Nucleic acid aptamers for capture and detection of Listeria spp

The purpose of this study was to identify biotinylated single-stranded (ss) DNA aptamers with binding specificity to Listeria and use these for capture and subsequent qPCR detection of the organism. For aptamer selection, SELEX (systematic evolution of ligands by exponential enrichment) was applied to a biotin-labeled ssDNA combinatorial library. After multiple rounds of selection and counter-selection, aptamers separated, sequenced, and characterized by flow cytometry showed binding affinities to L. monocytogenes of 18–23%. Although selected for using L. monocytogenes, these aptamers showed similar binding affinity for other members of the Listeria genus and low binding affinity for non-Listeria species. One aptamer, Lbi-17, was chosen for development of a prototype capture and detection assay. When Lbi-17 was conjugated to magnetic beads and used in a combined aptamer magnetic capture (AMC)-qPCR assay, the pathogen could be detected at concentrations <60 CFU/500 μl buffer in the presence of a heterogeneous cocktail of non-Listeria bacterial cells, with a capture efficiency of 26–77%. Parallel experiments using immunomagnetic separation (IMS)-qPCR produced the same detection limit but lower capture efficiency (16–21%). Increasing assay volume to 10 and 50 ml resulted in reduced capture efficiency and higher limits of detection, at 2.7 and 4.8 log₁₀ CFU L. monocytogenes per sample, respectively, for the AMC-qPCR assay. Biotinylated ssDNA aptamers are promising ligands for food-borne pathogen concentration prior to detection using molecular methods.     

Selection and characterization of DNA aptamers specific for Listeria species

Single-stranded (ss) DNA aptamers with binding affinity to Listeria spp. were selected using a whole-cell SELEX (Systematic Evolution of Ligands by EXponential enrichment) method. Listeria monocytogenes cells were grown at 37 °C and harvested at mid-log phase or early stationary phase to serve as the targets in SELEX. A total of 10 unique aptamer sequences were identified, six associated with log phase cells and four with stationary phase cells. Binding affinity of the aptamers was determined using flow cytometry and ranged from 10% to 44%. Four candidates having high binding affinity were further studied and found to show genus-specific binding affinity when screened against five different species within the Listeria genus. Using sequential binding assays combined with flow cytometry, it was determined that three of the aptamers (LM6-2, LM12-6, and LM12-13) bound to one apparent cell surface moiety, while a fourth aptamer (LM6-116) appeared to bind to a different cell surface region. This is the first study in which SELEX targeted bacterial cells at different growth phases. When used together, aptamers that bind to different cell surface moieties could increase the analytical sensitivity of future capture and detection assays.     

In Silico Reconstitution of Listeria Propulsion Exhibits Nano-Saltation

To understand how the actin-polymerization-mediated movements in cells emerge from myriad individual protein–protein interactions, we developed a computational model of Listeria monocytogenes propulsion that explicitly simulates a large number of monomer-scale biochemical and mechanical interactions. The literature on actin networks and L. monocytogenes motility provides the foundation for a realistic mathematical/computer simulation, because most of the key rate constants governing actin network dynamics have been measured. We use a cluster of 80 Linux processors and our own suite of simulation and analysis software to characterize salient features of bacterial motion. Our “in silico reconstitution” produces qualitatively realistic bacterial motion with regard to speed and persistence of motion and actin tail morphology. The model also produces smaller scale emergent behavior; we demonstrate how the observed nano-saltatory motion of L. monocytogenes, in which runs punctuate pauses, can emerge from a cooperative binding and breaking of attachments between actin filaments and the bacterium. We describe our modeling methodology in detail, as it is likely to be useful for understanding any subcellular system in which the dynamics of many simple interactions lead to complex emergent behavior, e.g., lamellipodia and filopodia extension, cellular organization, and cytokinesis.     

