一种可变长子片段对拼接的DNA双序列局部比对算法

提出一种基于可变长子片段对拼接的DNA双序列局部比对算法。该算法以最长的子片段对为中心,拼接相邻的相容子片段对来得到最优局部比对,并允许用户输入比对调控因子适当调整比对结果以提高算法的灵活性。实验结果表明算法在时间和空间复杂性方面都得到了较大的改善。

一种基于聚类的视频子片段分割方法

视频的子片段检测和分割是视频分析的一个重要步骤,提取视频中的关键信息能大大减少视频索引的数据量。基于此,简要介绍了传统的特征聚类技术,在聚类算法的基础上,提出一种聚类评估的方法,通过数值表示聚类的匹配程度,并对结果进行优化得到最佳聚类中心个数,保证了视频子片段检测的精度。实验证明该方法可较好地分割视频子片段。

融合时序特征和关键帧的视频检索方法

针对已有视频检索方法存在的诸多问题,提出了一种融合视频时序特征和关键帧的视频检索方法。该方法首先提取视频的时序特征,通过匹配两段视频的时序特征可直接实现画面变化率高的视频(如广告等)的检索,大大减小了视频检索的运算量。在此基础上,对于画面内容变化率较低的视频(如电视剧等),进一步将其划分为若干个子片段,每个子片段中提取出关键帧用于检索。实验结果表明,该方法检索效果好,稳健性高,应用范围广。

大数据视频图像关键帧的检索模型优化仿真

传统的检索方法在建模时,主要通过视频图像特征提取视频图像的关键帧,忽略了视频图像采集过程中受到光照等因素的影响,使得图像特征发生变化情况,导致建模误差大的问题。提出基于视频元数据信息的大数据视频图像关键帧的检索建模方法。先对采集的样例大数据视频进行图像划分,获取图像子区域的灰度均值,将编号相同的子区域直接进行连接,组成大数据图像视频的关键帧时序特征曲线,通过异常因子去除视频图像中的突变干扰,在引入视频元数据信息算法计算视频图像关键帧元数据,并进行视频元数据信息对比,建立大数据视频图像关键帧的检索模型。仿真结果表明,采用改进算法检索效果好,误差低。

一种支持不同时间尺度的视频相似性匹配算法

针对不同时间尺度视频间的匹配问题,如人为再编辑(快进、慢放等)视频与原始视频间的匹配以及不同帧率视频间的检索等,提出了一种基于动态时间规划的最优匹配算法。在子片段的基础上进行视频相似性匹配,通过极小化两段视频的整体距离建立视频之间的子片段对应关系,引入搜索门限值,将全局搜索转变为在门限区域内的局部搜索,保持视频内部各子片段之间的时序关系并能处理非线性偏移。该算法能够成功地匹配不同时间尺度的相似视频,并能实现海量视频的快速检索。实验结果证明了该算法比传统的基于视觉相似性的视频片段检索算法更快速有效。

一种基于RFT和分段处理的高速机动目标相参积累算法

高速机动目标会在短时间内跨越距离单元(Range Migration,RM),并且由于目标机动性产生跨多普勒单元(Doppler Spread,DS)等问题。基于搜索的传统处理算法通过时间和计算量换取积累性能,不利于工程应用。本文提出一种通过分段处理方式对回波进行相参积累的算法。该算法在保证子片段内回波RM和DS问题可以忽略的前提下,将积累时间划分为若干个子片段。在该分段准则下通过Radon-Fourier Transform(RFT)对子片段进行处理。随后,根据各子片段RFT积累峰值位置分布特性和相位差异,设计一种子片段间的相参积累方案,实现多个子片段间峰值能量的相参积累。所提算法在子片段内可以忽略目标机动性的影响,避免了子片段内目标机动参数(加速度项)的搜索,可在积累性能和计算效率之间取得良好平衡。

Discussion on AFLP Molecular Markers in Piper methysticum and Pepper

The aim of the research was to discuss the genetic relationships between Piper methysticum, Pepper and other wild species in Pepper genus. DNA was extracted from leaves which belonged to 28 germplasms including 6 materials of P. methysticum, 21 maerials of cultivated and wild Pepper, 1 material of Peperomia pellucida belonged to different genus. Premiers with good band-type and high polymorphism and resolution were selected from 64 pairs of primers for AFLP amplification and the clustering analysis was conducted with MVSP3.13f software. 191 bands were amplified by 4 pairs of premiers, 189 of which had polymorphism, being 98.6%. 28 germplasms were classified into 6 different groups at the genetic similarity coefficient of 0.52 by silver staining AFLP, in which 6 materials of Piper methysticum were clustered into a single group, indicating that P. methysticum belonged to Pepper family of Pepper genus but were distantly related to the others. The research provided the basis for selecting rootstocks for P. methysticum graft, molecular identification of P. methysticum and the fingerprint construction of P. methysticum.

