CloneIRD:面向代码溯源的克隆代码继承关系判定方法

随着开源软件的广泛使用,代码溯源成为管理软件源代码、降低潜在风险的重要技术手段。基于代码克隆检测的大规模代码溯源分析,从其检测结果中鉴别代码克隆对之间的继承关系,对代码来源追踪、组件依赖关系分析、软件脆弱性分析以及代码缺陷修复等具有重要意义。目前,已有方法在原始代码片段存在微小修改的情况下,会产生许多误判,并且检测克隆对的效率也有待提高。针对上述问题,提出了代码溯源中克隆代码继承关系的判定方法CloneIRD,包括一个基于自研快速分布式克隆检测工具FastDCF的代码溯源分析框架,以及该框架的核心算法——基于代码演化信息的克隆代码继承关系判定算法EIHR。为验证框架和算法的有效性,首先设计并实现了CloneIRD方法,并在Linux内核V4.9和V4.12的开源代码上进行了实验。实验结果表明,CloneIRD方法能够有效判定代码溯源结果中克隆对的继承关系,且基于FastDCF的溯源分析框架能够胜任大规模代码的溯源分析任务。

Selection of Media for Hardwood Cuttings Container Seedling-raising of Triploid Clones of Populus tomentosa

[Objective] The experiment was aimed to select effective and economical media for container seedling of triploid clones of Populus tomentosa that was carried out. [Method] The sandy loam, peat, perlite, vermiculite, riversand, sludge were taken as media of hardwood cutting and survival rate, seedling height were taken as indexes to select media for container seedling of triploid clones of Populus tomentosa. [Result] Different mixedmedia had great influence on survival rates of container seedlings. Taking peat and vermiculite with the proportion of 5∶2 (M10) or peat ,vermiculite with the proportion of 7∶2 (M11) or sandy loam (M1) as media would generate higher cutting survival rate that was higher than 90.0%. There were significant differece in height increments of container seedlings. Taking sandy loam, peat and vermiculite with the proportion of 6∶2∶2(M5)or sandy loam (M1), seedling height of 60-days the seedling was over 37.0 cm. [Conclusion] According to cost analysis of nursery medium, the optimum medium for hardwood cuttings container seedling-raising of triploid clones of Populus tomentosa was sandy loam.

戊地昔布抑制clone 26肿瘤细胞增生及机制

目的探讨戊地昔布对小鼠肠癌clone26细胞的生长抑制作用及机制。方法用噻唑蓝（MTT）法检测戊地昔布对clone26细胞生长的作用。用流氏细胞仪检测clone26细胞凋亡率和细胞周期分布。用Western blot检测clone26细胞caspase-3，PCNA和COX-2的表达．结果①戊地昔布可抑制clone26细胞生长并呈时间和浓度依赖性。②50-400μmol·L^-1戊地昔布可明显提高clone26细胞的凋亡率，从对照的3．1％提高到4．4％～11．0％。给予戊地昔布后，细胞的增殖指数，S期的细胞比例和G2／M期细胞有下降趋势，但只有在400μmol·L^-1戊地昔布组时才有统计学意义。③给予戊地昔布后，细胞PCNA的表达降低，caspase-3的表达升高，COX-2的表达没有变化。结论戊地昔布通过诱导凋亡和细胞周期停滞而抑制clone26细胞生长，小剂量时主要与凋亡有关，大剂量时与诱导凋亡和细胞周期停滞有关、Caspase-3参与戊地昔布诱导的凋亡。

Study on Tissue Culture and Effective Clone Establishment of Hemistepta lyrata Bunge