Evaluation of immunomagnetic separation in combination with ALOA Listeria chromogenic agar for the isolation and identification of Listeria monocytogenes in ready-to-eat foods

A study was conducted to evaluate the performance of the ALOA (chromogenic media) in combination with immunomagnetic separation (IMS) for the detection of Listeria monocytogenes in ready-to-eat food products. IMS-ALOA method was found to be equivalent to Health Canada's reference culture method as well as comparable to BAX-PCR method in terms of the sensitivity of the methods for the detection of L. monocytogenes in ready-to-eat foods such as turkey roast, beef roast, mixed vegetable salads, potato and egg salad, soft cheese and smoked salmon. The IMS-ALOA method gave 100% sensitivity in the inclusivity tests with 42 pure L. monocytogenes strains. Exclusivity testing with five other species of Listeria genus and 29 pure non-L. monocytogenes strains from 21 different genera showed 97% specificity. The method was able to detect L. monocytogenes at levels near or below 1 cfu/25 g regulatory limit in ready-to-eat food matrices after 24 h enrichment, with a turnaround time of 3 days compared to 7-8 days for culture method. IMS-ALOA method is a valuable alternate test method for the screening of L. monocytogenes in a variety of foods especially ready-to-eat foods.     

浅析新版《基本医疗保险药品目录》的制定

《基本医疗保险药品目录》是医保基金支付参保人员药品费用和强化医疗保险医疗服务管理的政策依据及标准。其根本目的是保证参保人员的合理用药需求,保障参保人员的合法权益,降低不合理用药支出。通过对新版《基本医疗保险药品目录》的新特点以及存在不足的分析,提出完善《基本医疗保险药品目录》制定的政策建议。     

Direct Measurement of Helical Cell Motion of the Spirochete Leptospira

Leptospira are spirochete bacteria distinguished by a short-pitch coiled body and intracellular flagella. Leptospira cells swim in liquid with an asymmetric morphology of the cell body; the anterior end has a long-pitch spiral shape (S-end) and the posterior end is hook-shaped (H-end). Although the S-end and the coiled cell body called the protoplasmic cylinder are thought to be responsible for propulsion together, most observations on the motion mechanism have remained qualitative. In this study, we analyzed the swimming speed and rotation rate of the S-end, protoplasmic cylinder, and H-end of individual Leptospira cells by one-sided dark-field microscopy. At various viscosities of media containing different concentrations of Ficoll, the rotation rate of the S-end and protoplasmic cylinder showed a clear correlation with the swimming speed, suggesting that these two helical parts play a central role in the motion of Leptospira. In contrast, the H-end rotation rate was unstable and showed much less correlation with the swimming speed. Forces produced by the rotation of the S-end and protoplasmic cylinder showed that these two helical parts contribute to propulsion at nearly equal magnitude. Torque generated by each part, also obtained from experimental motion parameters, indicated that the flagellar motor can generate torque >4000 pN nm, twice as large as that of Escherichia coli. Furthermore, the S-end torque was found to show a markedly larger fluctuation than the protoplasmic cylinder torque, suggesting that the unstable H-end rotation might be mechanically related to changes in the S-end rotation rate for torque balance of the entire cell. Variations in torque at the anterior and posterior ends of the Leptospira cell body could be transmitted from one end to the other through the cell body to coordinate the morphological transformations of the two ends for a rapid change in the swimming direction.     

Formulation of Statistical Equation of Motion of Blood

A general form of the statistical equation of motion of the blood is derived by averaging the motion of individual elements of the blood over a small volume in space. This equation can be transformed into an explicit form to find the constitutive equations of the blood provided the detailed motion of the plasma in some neighborhood of a suspended particle is known. As a demonstration of such transformation, the general form of the statistical equation of motion is applied to the suspension of sphere with a very low concentration to find the effective viscosity.     

Peristaltic Motion of Johnson-Segalman Fluid in a Curved Channel with Slip Conditions

Slip effects on the peristaltic transport of Johnson-Segalman fluid through a curved channel have been addressed. The influence of wall properties is also analyzed. Long wavelength and low Reynolds number assumptions have been utilized in the mathematical formulation of the problem. The equations so formed have been solved numerically by shooting method through computational software Mathematica 8. In addition the analytic solution for small Weissenberg number (elastic parameter) is computed through a regular perturbation method. An excellent agreement is noticed between the two solutions. The results indicate an increase in the magnitude of velocity with an intensification in the slip effect. Moreover the size and circulation of the trapped boluses increase with an increase in the slip parameter. Unlike the planar channel, the profiles of axial velocity are not symmetric about the central line of the channel.     

