A hybrid class- and prototype-based object model to support language-neutral structural intercession

ContextDynamic languages have turned out to be suitable for developing specific applications where runtime adaptability is an important issue. Although .Net and Java platforms have gradually incorporated features to improve their support of dynamic languages, they do not provide intercession for every object or class. This limitation is mainly caused by the rigid class-based object model these platforms implement, in contrast to the flexible prototype-based model used by most dynamic languages.ObjectiveOur approach is to provide intercession for any object or class by defining a hybrid class- and prototype-based object model that efficiently incorporates structural intercession into the object model implemented by the widespread .Net and Java platforms.MethodIn a previous work, we developed and evaluated an extension of a shared-source implementation of the .Net platform. In this work, we define the formal semantics of the proposed reflective model, and modify the existing implementation to include the hybrid model. Finally, we assess its runtime performance and memory consumption, comparing it to existing approaches.ResultsOur platform shows a competitive runtime performance compared to 9 widespread systems. On average, it performs 73% and 61% better than the second fastest system for short- and long-running applications, respectively. Besides, it is the JIT-compiler approach that consumes less average memory. The proposed approach of including a hybrid object-model into the virtual machine involves a 444% performance improvement (and 65% less memory consumption) compared to the existing alternative of creating an extra software layer (the DLR). When none of the new features are used, our platform requires 12% more execution time and 13% more memory than the original .Net implementation.ConclusionOur proposed hybrid class- and prototype-based object model supports structural intercession for any object or class. It can be included in existing JIT-compiler class-based platforms to support common dynamic languages, providing competitive runtime performance and low memory consumption.     

Screening new gene markers for gluten detection in foods

In the present work, three DNA sequences encoding wheat proteins (α2-gliadin, agglutinin isolectin and thioredoxin h) were compared to trace gluten-containing cereals in food products. Quantitative real-time PCR methods using hydrolysis probes were successfully developed to target the three sequences for the detection of wheat DNA. The comparison of the three systems highlights the best sensitivity when tracing the α2-gliadin marker sequence, showing an absolute limit of detection (LOD) of 2 pg of wheat DNA and a relative LOD of 0.005% (50 mg/kg) of wheat in soybean, which corresponds to 4.5 mg/kg of gluten. All the systems reveal high specificity for detecting other gluten-containing cereals, such as barley and rye. Therefore, the developed real-time PCR systems can be used as non-immunological tools to confirm the presence of gluten-containing cereals in foods, towards the safety of celiac patients and wheat allergic individuals.     

化妆品中动物源性成分多重实时荧光PCR检测方法的研究

使用优化的Chelex-100结合玻璃奶法提取膏状、液态和固态化妆品中的动物源性DNA;根据驴、马和牛线粒体16S rRNA基因序列设计通用引物和特异性探针,建立了一次性检测化妆品中驴、马和牛3种动物源性成分的多重实时荧光PCR体系,检出限均为0.001 ng。并对市售的面霜、洗面奶和面膜进行盲样检测,验证了体系的可靠性和准确性。     

一种特异性检测单增李斯特菌的质粒DNA标准物质

研制了一种质粒DNA标准物质,包含目前单增李斯特菌检测常用的靶基因序列——内化素基因(Inl A)序列,可适用于扩增Inl A基因的单增李斯特菌PCR相关检测方法。采用紫外分光光度法(UV)和高分辨电感耦合等离子体质谱(HR-ICP-MS)两种方法,多家实验室联合定值的方法,对该套标准物质的均匀性、稳定性、量值以及不确定度进行详细的考察,质粒DNA标准物质的最终定值结果为94.9(±5.1)ng/μL。该质粒DNA标准物质可用于微生物实验室对单增李斯特菌PCR相关检测进行检测结果质量控制、开展方法比对和能力验证等。     

Apple Allergy: The cDNA Sequence of the Major Allergen of Apple,Determined by Performing PCR with a Primer Based on the N-Terminal Amino Acid Sequence,is Highly Homologous to the Sequence of the Major Birch Pollen Allergen

Considering the known N-terminal amino acid sequence of the major apple allergen, a polymerase chain reaction (PCR) primer was selected to amplify cDNA encoding this protein. A single PCR product was obtained, cloned into Escherichia coli and subsequently sequenced. The missing 5′-end of the apple cDNA sequence was obtained by a 5′-RACE method. The cDNA sequence showed 72% identity with the coding region of one of the known isoforms of Bet v 1, the major allergen of birch pollen. The deduced amino acid sequence resulted in a 158-residue protein with a calculated molecular mass of 17·5 kDa and 63% amino acid sequence identity to Bet v 1. In addition, further protein alignments showed a high degree of identity with allergens from other tree pollens and some ‘pathogenesis-related proteins’ from food plants. According to international regulations the allergen was termed Mal d 1 for this protein, it being the first major allergen discovered and characterised in fruits of apple (Malus domestica).     