[Objective] The research aimed to study the rapid propagation technology and establish effective clone of Hemistepta lyrata Bunge. [Method] With tender stem of Hemistepta lyrata Bunge as material, the conditions needed in calluses induction and differentiation, adventitious bud differentiation and radication, test tube seedling cutting and transplantation were studied. [ Result] The results showed that the optimum medium for granulated calluses induction from tender stem was MS ＋ BA 0.3 mg/L ＋2,4-D 1 -1.5 mg/L, for granulated calluses and adventitious bud differentiation was MS ＋ AgNO31.5 mg/L ＋ BA 0.4 mg/L ＋ NAA 0.1 mg/L. 1/2 MS ＋ IAA 0.6 mg/L was suitable for test tube seedling rooting and regeneration, and cinder was used as transplantation and cutting substrate. [ Conclusion]This study will provide the scientific reference for choosing the feasible medium in tissue culture of Hemistepta lyrata Bunge.

Effects of Drought Stress on Osmotic Regulation Substances of Five Catalpa bungei Clones

[Objective] This study aimed to investigate the effects of drought stress on osmotic regulation substances of Catalpa bungei clones. [Method] Potting experimental was carried out with plastic film sealing method, to differentiate the degrees of drought stress based on changes in soil water content and leaf water potential and investigate variations in contents of osmotic regulation substances（free proline,soluble sugar and soluble protein） in leaves of five Catalpa bungei clones under different degrees of drought stresses. [Result] According to changes in soil water content and leaf water potential, the whole process of drought stress was divided into normal level（CK, with soil water content of 97.49% and leaf water potential of-0.54MPa）, light drought（LD with soil water content of 59.96% and leaf water potential of-1.28 MPa）, mediate drought（MD with soil water content of 34.19% and leaf water potential of-2.32 MPa） and severe drought（SD with soil water content of 14.52%and leaf water potential of-2.99 MPa）. The soil water content and leaf water potential of five Catalpa bungei clones reached the highest correlation in exponential fitting, with an average R2of 0.989 3（P0.001）. The free proline content in leaves of five Catalpa bungei clones increased rapidly with the increasing degree of drought stress（P 0.001）. To be specific, free proline contents of Catalpa bungei clones015-1 and 7080 were 34.39 and 33.41 times of the normal level under severe drought conditions, which reached an extremely significant level（P0.001）; the free proline content of Catalpa bungei clone 1-3 rapidly increased to（855.46±227.52） μg/g Fw under light drought conditions. The soluble protein content in leaves showed different variation trends. To be specific, the soluble protein content of Catalpa bungei clone 7080 was the lowest at various drought stages and reached（1.644 ±0.137）mg/g Fw under normal conditions; the soluble protein content of Catalpa bungei clone 1-3 was relatively high under normal conditions and was reduced rapidly under light drought conditions, showing different response patterns. [Conclusion] Osmotic regulation substances in leaves of five Catalpa bungei clones all have certain response to drought stress. Free proline is the most important osmotic regulation substance, followed by soluble protein, while soluble sugar makes no significant contribution. According to changes in content of osmotic regulation substances, Catalpa bungei clone 7080 has relatively high capacity and good drought resistance, while Catalpa bungei clone 1-3 has the rapidest response to drought stress.

Study on Phenological Character in Seedling Period of Introduced Populus deltoids Clones

In order to provide directionally genetically improved breeding materials of poplar by exploring the phenological traits genetic variation level and its develop- ment potential of Populus deltoides and the resource evaluation was carried out; 8 phenological phases in seedling period were observed and analyzed of 60 Populus deltoids clones introduced from America. The results showed that： （1） there was obvious difference in phonological character among clones, especially in leaf-spread- ing peak stage and the end term of leaf-falling stage, with the largest variation co- efficient of 14.97% and the minimum of 3.83% respectively. （2） Leaf-spreading peak stage scattered but the end term of leaf-falling stage concentrated the most. The phonological character in early stage of seedling growth was the main factor influ- encing the length of growing season. （3） By principal component analysis, pheno- logical phases were classified into 3 typical periods, including germination stage, leaf-spreading peak stage and leaf-falling stage. （4） Totaling 60 clones were classi- fied into 4 types by using clustering analysis in phenological time variables of clones.

