Study of Implosion of Twisted Nested Arrays at the Angara-5-1 Facility

Results are presented from experimental studies of the implosion of twisted nested arrays in which the wires of the outer and inner arrays are twisted about the array axis in opposite directions (clockwise and counterclockwise). Experiments with twisted arrays were carried out at the Angara-5-1 facility at currents of up to 4 MA. The currents through the arrays were switched either simultaneously or the current pulse through the outer array was delayed by 10–15 ns with the help of an anode spark gap. It is shown that, in such arrays, the currents flow along the inclined wires and, accordingly, there are both the azimuthal and axial components of the discharge current. The process of plasma implosion in twisted arrays depends substantially on the value of the axial (longitudinal) magnetic field generated inside the array by the azimuthal currents. Two-dimensional simulations of the magnetic field in twisted nested arrays were performed in the (r, z) geometry with allowance for the skin effect in the discharge electrodes. It is shown that, depending on the geometry of the discharge electrodes, different configurations of the magnetic field can be implemented inside twisted nested arrays. The calculated magnetic configurations are compared with the results of measurements of the magnetic field inside such arrays. It is shown that the configuration of the axial magnetic field inside a twisted nested array depends substantially on the distribution of the azimuthal currents between the inner and outer arrays.     

基因表达芯片探针选择的一种有效方法

为了减少基因表达芯片探针选择的计算量,采用最大共有序列准则大大减少了需要计算的候选探针数量,并通过不断扩大进行计算的探针数目保证探针选择的效果．结果表明该方法是十分有效的,探针选择的结果也是令人满意的．     

Nested Inverse Polymerase Chain Reactions: An Effective Method for Cloning of Full-Length Sequences of Chalcone Synthase

Chalcone synthase is the key enzyme in biosynthesis of flavonoids, which play roles in pigmentation of flowers and protection against ultraviolet and pathogens. Inverse polymerase chain reaction (IPCR) is a method for the rapid in vitro amplification of DNA sequences that flank a region of known sequence. In this study, IPCR united with nested PCR was successfully applied in cloning full-length sequences of three Phalaenopsis chalcone synthase genes (phchs3, phchs4, and phchs5, respectively). Firstly, routine PCR with homologous primers were performed, and gene fragments of phchs3 (1 kb), phchs4 (1.2 kb), and phchs5 (800 bp) were obtained and then sequenced. Then, inverse PCR were carried out for cloning full-length sequence of each gene. Because products were not unique in single round inverse PCR, nested PCR were performed, and the specificity was much enhanced. At last, full-length sequences of 2,499 bp for phchs3, 2,502 bp for phchs4, and 1,855 bp for phchs5 were obtained. This study proved that IPCR could be more efficient if being united with nested PCR.     

A Method for Increasing the Number of Mitoses Available for Cytogenetic Analysis in Rainbow Trout

A new method for the cytogenetic analysis of fishes with special interest for the rainbow trout (Salmo gairdneri Rich.) is described. This reliable method that includes treatment with a yeast solution provides high quality spreads of a great number of metaphases.     

A Novel Method for Generating Nested Deletions Using the in Vitro Bacteriophage T3 DNA Packaging System

To sequence a DNA segment inserted into a cosmid vector underthe directed sequencing strategy, we established a simple andrapid method for generating nested deletions which uses thein vitro packaging system of bacteriophage T3 DNA. The principleis based on the previous finding that this system can translocateany linear double-stranded DNA up to 40 kb into the phage capsidin a time-dependent manner and the encapsulated DNA becomesDNase-resistant. For this purpose, we constructed a cosmid vectorthat carries two different antibiotic selection markers at bothsides of the multiple cloning site, and after insertion of aDNA segment, the clone was linearized by -terminase at the cossite. After the packaging reaction in vitro followed by DNasetreatment, the encapsulated DNA was introduced into Escherichiacoli cells to give clones with unidirectional deletions by differentialantibiotic selection. Restriction and sequence analyses of deletionclones demonstrated that an ordered set of clones with nesteddeletions, ranging from less than 1 kb to 25 kb, was createdfrom either the end of the DNA segment. Thus, nested deletionclones that cover the entire region of a 40-kb cosmid insertcan be obtained by a single packaging reaction, and its restrictionmap can be simultaneously obtained.     