核酸固相分离方法及其在病原PCR诊断中的应用综述

病原PCR(Polymerase Chain Reaction)诊断具有快速、灵敏、高修改灵活性等优势,在传染病控制、农业病害防治和食品安全等领域发挥着重要作用.核酸分离作为分子诊断技术的关键步骤,影响着PCR诊断的整体效率、检测灵敏度和准确性,是PCR诊断局限于实验室使用的关键制约因素之一.核酸固相分离可以避免传统液...     

不同年份对虾白斑综合征病毒基因组差异的微阵列分析

根据对虾白斑综合征病毒(white spot syndrome virus,WSSV)全基因组序列的分析与应用,设计了190对引物,覆盖全基因组绝大多数可预测的开放读框(ORF).扩增相应基因片段,在尼龙膜上点样,制备成为DNA微阵列.收集了1996年和2002年感染阳性对虾,分别提取纯病毒基因组DNA,用地高辛标记后与DNA微阵列杂交.与1996年病毒株相比较,2002年病毒株缺失了wsv479、wsv482、wsv489和wsv493.运用PCR技术验证了DNA微阵列杂交结果的可靠性.     

Comparison of Automated Ribotyping,spa Typing,and MLST in 108 Clinical Isolates of Staphylococcus aureus from Orthopedic Infections

108 isolates of Staphylococcus aureus, belonging to six large ribogroups according to the automated Ribo-Printer^® system, were studied with two highly used molecular methods for epidemiological studies, namely multi-locus sequence typing (MLST) and spa typing, followed by BURP and eBURST v3 analysis for clustering spa types and sequence (ST) types. The aim was to evaluate whether automated ribotyping could be considered a useful screening tool for identifying S. aureus genetic lineages with respect to spa typing and MLST. Clarifying the relationship of riboprinting with these typing methods and establishing whether ribogroups fit single clonal complexes were two main objectives. Further information on the genetic profile of the isolates was obtained from agr typing and the search for the mecA, tst genes, and the IS256 insertion sequence. Automated ribotyping has been shown to predict spa clonal complexes and MLST clonal complexes. The high cost and lower discriminatory power of automated ribotyping compared to spa and MSLT typing could be an obstacle to fine genotyping analyzes, especially when high discriminatory power is required. On the other hand, numerous advantages such as automation, ease and speed of execution, stability, typeability and reproducibility make ribotyping a reliable method to be juxtaposed to gold standard methods.     

丙型肝炎病毒RNA室内质控品的制备及其临床应用评估

目的探讨自制丙型肝炎病毒(hepatitis C Virus,HCV)RNA定量检测室内质控品的可行性,并评估其临床应用价值。方法收集已发过HCV-RNA临床报告的血浆样本,分别将HCV-RNA阴性血浆(<50 IU/mL)、弱阳性血浆(102~103 IU/mL)和强阳性血浆(105~106 IU/mL)混合、离心后,获得阴性质控品(HCV-RNA-N)、弱阳性质控品(HCV-RNA-L)和强阳性质控品(HCV-RNA-H),小量分装后于-80℃冻存。确定靶值后,评价其均一性、重复性、准确性和稳定性。结果自制HCV RNA室内质控品具有良好的均一性、重复性和准确性,可在-80℃保持稳定至少12个月。结论HCV RNA室内质控品制备过程简单,样品均一,重复性好,准确性高,稳定性良好,可用于临床检测HCV-RNA。     

Narrow Genetic Diversity of Wolbachia Symbionts in Acrididae Grasshopper Hosts (Insecta,Orthoptera)

Bacteria of the Wolbachia genus are maternally inherited symbionts of Nematoda and numerous Arthropoda hosts. There are approximately 20 lineages of Wolbachia, which are called supergroups, and they are designated alphabetically. Wolbachia strains of the supergroups A and B are predominant in arthropods, especially in insects, and supergroup F seems to rank third. Host taxa have been studied very unevenly for Wolbachia symbionts, and here, we turn to one of largely unexplored insect families: Acrididae. On the basis of five genes subject to multilocus sequence typing, we investigated the incidence and genetic diversity of Wolbachia in 41 species belonging three subfamilies (Gomphocerinae, Oedipodinae, and Podisminae) collected in Turkey, Kazakhstan, Tajikistan, Russia, and Japan, making 501 specimens in total. Our results revealed a high incidence and very narrow genetic diversity of Wolbachia. Although only the strains belonging to supergroups A and B are commonly present in present, the Acrididae hosts here proved to be infected with supergroups B and F without A-supergroup variants. The only trace of an A-supergroup lineage was noted in one case of an inter-supergroup recombinant haplotype, where the ftsZ gene came from supergroup A, and the others from supergroup B. Variation in the Wolbachia haplotypes in Acrididae hosts within supergroups B and F was extremely low. A comprehensive genetic analysis of Wolbachia diversity confirmed specific features of the Wolbachia allelic set in Acrididae hosts. This result can help to elucidate the crucial issue of Wolbachia biology: the route(s) and mechanism(s) of Wolbachia horizontal transmission.