vector expressing shRNA that targets to the oncogene iASPP was constructed successfully.HepG2 infected with the lentivirus expressing shRNA against iASPP inhibited the expression of iASPP in the presence of doxycycline, which resulted in the repression of tumor cell proliferation and anchorage-independent growth potential.Conclusions:The lentiviral vector-mediated tet-on system demonstrates efficient and inducible knockdown of iASPP in hepatocellular carcinoma cells.iASPP gene may be involved in tumorigenesis and progression of human tumors.

New challenges in hepatocellular carcinoma:A role for PIWIinteracting RNAs?

Hepatocellular carcinoma(HCC)is the most common and deadliest subtype of liver cancer worldwide and,therefore,poses an enormous threat to global health.Understanding the molecular mechanisms underlying the development and progression of HCC is central to improving our clinical approaches.PIWIinteracting RNAs(piRNAs)are a class of small non-coding RNAs that bind to PIWI family proteins to regulate gene expression at transcriptional and posttranscriptional levels.A growing body of work shows that the dysregulation of piRNAs plays a crucial role in the progression of various human cancers.In this editorial,we report on the current knowledge of HCC-associated piRNAs and their potential clinical utility.Based on the editorial by Papadopoulos and Trifylli,on the role and clinical evaluation of exosomal circular RNAs in HCC,we highlight this other emerging class of non-coding RNAs.