Hind-Casting the Quantity and Composition of Discards by Mixed Demersal Fisheries in the North Sea

Many commercial fisheries seek to maximise the economic value of the catch that they bring ashore and market for human consumption by discarding undersize or low value fish. Information on the quantity, size and species composition of discarded fish is vital for stock assessments and for devising legislation to minimise the practice. However, except for a few major species, data are usually extremely sparse and reliant on observers aboard a small sample of fishing vessels. Expanding these data to estimate total regional discards is highly problematic. Here, we develop a method for utilising additional information from scientific trawl surveys to model the quantities of fish discarded by the commercial fisheries. As a case-study, we apply the model to the North Sea over the period 1978-2011, and show a long-term decline in the overall quantity of fish discarded, but an increase in the proportion of catch which is thrown away. The composition of discarded catch has shifted from predominantly (∼80%) roundfish, to >50% flatfish. Undersized plaice constitute the largest single fraction of discards, unchanged from the beginning of the 20th century. Overall, around 60% of discarded fish are rejected on the basis of size rather than for reasons of species value or quota restrictions. The analysis shows that much more information can be gained on discarding by utilising additional sources of data rather than relying solely on information gathered by observers. In addition, it is clear that reducing fishing intensity and rebuilding stocks is likely to be more effective at reducing discards in the long term, than any technical legislation to outlaw the practice in the short term.     

Method for Increasing the Regularity of Isolation of Infectious Ribonucleic Acid from Influenza Virus

A more effective method of isolating infectious ribonucleic acid (RNA) from influenza virus was evaluated based on the enzymatic disintegration of the viral coat by Pronase, followed by phenol-detergent extraction of the RNA from susceptible and from resistant cells.     

The Role of Formulation Additives in Increasing the Potency of Cydia pomonella Granulovirus for Codling Moth Larvae,in Laboratory and Field Experiments

Studies were undertaken to improve the biological efficacy of the granulovirus (CpGV) of the codling moth, Cydia pomonella , by evaluating the performance of some formulation additives that might improve virus persistence and/or virus uptake by first instar larvae. Laboratory studies, using a leaf disc bioassay, demonstrated that 15% cane molasses incorporated within a formulation of purified CpGV dramatically reduced the median lethal exposure time (LET 50 ) to CpGV for neonate larvae at a CpGV dosage rate of 10 7 occlusion bodies (OBs) ml -1 . Screening of a range of other compounds showed that sucrose, fructose and sorbitol (at 10% concentrations) and extracts of apple flesh and skin also gave significant reductions in the LET 50 of CpGV formulations containing these ingredients. Pectin, malic acid and &#102 -farnesene did not significantly reduce the LET 50 . In a field trial, molasses included at 15% (v/v) in a CpGV formulation, containing a dosage rate of 10 12 OBs ha -1 , gave as good control of codling moth damage as virus formulations containing the 'sticker' 0.2% skimmed milk at higher dosage rates of 10 13 and 10 14 OBs ha -1 . Studies of CpGV persistence on foliage revealed no significant improvement of virus persistence on apple foliage using 10% or 15% molasses formulations. A second field trial demonstrated that 10% molasses, 10% sorbitol or 0.08% &#102 -farnesene significantly reduced codling moth deep damage to fruit when these ingredients were added to formulations of pure CpGV. Substantial sooty-mould growth ( Cladosporium spp.) was observed on apple foliage treated with formulations containing molasses, indicating that this formulation additive has secondary consequences that would need to be taken into account if molasses was to be used in commercial CpGV formulations. Nonetheless, these studies clearly demonstrate that major biological improvements in CpGV performance can be achieved by the incorporation of formulation additives, including molasses and several other compounds, that probably function as attractants and/or feeding stimulants for codling moth larvae.     