A new role for the SHATTERPROOF genes during Arabidopsis gynoecium development

Gynoecium development is a complex process which is regulated by key factors that control the spatial formation of the apical, medial and basal parts. SHATTERPROOF1 (SHP1) and SHP2, two closely related MADS-box genes, redundantly control the differentiation of the dehiscence zone and promote the lignification of adjacent cells. Furthermore, SHP1 and SHP2 have shown to play an important role in ovule identity determination. The present work identifies a new function for these two genes in promoting stigma, style and medial tissue development. This new role was discovered by combining the shp1 shp2 double mutant with the aintegumenta (ant) and crabs claw (crc) mutants. In quadruple mutant flowers, the inner whorl is composed of unfused carpels which lack almost completely apical and medial tissues, a phenotype similar to the previously reported fil ant and lug ant double mutants.     

A medium for the maintenance of Chironomus tentans salivary glands in vitro

A synthetic medium based upon the chemical composition of fourth instar Chironomus haemolymph was formulated for the in vitro culture of Chironomus tentans salivary glands.Salivary glands maintained in the medium for up to 4 days appeared morphologically normal. Secretion-free glands, obtained from pilocarpine-treated larvae, accumulated proteinaceous material in the gland lumen and exhibited a 46% increase in total gland protein after 24 hr in the medium. Cycloheximide almost totally inhibited the accumulation of secretion material and the increase in total gland protein by cultured glands.Glands cultured for up to 4 days continued to incorporate ¹⁴C-leucine into acid-insoluble total protein and ³H-uridine into total RNA, but at reduced levels. The incorporation of both isotopes was almost completely inhibited by cycloheximide.Autoradiographic squash preparations of glands pulse-labelled with ³H-thymidine after 3 days in culture revealed a normal pattern of asynchronous chromosomal DNA replication. Glands cultured for up to 4 days exhibited ³H-uridine incorporation into nucleoli and into distinct chromosomal regions which corresponded with sites of cytochemically demonstrable acidic protein.The chromosomes of cultured glands appeared morphologically and cytochemically normal, except for some regression of the Balbiani rings. Addition of ecdysterone to media containing glands previously cultured for 3 days resulted in puff induction at the IV-2-B chromosomal locus.     

苏州文人园林曲桥路径对视线引导的实验研究

选取3处苏州园林的曲桥路径,现场邀请游人取景拍照,获取其游园过程中关注景物、视线方向等信息,结合路径与景物关系,通过实验方法分析曲桥路径中游人赏景的视觉行为特征。通过定量分析发现,苏州文人园林中曲桥转折间带来的空间位置变化影响着人们的视觉行为,其中景物视距与方向对人们的观景兴致存在显著影响,视距在3~33 m时,游人观景兴致最佳;同时路径方向与观景方向的垂直关系、路径对景物的指向关系可增强游人对相应景观的观赏兴致,曲桥中对垂直与指向关系的运用存在一定的规律。     

A metabolomics-based method for studying the effect of yfcC gene in Escherichia coli on metabolism

Metabolomics is a potent tool to assist in identifying the function of unknown genes through analysis of metabolite changes in the context of varied genetic backgrounds. However, the availability of a universal unbiased profiling analysis is still a big challenge. In this study, we report an optimized metabolic profiling method based on gas chromatography–mass spectrometry for Escherichia coli. It was found that physiological saline at −80 °C could ensure satisfied metabolic quenching with less metabolite leakage. A solution of methanol/water (21:79, v/v) was proved to be efficient for intracellular metabolite extraction. This method was applied to investigate the metabolome difference among wild-type E. coli, its yfcC deletion, and overexpression mutants. Statistical and bioinformatic analysis of the metabolic profiling data indicated that the expression of yfcC potentially affected the metabolism of glyoxylate shunt. This finding was further validated by real-time quantitative polymerase chain reactions showing that expression of aceA and aceB, the key genes in glyoxylate shunt, was upregulated by yfcC. This study exemplifies the robustness of the proposed metabolic profiling analysis strategy and its potential roles in investigating unknown gene functions in view of metabolome difference.     