Comparative Study on Photosynthetic Characteristics of Different Catalpa bungei Clones

[Objective] This study aimed to provide scientific basis for the early selec-tion and breeding of excellent Catalpa bungei clones. [Method] The Li-6400 portable photosynthesis system was used to analyze the photosynthetic characteristics of five Catalpa bungei clones （1-3, 1-4, 004-1, 015-1 and 7080）. [Result] Al five Catalpa bungei clones had similar change trends of light response curves, but their maxi-mum net photosynthetic rates （Pmax） were in the order of 1-3＆gt;7080＆gt;015-1＆gt;004-1＆gt;1-4, showing that clone 1-3 and clone 7080 had strong light environmental adapt-ability with the light saturation points （LSP） of 1 147.97 μmol/m2＆#183;s and 1 196.31μmol/m2＆#183;s, respectively, while clone 1-4 had the narrowest range of adaptation to light. There were differences in the total photosynthetic amount per area among the five clones that clone 1-4 was the best of 433 974.24 μmol/m2, fol owed by clone 1-3 of 401 290.20 μmol/m2. The transpiration rates （Tr） and stomatal conductances （Cond） of the five clones presented the same change trend. And the diurnal varia-tion curves of net photosynthetic rate （Pn） of clone 1-3, 1-4 and 015-1 showed two typical peaks with obvious midday depression, while clone 004-1 and 7080 didn’t. [Concluson] Considering a variety of photosynthetic characteristics of indica-tors, photosynthetic capacity of clone 1-3 was the best among the five Catalpa bungei clones.

Study on Cutting Propagation of Toona ciliata Clones

Cutting propagation rhizogenesis of Toona ciliata clone cutting orchard were studied, and the results were as fol ows： Rooting type included both cal us rooting and cortex rooting. About 17 in 22 of clones were dominated by cortex rooting, accounting for the 77% of clones. There were 5 clones which occurred with both cal us rooting and cortex rooting during rooting process. The rooting efficiency index （REI） showed a positive correlation with the rooting rate. Under natural tem-perature condition, keeping moisture and shading, we found that the highest survival rate occurred in early June, September, and October.

Field test of new poplar clone in Shangdong Province

Poplar is one of the dominant tree species for the establishment of fast growing plantations in Shandong Province. Eighteen poplar clones belonging to Populus aigeiros section were introduced from Italy, Turkey and domestic regions. Populus deltoides cv. 慙ux?I-69/55 (I-69), which was widely used in Shandong Province, China, was taken as control clone (I-69). Following a randomized complete block design, seedling test and controlled afforestation trials were carried out at Juxian County, Caoxian County and Laiyang City. The results showed that the poplar clone (Populus ?euramericana cv. ?02/74?, namely 102/74, performed well both in terms of adaptability and growth rate. The mean height of 13.9 m (H), diameter at breast height of 18.0 cm (DBH) and volume growth of 0.1445 m3 (V) were 2.2 %, 21.6% and 52.9 % higher than those of I-69 (CK), respectively, at the age of 5 years at three experimental sites. Moreover, the clone can be propagated easily and showed high resistance to poplar disease, pest as well as salinity and had longer growing period. Furthermore, wood basic density and fiber length of new poplar clone (102/74) were as same as I-69 (CK). It was concluded that the selected clone (102/74) was ideal for the estab-lishment of fast-growing poplar plantations, especially for the pulpwood plantations in Shandong Province.

