Structure of the Large Subunit rDNA from a Diatom, and Comparison Between Small and Large Subunit Ribosomal RNA for Studying Stramenopile Evolution

The aim of this study was to compare the usefulness of complete small and large subunit rRNA, and a combination of both molecules, for reconstructing stramenopile evolution. To this end, phylogenies from species of which both sequences are known Acre constructed with the neighbor-joining, maximum parsimony, and maximum likelihood methods. Also the use of structural features of the rRNAs was evaluated. The large subunit rRNA from the diatom Skeletonema pseudocostatum was sequenced in order to have a more complete taxon sampling, and a group I intron was identified. Our results indicated that heterokont algae are monophyletic, with diatoms diverging first. However, as the analysis was restricted to a particular data set containing merely six taxa, the outcome has limited value for elucidating stramenopile relationships. On the other hand, this approach permits comparison of the performance of both rRNA molecules without interference from other factors, such as a different species selection for each molecule. For the taxa used, the large subunit rRNA clearly contained more phylogenetic information than the small subunit rRNA. Although this result can definitely not be generalized and depends on the phvlogeny to be studied, in some cases determining complete large subunit rRNA sequences certainly seems worthwhile.     

Developmental potential of avian trunk neural crest cells in situ

To analyze the developmental potential of individual neural crest cells or their precursors, we have microinjected a vital dye, lysinated rhodamine dextran (LRD), into single cells in the dorsal neural tube. The phenotypes of the descendants that inherited the LRD from the injected cells were evaluated based upon their position, morphology, and neurofilament expression. Individual neural crest cells labeled before or as they emigrated from the neural tube gave rise to both sensory and sympathetic neurons as well as nonneuronal cells, some of which had the morphological characteristics of Schwann cells or pigment cells. In numerous cases, the descendants of a single cell included both neural crest- and neural tube-derived neurons, suggesting that some cells of the peripheral and central nervous systems share a common lineage. Our data demonstrate definitively that both emigrating and premigratory trunk neural crest cells can be multipotent, giving rise not only to cells in multiple neural crest derivatives, but also to both neuronal and nonneuronal elements within a given derivative.     

Olfactory functioning and callosotomy: a report of two cases

Two callosotomy patients with presumably intact anterior commissures were evaluated on a battery of olfactory tasks including sensitivity, discrimination, memory, identification, cross-modality matching, bilateral summation (dirhinic vs. monorhinic thresholds), and localization of odorants. One case was evaluated both pre- and post-surgery. He showed marked decrements after surgery in odor memory and in matching across modalities. After surgery, both patients were better able to name odorants presented to the left nostril than the right nostril. The patient who was asked to remember odorants that could be readily labeled was better able to remember those odorants presented to the left nostril. The findings that both cases performed equally well whether olfactory and tactile information was projected to the same hemisphere or a different one, that some bilateral summation was evident, and that the cases were unable to localize odorants suggests that the remaining neuronal pathways allow for some communication between hemispheres.     

Is it better to give information, receive it, or be ignorant in a two-player game?

The standard approach in a biological two-player game is toassume both players choose their actions independently of oneanother, having no information about their opponent's action(simultaneous game). However, this approach is not realisticin some circumstances. In many cases, one player chooses hisaction first and then the second player chooses her action withinformation about his action (Stackelberg game). We comparethese two games, which can be mathematically analyzed into twotypes, depending on the direction of the best response function(BRF) at the evolutionarily stable strategy in the simultaneousgame (ESS_sim). We subcategorize each type of game into two cases,depending on the change in payoff to one player, when both playersare at the ESS_sim, and the other player increases his action.Our results show that in cases where the BRF is decreasing atthe ESS_sim, the first player in the Stackelberg game receivesthe highest payoff, followed by both players in the simultaneousgame, followed by the second player in the Stackelberg game.In these cases, it is best to be the first Stackelberg player.In cases where the BRF is increasing at the ESS_sim, both Stackelbergplayers receive a higher payoff than players in a simultaneousgame. In these cases, it is better for both players to playa Stackelberg game rather than a simultaneous game. However,in some cases the first Stackelberg player receives a higherpayoff than the second Stackelberg player, and in some casesthe opposite is true.     

Inhibitory effect of theophylline on repair of potentially lethal MMS-induced damages to DNA in V79 cells

Vanillin and its isomer o-vanillin have an effect on the adaptive and SOS responses, as well as mutagenesis, induced in Escherichia coli by N-methyl-N-nitrosourea (MNU) and UV irradiation, potentiating in some cases and suppressing in others. o-Vanillin markedly inhibited the MNU-induced adaptive response, while both vanillins potentiated the UV-induced SOS response. These phenomena appear to be responsible for the comutagenic or antimutagenic role of these chemicals in MNU and UV mutagenesis.     