Direct Method for Determining the Viability of a Freshly Generated Mixed Bacterial Aerosol

A direct method was developed to determine the viability of a freshly generated mixed bacterial aerosol. A mixed suspension of (32)P-labeled Staphylococcus aureus and (35)S-labeled Proteus mirabilis was nebulized, and the aerosol was collected and separated according to particle size with an Andersen sampler. Quantitative and qualitative bacteriological and radioisotopic techniques were used to obtain ratios of bacterial to radioactive counts for each organism in samples of the nebulizer suspension and aerosol. Loss of viability was calculated from the change that occurred between the ratio of the nebulizer suspension and the ratio of the aerosol. The viability of S. aureus was unaffected by aerosolization, whereas the viability of P. mirabilis declined by 20 to 60% and was inversely proportional to particle size. The advantages of this method over present indirect methods, as well as potential applications of the method, are discussed.     

Integration of Experiments across Diverse Environments Identifies the Genetic Determinants of Variation in Sorghum bicolor Seed Element Composition

Seedling establishment and seed nutritional quality require the sequestration of sufficient element nutrients. The identification of genes and alleles that modify element content in the grains of cereals, including sorghum (Sorghum bicolor), is fundamental to developing breeding and selection methods aimed at increasing bioavailable element content and improving crop growth. We have developed a high-throughput work flow for the simultaneous measurement of multiple elements in sorghum seeds. We measured seed element levels in the genotyped Sorghum Association Panel, representing all major cultivated sorghum races from diverse geographic and climatic regions, and mapped alleles contributing to seed element variation across three environments by genome-wide association. We observed significant phenotypic and genetic correlation between several elements across multiple years and diverse environments. The power of combining high-precision measurements with genome-wide association was demonstrated by implementing rank transformation and a multilocus mixed model to map alleles controlling 20 element traits, identifying 255 loci affecting the sorghum seed ionome. Sequence similarity to genes characterized in previous studies identified likely causative genes for the accumulation of zinc, manganese, nickel, calcium, and cadmium in sorghum seeds. In addition to strong candidates for these five elements, we provide a list of candidate loci for several other elements. Our approach enabled the identification of single-nucleotide polymorphisms in strong linkage disequilibrium with causative polymorphisms that can be evaluated in targeted selection strategies for plant breeding and improvement.Sorghum (Sorghum bicolor) is a globally cultivated source of food, feed, and fiber. Contrasting needs for elemental nutrient accumulation limit crop yield and quality for sorghum marketed to different sectors. The seed-bearing reproductive organs, or panicles, in sorghum represent up to 30% of the total dry matter yield (Amaducci et al., 2004). Plant-based diets, in which grains compose the major food source, require the accumulation of bioavailable essential elements in the plant seeds. Currently, iron (Fe) and zinc (Zn) deficiencies negatively affect the health of over two billion people worldwide (World Health Organization, 2002). Increased bioavailable elemental nutrient content in the edible portions of sorghum for human and animal nutrition could ameliorate this nutritional crisis (Graham et al., 1999; World Health Organization, 2002). Additional global health benefits could be achieved by increasing magnesium (Mg), selenium (Se), calcium (Ca), and copper (Cu; White and Broadley, 2005) while reducing the concentration of toxic elements, including arsenic (As) and cadmium (Cd; Ma et al., 2008).Seed element accumulation results from interconnected biological processes, including element uptake by the roots, translocation and remobilization within the plant, and ultimately import, deposition, and assimilation/storage in the seeds. Element availability is further affected by the accumulation of metabolites in seeds (Vreugdenhil et al., 2004). High-throughput ionomic analysis, or concurrent measurement of multiple elements, allows for the quantitative and simultaneous measurement of an organism’s elemental composition, providing a snapshot of the functional state of an organism under different experimental conditions (Salt et al., 2008). Most studies of the plant ionome utilize inductively coupled plasma mass spectroscopy (ICP-MS). Briefly, inductively coupled plasma (ICP) functions to ionize the analyte into atoms, which are then detected by mass spectroscopy. Reference standards are used to identify and quantitate each element of interest in the sample. ICP-MS analysis can be accomplished in as little as 1 min per sample, which allows for high-throughput processing of thousands of samples (Salt et al., 2008). Previous studies have demonstrated that several elements, including Fe, manganese (Mn), Zn, cobalt (Co), and Cd, share mechanisms of accumulation (Yi and Guerinot, 1996; Vert et al., 2002; Connolly et al., 2003). Ionomic signatures derived from multiple elements also have been shown to better predict plant physiological status for some elements than the measure of the element’s concentration, including essential nutrients like Fe (Baxter et al., 2008). Holistically examining the ionome provides significant insights into the networks underlying ion homeostasis beyond single-element studies (Baxter and Dilkes, 2012).There are over 45,000 catalogued lines of sorghum at the U.S. Department of Agriculture Germplasm Resource Information Network. This diverse collection of sorghum germplasm contains genetic variation with undiscovered impact on seed element composition (Das et al., 1997). Mapping quantitative trait loci for seed element concentration has been successful in a number of species, including Arabidopsis (Arabidopsis thaliana; Vreugdenhil et al., 2004; Waters and Grusak, 2008; Buescher et al., 2010), rice (Oryza sativa; Norton et al., 2010; Zhang et al., 2014), wheat (Triticum aestivum; Shi et al., 2008; Peleg et al., 2009), and maize (Zea mays; Simić et al., 2012; Baxter et al., 2013, 2014). Genome-wide association (GWA) mapping is well suited for uncovering the genetic basis for complex traits, including seed element accumulation. One of the key strengths of association mapping is that a priori knowledge is not necessary to identify new loci associated with the trait of interest. Furthermore, a GWA mapping population is composed of lines that have undergone numerous recombination events, allowing for a narrower mapping interval. Previous GWA studies in maize (Tian et al., 2011), rice (Huang et al., 2010), and sorghum (Morris et al., 2013) have been successful in identifying the genetic basis for various agronomic traits. Here, we analyzed the seed ionome from a community-generated association panel to identify potential loci underlying seed element accumulation in sorghum.     