Genetic Control of Air-Dried Wood Density, Mechanical Properties and Its Implication for Veneer Timber Breeding of New Triploid Clones in Populus tomentosa Carr

The wood samples of 9 triploid clones of Populus tomentosa Carr. taken from a 9 year old clonal test site were analyzed in order to investigate the genetic variation of wood properties, including air dried wood density and some mechanical properties. The results showed that significant or extremely significant difference in air dried wood density and the mechanical properties existed among the clones, this means these wood properties were under moderate or strong genetic controls and could be improved by genetic manipulations. The radial and vertical variation patterns of air dried wood density were also studied and the results were found to coordinate with other previous research results. The vertical variation patterns of most mechanical properties within the individual tree also conformed to the general wood theories except the modulus of elasticity and cross section hardness. Among the mechanical properties, modulus of elasticity (MOE) and tangent section hardness were under strong genetic control, with the clonal repeatabilities being 0 90 and 0 80, respectively. However, the clonal repeatabilities of other mechanical properties under study were a little lower than above two indexes. Genetic correlation analysis indicated that super clonal selection and breeding for veneer timber could be realized through indirect selection of wood density and form indexes.

Effects of Drought Stress on Contents of Endogenous Hormones in Leaves of Different Clones of Liriodendron chinense×L. tulipifera

[Objective] The aim was to study the effects of drought stress on contents of endogenous hormones in leaves of different clones of Liriodendron chinense×L. tulipifera. Drought-resistant Liriodendron chinense×L. tulipifera clones NE25,NE78 and drought-sensitive Liriodendron chinense×L. tulipifera clones NE04,NE23 were selected as experimental materials to study the content changes of four kinds of endogenous hormones such as abscisic acid （ABA）,indoleacetic acid （IAA）,ribosylzeatin （ZR） and jasmonic acid （JA） in leaves of different clones under drought stress. [Result] Under drought stress,ABA was accumulated I leaves of different clones,however,the content changes in drought-resistant clones were not obvious; IAA content showed a decreasing trend,and the content changes n drought-resistant clones during later period of drought stress was decreased; JA content showed an increasing trend in leaves of drought-sensitive clones,indicating that drought-sensitive clones had to maintain higher contents of JA to resist drought stress. [Conclusion] The result of this study had provided scientific basis for the screening,planting and application of drougt-resistant clones of Liriodendron chinense×L. tulipifera.

神经元限制性沉默因子在NTera2/CloneD1细胞向神经元分化模型中表达的检测

目的:建立NTera2/CloneD1细胞向神经元分化的模型,检测神经元限制性沉默因子(NRSF)经分化培养基诱导后表达的变化。方法:收集正常培养的NTera2/CloneD1细胞及经全反式维甲酸(RA)、阿糖胞苷(AraC)、尿苷分阶段诱导共28 d的细胞,显微镜下观察诱导前后细胞的形态学变化;免疫荧光法检测NTera2/CloneD1细胞诱导前后干性标志Nestin、Sox2和成熟神经元特异性标志NF-200、β-tubulinⅢ的表达情况;应用RT-PCR和免疫荧光法对NRSF进行mRNA和蛋白水平的检测。结果:显微镜下观察到正常培养的NTera2/CloneD1细胞呈克隆样生长,经分化培养基诱导后的NTera2/CloneD1细胞表现出典型的神经元样细胞形态。免疫荧光检测表明,未诱导的NTera2/CloneD1细胞表达神经干细胞的标志Sox2、Nestin,不表达成熟神经元特异性蛋白NF-200、β-tubulinⅢ;而经RA等诱导分化的细胞则不表达Sox2、Nestin,表达NF-200、β-tubulinⅢ。RT-PCR和免疫荧光检测显示,NRSF在诱导分化后的NTera2/CloneD1细胞中的表达量显著降低。结论:建立了NTera2/CloneD1细胞向神经元分化的模型,NRSF在诱导后的NTera2/CloneD1细胞中表达量显著下调,提示NTera2/CloneD1细胞在诱导过程中可能通过下调NRSF,使受到NRSF负性调控的神经元特异性蛋白启动表达并上调,进而实现NTera2/CloneD1细胞向神经元的定向分化。

Effects of Light Stress on Oxygen Evolution and Photochemical Energy Stor age of Hybrid Poplar Clones Determined by Photoacoustic Technique