Formulation of Eco-friendly Medicated Chewing Gum to Prevent Motion Sickness

An attempt was made to formulate medicated chewing gum to prevent motion sickness using natural gum base for faster onset of action and easy administration, anywhere and anytime, without access to water. To avoid the discard issue of gum cud, natural gum base of Triticum aestivum (wheat grain) was explored because of its biodegradable and biocompatible nature and easy availability. Prolamin, extracted from wheat, showed good chewing capacity, elasticity, high water retention capacity, antifungal activity, and compatibility with the drug. Formulations were prepared based on a two-factor and three-level factorial design. Amount of calcium carbonate (texturizer) and gum base were selected as independent variables. Elasticity and drug release were considered as the dependent variables. All batches were evaluated for the content uniformity, elasticity study, texture study, in vitro drug release study, and chewiness study. Results revealed that medicated chewing gum containing 80 mg of calcium carbonate and 500 mg of gum base showed good elasticity and more than 90% drug release within 16 min. Thus, this study suggested that both good elasticity and chew ability and abundant availability of wheat grain can act as a potential gum base for medicated chewing gum.KEY WORDS: biodegradable gum, gum base, medicated chewing gum, plasticizer, wheat prolamin     

Functional polymorphisms in the CYP3A4, CYP3A5, and CYP21A2 genes in the risk for hypertension in pregnancy

An intronic single nucleotide polymorphism (SNP) in the CYP3A5 gene (CYP3A5∗3; SNP rs776746) affects RNA splicing and enzymatic activity. The CYP3A5∗3 frequency increased with distance from the equator and natural selection has been proposed to explain the worldwide distribution of this allele. CYP3A activity has been related with the risk for hypertension in pregnancy, a major cause of morbidity and mortality among women, and CYP3A5∗3 could reduce the risk for this disease in populations from regions with high sodium and water availability. The CYP3A5 genotype was related with blood pressure in the general population, but the effect on the risk for hypertension in pregnancy has not been evaluated.We compared the allele and genotype frequencies of three functional SNPs in the CYP3A5 (rs776746), CYP3A4 (rs2740574), and CYP21A2 (rs6471) genes between pregnant women who developed hypertension (n = 250) or who remained normotensive (control group, n = 250). In addition, we sequenced the full CYP3A5 coding sequence in 40 women from the two groups to determine whether some gene variants could explain the risk for hypertensive pregnancies in our population.Allele and genotype frequencies did not differ between hypertensive and normotensive women for the three CYP variants. We did not find CYP3A5 nucleotide changes that could explain a higher risk for hypertension in pregnancy. Our data suggests that the variation in CYP3A5, CYP3A4, and CYP21A2 did not contribute to the risk for hypertension in pregnancy in our population.     

A Microscopic Phenotypic Assay for the Quantification of Intracellular Mycobacteria Adapted for High-throughput/High-content Screening

Despite the availability of therapy and vaccine, tuberculosis (TB) remains one of the most deadly and widespread bacterial infections in the world. Since several decades, the sudden burst of multi- and extensively-drug resistant strains is a serious threat for the control of tuberculosis. Therefore, it is essential to identify new targets and pathways critical for the causative agent of the tuberculosis, Mycobacterium tuberculosis (Mtb) and to search for novel chemicals that could become TB drugs. One approach is to set up methods suitable for the genetic and chemical screens of large scale libraries enabling the search of a needle in a haystack. To this end, we developed a phenotypic assay relying on the detection of fluorescently labeled Mtb within fluorescently labeled host cells using automated confocal microscopy. This in vitro assay allows an image based quantification of the colonization process of Mtb into the host and was optimized for the 384-well microplate format, which is proper for screens of siRNA-, chemical compound- or Mtb mutant-libraries. The images are then processed for multiparametric analysis, which provides read out inferring on the pathogenesis of Mtb within host cells.     

A cis-encoded sRNA controls the expression of fabH2 in Yersinia

YsrH is a novel cis-encoded sRNA located on the opposite strand to fabH2, which is essential for fatty acid biosynthesis in bacteria. In this study, YsrH-mediated regulation of fabH2 expression was investigated in Yersinia pseudotuberculosis. Constitutive and inducible over-expression of YsrH decreased the mRNA level of fabH2, while expression of downstream fabD and fabG remained unaffected. Polynucleotide phosphorylase (PNPase) also played an important role in this regulation process by mediating YsrH decay in the exponential phase. Thus, our data defines a cis-encoded sRNA that regulates fatty acid synthesis via a regulatory mechanism also involving PNPase.