壮阳药效动物实验评价方法的改进

目的对壮阳药效评价方法进行优化,以探求更为有效的候选药物筛选方法。方法模型组大鼠均灌胃给予西地那非10 mg/kg,对照组大鼠给予相同容量的生理盐水灌胃,每天1次,连续灌胃给药14 d。每次给药后连续记录2 h内大鼠阴茎勃起、阴部理毛、爬背次数和参与动物数,并计算PEI值。采用改良的壮阳药效评价方法,整个过程采用摄像头观察并在不同时间段给予雌鼠诱导。结果在雌鼠诱导组中,模型组大鼠给药后2 h PEI值较对照组明显升高（P〈0.05）。在模型组中,与人为观察组相比,摄像头观察组大鼠给药后2 h PEI值明显升高（P〈0.05）;与非雌鼠诱导组相比,雌鼠诱导组大鼠给药后2 h PEI值明显升高（P〈0.05）;与持续诱导组相比,间断诱导组2h PEI值无明显差异,但60～120 min时间段PEI值明显升高（P〈0.05）。结论优化后的壮阳药效评价方法能更为有效的评价候选药物的壮阳药效。     

Nested Sampling for Bayesian Model Comparison in the Context of Salmonella Disease Dynamics

Understanding the mechanisms underlying the observed dynamics of complex biological systems requires the statistical assessment and comparison of multiple alternative models. Although this has traditionally been done using maximum likelihood-based methods such as Akaike''s Information Criterion (AIC), Bayesian methods have gained in popularity because they provide more informative output in the form of posterior probability distributions. However, comparison between multiple models in a Bayesian framework is made difficult by the computational cost of numerical integration over large parameter spaces. A new, efficient method for the computation of posterior probabilities has recently been proposed and applied to complex problems from the physical sciences. Here we demonstrate how nested sampling can be used for inference and model comparison in biological sciences. We present a reanalysis of data from experimental infection of mice with Salmonella enterica showing the distribution of bacteria in liver cells. In addition to confirming the main finding of the original analysis, which relied on AIC, our approach provides: (a) integration across the parameter space, (b) estimation of the posterior parameter distributions (with visualisations of parameter correlations), and (c) estimation of the posterior predictive distributions for goodness-of-fit assessments of the models. The goodness-of-fit results suggest that alternative mechanistic models and a relaxation of the quasi-stationary assumption should be considered.     