The oxygen evolution, thermal dissipation, and photochemical energy storage of three hybrid poplar clones, namely the triploid clone B342, the diploid clone B11 [(Populus alba×P. glandulosa)×(P.tomentosa×P.bolleana)], and the triploid clone B346 [(P.tomentosa×P. bolleana)×(P. alba×P.glandulosa)], under light stress were studied using photoacoustics. The oxygen evolution signal and photochemical energy storage varied negatively with the pretreatment_PFD (photon flux density), whereas the thermal signal varied positively with the pretreatment_PFD. Photochemical energy storage was reallocated to PSⅡ more than to PSⅠ, while the photochemical energy storage in PSⅠ was more stable than that in PSⅡ when subjected to light stress. The inhibitors streptomycin (SM), dithiothreitol (DTT) and sodium fluoride (NaF) could all affect the oxygen evolution signal. Clones B11 and B342 were more resistant to light stress than clone B346.

Clone30与Lasota疫苗对雏鸡免疫后HI抗体消长规律的试验

以血凝抑制试验方法,对同日龄雏鸡群,在同样饲养管理条件下,分别以Clone 30,Lasota两种新城疫弱毒疫苗,采用不同免疫途径,比较其免疫后的血清中HI抗体滴度的消长规律。结果表明,两种疫苗免疫后HI抗体消长规律基本相同。

Physical Location of the Rice Pi-5(t), Glh and RTSV Genes by ISH of BAC Clones

Mapping of low or single-copy sequences on plant chromosomes has proven difficult because of very low frequency of signal detection. Rice BAC library is being used widely in rice genome research due to its distinctive advantages over other library systems. In this study, two biotin-labeled rice BAC clones closely linked to a rice blast resistance, green leafhopper resistance and tungro spherical virus resistance gene,Pi-5(t), Glh, RTSV, werein situ hybridized to rice chromosomes. They were located on the long arm and short arm of chromosome 4 with FL value of 40%and 100%respectively. The frequency of signal detection reached 46.8%and 59.2%. The signal location were consistent with the selective marker on rice saturated molecular map. The results demonstrated the advantages to locate BAC clones to chromosomes byin situ hybridization and will facilitate the rice low or single-copy gene location by using the BAC library.

Establishment of cell clones with different metastatic potential from the metastatic hepatocellular carcinoma cell line MHCC97

AIM: To establish clone cells with different metastatic potential for the study of metastasis-related mechanisms. METHODS: Cloning procedure was performed on parental hepatocellular carcinoma (HCC) cell line MHCC97, and biological characteristics of the target clones selected by in vivo screening were studied. RESULTS: Two clones with high (MHCC97-H) and low (MHCC97-L) metastatic potential were isolated from the parent cell line. Compared with MHCC97-L, MHCC97-H had smaller cell size (average cell diameter 43 microm vs 50 microm) and faster in vitro and in vivo growth rate (tumor cell doubling time was 34.2h vs 60.0h). The main ranges of chromosomes were 55-58 in MHCC97-H and 57-62 in MHCC97-L. Boyden chamber in vitro invasion assay demonstrated that the number of penetrating cells through the artificial basement membrane was (37.5 +/- 11.0) cells/field for MHCC97-H vs (17.7 +/- 6.3)/field for MHCC97-L. The proportions of cells in G0-G1 phase, S phase, and G2-M phase for MHCC97-H/MHCC97-L were 0.56/0.65, 0.28/0.25 and 0.16/0.10, respectively, as measured by flow cytometry. The serum AFP levels in nude mice 5wk after orthotopic implantation of tumor tissue were (246 +/- 66) microg.L(-1) for MHCC97-H and (91 +/- 66) microg.L(-1) for MHCC97-L. The pulmonary metastatic rate was 100% (10/10) vs 40% (4/10). CONCLUSION: Two clones of the same genetic background but with different biological behaviors were established, which could be valuable models for investigation on HCC metastasis.