Effects of Fragmentation Intensity of Perennial Roots and Their Burial Depth on Sprouting and Early Growth of Alternanthera philoxeroides(Mart.)Griseb

[Objective] The aim was to provide theoretical basis for the prevention and control of the invasion of Alternanthera philoxeroides（Mart.）Griseb.[Method] Effects of fragmentation intensity of fresh roots and their burial depth on sprouting and early growth of A.philoxeroides were studied by control test.[Result] More sprouts of A.philoxeroides emerged when the fragmentation intensity of fresh roots was higher,while if the fragmentation intensity of fresh roots was lower,the early growth of A.philoxeroides was more rapid.The soil buried depth had significant effect on fresh root sprouts＇ emergence,but once fresh root sprouts could reach the soil surface and were given enough growth time,even if the fresh roots were buried in different depths,soil buried depth had no significant effect on its young plant growth.[Conclusion] If different fragmentation intensities of fresh roots present,there is a kind of trade-off strategy between root sprouts＇ emergence and plant＇ early growth,by which A.philoxeroides can invade new habitat successfully.To control the invasion of A.philoxeroides,it is critical to prevent its fresh root sprouts from emerging to soil surface,that is,to bury the fresh roots at a further soil depth.

Preliminary Analysis of Population Genetic Diversity of Cultivated Laminaria japonica Sporophyte via AFLP Technique

The amplified fragment length polymorphic DNA (AFLP) technique was adopted to estimate the population genetic polymorphism among 30 sporophytes of Laminaria japonica collected from a cultivating farm in Rongcheng,China.Three methods were used for genomic DNA extraction from Laminaria japonica sporophyte and only the products obtained using the improved genomic DNA extraction kit method proved qualified for AFLP analysis.The parameters of the method were optimized.Samples of forty milligrams and the cell lysis time of 120 min were suggested to replace the parameters recommended by the manufacturer.Thirty individuals of Laminaria japonica from the same cultivating site were investigated using one pair of selective primers.A total of 21 loci were obtained and 17 of them were polymorphic.The mean percent age of polymorphic loci of this population was 80.95%.The Nei's gene diversity (H) within this population was 0.3028 and the average Shannon's Information index (I) was 0.4498.A genetic distance matrix among different individuals was constructed as well.Through this study,an applicable AFLP genetic analysis working system for Laminaria japonica sporophyte was established.The results of this research also revealed a high level of genetic diversity within the studied population.

Investigation of oil-air two-phase mass flow rate measurement using Venturi and void fraction sensor

Oil-air two-phase flow measurement was investigated with a Venturi and void fraction meters in this work. This paper proposes a new flow rate measurement correlation in which the effect of the velocity ratio between gas and liquid was considered. With the pressure drop across the Venturi and the void fraction that was measured by electrical capacitance tomography apparatus, both mixture flow rate and oil flow rate could be obtained by the correlation. Experiments included bubble-, slug-, wave and annular flow with the void fraction ranging from 15% to 83%, the oil flow rate ranging from 0.97 kg/s to 1.78 kg/s, the gas flow rate ranging up to 0.018 kg/s and quality ranging nearly up to 2.0%. The root-mean-square errors of mixture mass flow rate and that of oil mass flow rate were less than 5%. Furthermore, coefficients of the correlation were modified based on flow regimes, with the results showing reduced root-mean-square errors.

Development of a SCAR marker for male gametophyte of Gracilariopsis lemaneiformis based on AFLP technique

The red alga Gracilariopsis lemaneiformis(Bory) is an economically valuable macroalgae. As a means to identify the sex of immature Gracilariopsis lemaneiformis, the amplifi ed fragment length polymorphism(AFLP) technique was used to search for possible sex- or phase-related markers in male gametophytes, female gametophytes, and tetrasporophytes, respectively. Seven AFLP selective amplifi cation primers were used in this study. The primer combination E-TG/M-CCA detected a specifi c band linked to male gametophytes. The DNA fragment was recovered and a 402-bp fragment was sequenced. However, no DNA sequence match was found in public databases. Sequence characterized amplifi ed region(SCAR) primers were designed from the sequence to test the repeatability of the relationship to the sex, using 69 male gametophytes, 139 female gametophytes, and 47 tetrasporophytes. The test results demonstrate a good linkage and repeatability of the SCAR marker to sex. The SCAR primers developed in this study could reduce the time required for sex identifi cation of Gracilariopsis lemaneiformis by four to six months. This can reduce both the time investment and number of specimens required in breeding experiments.