用逆转录套式PCR检测临床标本中的腮腺炎病毒RNA

流行性腮腺炎是儿童常见呼吸道传染病,并发症多为睾丸炎、无菌脑炎等。个别患者甚至因严重的脑炎并发症而死亡［１］。故有必要对患者进行早期病原诊断,以利于早期治疗。腮腺炎病毒ＲＮＡ中小疏水蛋白（ＳＨ）基因作为高变区在不同毒株的分子特性鉴别中比其它基因片段更...     

DNA-based方法及其在研究动物食物组成中的应用

了解动物的食物组成是研究生态系统的多样性和生态系统功能的基本要求,在动物生态学的研究中至关重要。DNA-based方法包括样本采集、DNA提取、PCR扩增、序列比对分析等一系列步骤,实验的成败取决于标记基因的选择、引物的设计及每个步骤的优化。文章综述了DNA-based方法的各个基本步骤及其优化方法,并对该方法在今后用于国内相关研究的可能性进行展望,关注用于研究国内三峡大坝这个大型水域生态系统的可能性,期望推动国内该领域的研究。     

A Mixed Methods and Triangulation Model for Increasing the Accuracy of Adherence and Sexual Behaviour Data: The Microbicides Development Programme

Background

The collection of accurate data on adherence and sexual behaviour is crucial in microbicide (and other HIV-related) research. In the absence of a “gold standard” the collection of such data relies largely on participant self-reporting. After reviewing available methods, this paper describes a mixed method/triangulation model for generating more accurate data on adherence and sexual behaviour in a multi-centre vaginal microbicide clinical trial. In a companion paper some of the results from this model are presented [1].

Methodology/Principal Findings

Data were collected from a random subsample of 725 women (7.7% of the trial population) using structured interviews, coital diaries, in-depth interviews, counting returned gel applicators, focus group discussions, and ethnography. The core of the model was a customised, semi-structured in-depth interview. There were two levels of triangulation: first, discrepancies between data from the questionnaires, diaries, in-depth interviews and applicator returns were identified, discussed with participants and, to a large extent, resolved; second, results from individual participants were related to more general data emerging from the focus group discussions and ethnography. A democratic and equitable collaboration between clinical trialists and qualitative social scientists facilitated the success of the model, as did the preparatory studies preceding the trial. The process revealed some of the underlying assumptions and routinised practices in “clinical trial culture” that are potentially detrimental to the collection of accurate data, as well as some of the shortcomings of large qualitative studies, and pointed to some potential solutions.

Conclusions/Significance

The integration of qualitative social science and the use of mixed methods and triangulation in clinical trials are feasible, and can reveal (and resolve) inaccuracies in data on adherence and sensitive behaviours, as well as illuminating aspects of “trial culture” that may also affect data accuracy.     

Experiments on the central pattern generator for swimming in amphibian embryos

The central nervous system of paralysed Xenopus laevis embryos can generate a motor output pattern suitable for swimming locomotion. By recording motor root activity in paralysed embryos with transected nervous systems we have shown that: (a) the spinal cord is capable of swimming pattern generation; (b) swimming pattern generator capability in the hindbrain and spinal cord is distributed; (c) caudal hindbrain is necessary for sustained swimming output after discrete stimulation. By recording similarly from embryos whose central nervous system was divided longitudinally into left and right sides, we have shown that: (a) each side can generate rhythmic motor output with cycle periods like those in swimming; (b) during this activity cycle period increases within an episode, and there is the usual rostrocaudal delay found in swimming; (c) this activity is influenced by sensory stimuli in the same way as swimming activity; (d) normal phase coupling of the left and right sides can be established by the ventral commissure in the spinal cord. We conclude that interactions between the antagonistic (left and right) motor systems are not necessary for swimming rhythm generation and present a model for swimming pattern generation where autonomous rhythm generators on each side of the nervous system drive the motoneurons. Alternation is achieved by reciprocal inhibition, and activity is initiated and maintained by tonic excitation from the hindbrain.