Effect of methamidophos on soil fungi community in microcosms by plate count,DGGE and clone library analysis

Methamidophos was widely used a pesticide in northern China. The potential influences of methamidophos on soil fungal community in black soil were assessed by plate count, 28S rDNA-PCR-DGGE, and clone library analysis. Three methamidophos levels （50, 150, and 250 mg/kg） were tested in soil microcosms. Results from plate count during a 60-d microcosm experiment showed that high concentrations of methamidophos （250 mg/kg） could significantly stimulate fungal populations. DGGE （denaturing gradient gel electrophoresis） fingerprinting patterns showed a significant difference between the responses of culturable and total fungi communities under the stress of methamidophos. Shannon diversity indices calculated from DGGE profiles indicated that culturable fungi in all microcosms with methamidophos treatment increased after 1 week of incubation. However, the diversity indices of total fungi decreased in the first week, as compared to the stimulation of culturable fungi. At the 8th week, however, all the microcosms treated by methamidophos were similar to the control microcosms in community structure as suggested by the Shannon diversity indices for both culturable and total fungi. In contrast, after 1 week the fungal structure of culturable and unculturable both were disturbed to different extent under the stresses of methamidophos by clustering analysis. Clone sequencing analysis indicated the stimulation of pathogenic and unculturable fungal populations by methamidophos treatment, suggetsing potential risks of plant disease outbreak.

Infectivity Analysis of Cloned Genomic DNA of P1 Agent in vitro

The ultrastructure of porcine kidney(PK)-15 cells was examined after lipofectamine-aided transfection of the molecular clone of the P1 agent.PK-15 cells transfected with the tandem dimer of the P1molecular DNA clone had numbers of intracytoplasmic inclusions,and a few cells had intranuclear inclusions.Intracytoplasmic inclusions were round to oval and 0.1-0.3μm in diameter,and intranuclear inclusions,which were more electron dense,were of two general types:the first were round and small(0.1μm approximately)and the second were hexagonal and larger(0.4-0.8μm in diameter).Cells transfected with the tandem dimer of the P1 molecular DNA clone tested positive for P1 DNA at passage 5.This is the first report that the P1 molecular clone has infectivity in vitro and it will provide fundamental materials for further study of the biological characterization of P1.

Qualitative analysis of catechins from green tea GMB-4 clone using HPLC and LC-MS/MS

Objective:To identify the bioactive compounds in catechins isolation and its components from green tea GMB-4 clone.Methods:Green tea GMB-4 clones were extracted with distilled water at 90C.Samples were eluted into the column with 10%ethanol.Subsequently,the column was eluted with95%ethanol and evaporated separately.Green tea extract was identified by thin layer chromatography.Catechins were separated by the stationary phase in column chromatography using polyamide with 10%ethanol eluent and 95%ethanol.The results of isolations were analyzed by high performance liquid chromatographic(HPLC)and LCMS/MS.Analysis of catechins by HPLC was done by external standard.Results:Fraction from 10%ethanol showed that four major peaks at retention time of1.663,2.367,2.950 and 4.890,indicated the presence of four catechins components including catechin,epicatechins,gallocatechin and epigallocatechin.Whereas,fraction from 95%ethanol showed two main peaks at retention time of 5.167 and 9.82,which indicated the presence of epigallocatechin gallate(EGCG)and epicatechin gallate(ECG).EGCG(m/z 459),epigallocatechin(m/z 307),ECG(m/z 443),and epicatechin(m/z 291)were isolated and separated successfully using HPLC and LC-MS/MS.Conclusions:The HPLC and LC-MS/MS methods were successfully tuned for the qualitative analysis of green tea extract with EGCG and ECG.Four major catechins were separated and identified by LC-MS/MS,such as EGCG,epigallocatechin,ECG and epicatechin.The result of HPLC analysis showed that EGCG and ECG were main components from catechins isolation of green tea GMB-4 clone.