TNF-α induces apoptosis of Molt-4 cells and cell cycle specificity of Bcl-2 phosphorylation

Objective： The aim of the study was to observe the expression of Bcl-2 and its phosphorylation in Molt-4 cells induced by tumor necrosis factor-α （TNF-α）, and to investigate the possible mechanism of cell cycle specificity of apoptosis. Methods： Exponentially growing Molt-4 cells were treated with TNF-α. Apoptosis was detected by DNA fragmentation assay. API method was applied to illustrate the cell cycle specificity of apoptotic cells. Cells of sub-phases were sorted by FACSvan- tage flow cytometer and then submitted to immunoblot. Results： Molt-4 cells which were treated with TNF-α went to apoptosis and showed a DNA ladder pattern. Most apoptosis happened in Gl-phase of cell cycle. Bcl-2 expression increased for the Molt-4 cells treated with TNF-α. The phosphorylation state of Bcl-2 was only presented in Gl-phase cells, in accordance with the specified time and cell cycle phase of apoptosis. Conclusion： The phosphorylation of Bcl-2 in the Molt-4 cells treated with TNF-α happened with the same cell cycle specificity as cell apoptosis. The cell cycle specificity of Bcl-2 phosphorylation was one of the mechanisms of receptor-mediated apoptosis. The cell cycle machine can trigger the apoptosis program.

Molecular characterization of a novel reovirus isolated from SARS patients with distinct S1 segment

We reported a novel mammalian reovirus, designed BYD1, isolated from throat swabs of patients with severe acute respiratory syndrome （SARS）, in 2003. In the present study, we firstly compared the genome electrophoretic migration patterns of reovirus BYD1 with 3 prototype reovirus strains by polyacrylamide gel electrophoresis （PAGE） and determined the complete nucleotide sequence of the S1 gene segment of BYD1 by single primer amplification technique. The electropherogram of BYD1 was different from those of the 3 prototype strains and any other reovirus isolates reported before. The entire S1 segment sequence of BYD1 is 1437 bp long with two meaningful open reading frames （ORFs）. The longest ORF encodes σ1, the cell attachment protein, and the second longest ORF supposedly encodes σ1s, an important nonstructural virulence factor. The terminal sequences of SI segment are 5＇GCUA and 3＇UCAUC, which are consistent with those of other mammalian reoviruses. The highest homology of deduced σ1 amino acid sequence is 64% identity with known mammalian reoviruses. Phylogenetic analysis of both S1 nucleotide sequence and σ1 amino acid sequence indicated the BYD1 isolate belonged to a new clade of serotype 2 group. The results of this study showed that the BYD1 S1 segment was markedly different from those of isolates reported before and BYD1 was a novel human reovirus isolate.

Association between EGF +61A/G polymorphism and gastric cancer in Caucasians

AIM: To investigate the association between epidermal growth factor (EGF) +61A/G polymorphism and susceptibility to gastric cancer, through a cross-sectional study. METHODS: Polymerase chain reaction resctriction fragment lenght polymorphism analyses were used to genotype EGF +61 in 207 patients with gastric lesions (162 patients with gastric adenocarcinomas, 45 with atrophy or intestinal metaplasia) and 984 controls. All subjects were Caucasian. RESULTS: Genotype distribution was 23.5% for GG and 76.5% for GA/AA in the control group, 18.4% for GG and 68.6% for GA/AA in the entire group with gastric lesions and 17.9% for GG and 82.1% for GA/AA in the group with gastric adenocarcinoma. No statistically significant associations were found between EGF +61 variants and risk for developing gastric cancer [odds ratios (OR) = 1.41, 95% confidence intervals (CI): 0.90-2.21, P = 0.116]. However, the stratification of individuals by gender revealed that males carrying A alleles (EGF +61A/G or AA) had an increased risk for developing gastric cancer as compared to GG homozygous males (OR = 1.55, 95% CI: 1.05-2.28, P = 0.021). CONCLUSION: In summary, we found that males who were A carriers for EGF +61 had an increased risk for developing gastric cancer. This result may be explained by the suggestion that women secrete less gastric acid than men.

Association of Fas/Apo1 gene promoter (-670 A/G) polymorphism in Tunisian patients with IBD

AIM： To detect a possible association between the polymorphism of the （-670 A/G） Fas/Apol gene promoter and susceptibility to Crohn＇s disease （CD） and ulcerative colitis （UC） in the Tunisian population. METHODS： The （-670 A/G） Fas polymorphism was analyzed in 105 patients with CD, 59 patients with UC, and 100 controls using the polymerase chain reaction restriction fragment length polymorphism method. RESULTS： Significantly lower frequencies of the Fas -670 A allele and A/A homozygous individuals were observed in CD and UC patients when compared with controls. Analysis of （-670 A/G） Fas polymorphism with respect to sex in CD and UC showed a significant difference in A/A genotypes between female patients and controls （P corrected = 0.004 ＂in CD patients＂ and P corrected = 0.02 ＂in UC patients＂, respectively）. Analysis also showed a statistically significant association between genotype AA of the （-670 A/G） polymorphism and the ileum localization of the lesions （P corrected = 0.048） and between genotype GG and the colon localization （P corrected = 0.009）. The analysis of IBD patients according to clinical behavior revealed no difference. CONCLUSION： Fas-670 polymorphism was associated with the development of CD and UC in the Tunisian population.

Polymorphisms in the Myostatin-1 gene and their association with growth traits in Ancherythroculter nigrocauda

Myostatin （MSTN） is a member of the transforming growth factor-β gene superfamily that negatively regulates skeletal muscle development and growth. In the present study, partial genomic fragments of Myostatin-1 （MSTN-1） in two commercial hatchery populations of Ancherythroculter nigrocauda, an economically important freshwater fish, were screened for single nucleotide polymorphisms （SNPs） and then genotyped by direct sequencing of PCR products. Five SNPs were identified in intron 1 and exon 2, including a non-synonymous mutation causing an amino acid change （Val to Ile） at position 180. Association analyses based on 300 individuals revealed that the g. 1129T〉C SNP locus was significantly associated with total length （TL）, body length （BL）, body height （BH） and body weight （BW） in 6- and 18-month-old populations, while the g. 1289G〉A locus was significantly associated with BH and BW in the 6-month-old population. Haplotype analyses revealed that fish with the genotype combinations TC/TC or TC/GA showed better growth performance. Our results suggest that g.l129T〉C and g.1289G〉A have positive effects on growth traits and may be candidate gene markers for marker-assisted selection in A. nigrocauda.

Specific killing effect of diphtheria toxin A fragment under control of DF3 promotor on human breast cancer cells

Objective: To study the effects of recombinant expression vector containing human breast cancer DF3 promotor and diphtheria toxin A fragment on human breast cancer cells. Methods: Constructing recombinant expression vector PGL3-DF3-DTA and transfecting it into human breast cancer cells of DF3 positive and negative. By means of RT-PCR to measure the expression of DTA in human breast cancer cells. MTT color-imetry was used to examine the effect of PGL3-DF3-DTA on growth of human breast cancer cells. By experiment on nude mice to observe the killing effect of PGL3-DF3-DTA on human breast cancer cells. Results: Recombinant expression vector PGL3-DF3-DTA was highly expressed in human breast cancer cell line of DF3 positive, and it could kill the human breast cancer cells not only in vitro but also in vivo. Conclusion: Recombinant expression vector PGL3-DF3-DTA could produce specific killing effect on human breast cancer cell line of DF3 positive.

Lack of correlation between p53 codon 72 polymorphism and anal cancer risk

AIM:To investigate the potential role of p53 codon 72 polymorphism as a risk factor for development of anal cancer. METHODS:Thirty-two patients with invasive anal carcinoma and 103 healthy blood donors were included in the study.p53 codon 72 polymorphism was analyzed in blood samples through polymerase chain reaction-restriction fragment length polymorphism and DNA sequencing. RESULTS:The relative frequency of each allele was 0.60 for Arg and 0.40 for Pro in patients with anal cancer, and 0.61 for Arg and 0.39 for Pro in normal controls. No significant differences in distribution of the codon 72 genotypes between patients and controls were found. CONCLUSION:These results do not support a role for the p53 codon 72 polymorphism in anal carcinogenesis.

Exploring genetic diversity in Northeastern Sika deer population （Cervus nippon hortulorum） by AFLP molecular markers

The genetic diversity of 27 different Cervus nippon hortulorum was studied to provide theoretical evidence for their identification and utilization. The genomie DNA of 27 different Cereus nippon hortulorum were analyzed by amplified fragment length polymorphism （AFLP）. 11,443 bands associated with genetic polymorphism among total 15,169 bands were obtained with 9 kinds of primer pairs and restriction endonuclease EcoRI/Msel, percentage of polymorphie band was 78.43%, 1,271 polymorphic locus were shown per primer pair. The AFLP data showed that average genetic similarity was 0.7841 （0.6809-0.8648）. 27 samples were classified into Group I and Group II with cluster analysis, and Group II was divided into five subgroups. The result of AFLP and cluster analysis concluded that there was high genetic variation, which associated with orientated artificial breed selection and breeding in the population. Genetic similarity of Group II-4 was the highest, more than 0.82, while genetic distance in this group was the shortest, from 0.1354 to 0.1563, which was coordinated with breeding record. All these showed that there was great genetic polymorphism among the deer population. The results laid the foundation for main quantitative trait locus （QTLs） of Cervus nippon hortulorum.