Characterization and Simulation of Uncertain Frequency Distributions: Effects of Distribution Choice,Variability, Uncertainty,and Parameter Dependence

We use bootstrap simulation to characterize uncertainty in parametric distributions, including Normal, Lognormal, Gamma, Weibull, and Beta, commonly used to represent variability in probabilistic assessments. Bootstrap simulation enables one to estimate sampling distributions for sample statistics, such as distribution parameters, even when analytical solutions are not available. Using a two-dimensional framework for both uncertainty and variability, uncertainties in cumulative distribution functions were simulated. The mathematical properties of uncertain frequency distributions were evaluated in a series of case studies during which the parameters of each type of distribution were varied for sample sizes of 5, 10, and 20. For positively skewed distributions such as Lognormal, Weibull, and Gamma, the range of uncertainty is widest at the upper tail of the distribution. For symmetric unbounded distributions, such as Normal, the uncertainties are widest at both tails of the distribution. For bounded distributions, such as Beta, the uncertainties are typically widest in the central portions of the distribution. Bootstrap simulation enables complex dependencies between sampling distributions to be captured. The effects of uncertainty, variability, and parameter dependencies were studied for several generic functional forms of models, including models in which two-dimensional random variables are added, multiplied, and divided, to show the sensitivity of model results to different assumptions regarding model input distributions, ranges of variability, and ranges of uncertainty and to show the types of errors that may be obtained from mis-specification of parameter dependence. A total of 1,098 case studies were simulated. In some cases, counter-intuitive results were obtained. For example, the point value of the 95th percentile of uncertainty for the 95th percentile of variability of the product of four Gamma or Weibull distributions decreases as the coefficient of variation of each model input increases and, therefore, may not provide a conservative estimate. Failure to properly characterize parameter uncertainties and their dependencies can lead to orders-of-magnitude mis-estimates of both variability and uncertainty. In many cases, the numerical stability of two-dimensional simulation results was found to decrease as the coefficient of variation of the inputs increases. We discuss the strengths and limitations of bootstrap simulation as a method for quantifying uncertainty due to random sampling error.     

Some general aspects regarding the interpretation of binding data by means of a Scatchard plot

The question is quantitatively examined which general information can be obtained from experimental data of ligand binding to macromolecules if represented by a Scatchard plot. In particular, the curvature as well as the intercepts and slopes at both coordinate axes are analyzed assuming rather general conditions including cooperative behavior (with applications to some simplified cases of interest in practice). The results should provide a basis for attempts to elucidate the binding mechanism of a system encountered in experimental work.     

USE AND ABUSE OF NASOGASTRIC INTUBATION

The value of nasogastric intubation in the treatment of paralytic ileus and in some cases of mechanical obstruction, as well as in the preparation of obstructed patients for operation, cannot be denied. However, it is felt that intubation is oftentimes employed unnecessarily, and that the complications of this procedure are not fully appreciated. Fluid and electrolyte loss, sinusitis, parotitis, laryngeal obstruction, esophagitis, knotting and difficulty in withdrawing tubes and perforations of the gastrointestinal tract are complications that can occur when nasogastric intubation is employed.Two hundred consecutive operations on the gallbladder and bile ducts were reviewed, and the need for intubation in these cases was evaluated. It was needed in only 7.5 per cent of the cases in the series. In light of the hazards and the rather rare necessity for nasogastric intubation, “routine” use should be eschewed.     

基于COMSTAT软件对微生物被膜进行定量分析的方法与意义

目的:微生物被膜是一种具有协调性、功能性和高度结构性的膜状复合物,它可以为微生物提供良好的生存环境,免受外界因素的干扰。研究发现,具有产生微生物被膜能力的细菌治病性明显增强,而现今缺乏一种分析微生物被膜的有效手段。本文探讨利用COMSTAT软件对微生物被膜进行定量分析的方法和意义,为对微生物被膜定性定量分析提供支持手段,从而为研究微生物被膜致病性提供方法理论基础。方法:以葡萄球菌为研究模型,利用激光扫描共聚焦显微镜成像技术,结合COMSTAT微生物被膜分析软件对微生物被膜的单位面积生物量、基质覆盖率、平均厚度、粗糙系数等方面进行定量分析,研究了该葡萄球菌的生物被膜生长变化过程,并考察了抗生素对其生物被膜的抑制作用。结果:在葡萄球菌生物被膜生长过程中,生物量、平均厚度以及平均扩散距离等结构指标数值都有明显增加,而粗糙度和表面积与生物量比值呈现降低趋势,表明了微生物被膜由发生向成熟的转化过程。与此同时,经10μg/mL和100μg/mL的卡那霉素处理得到的葡萄球菌微生物被膜生长受到明显抑制,且随着卡那霉素的浓度增加,抑制效果随之增加。结论:本文运用COMSTAT软件的分析方法首次从生物量、平均厚度等结构指标数值的角度描述了葡萄球菌生物被膜,从而有效评价微生物被膜发生、发展、成熟以及崩解的生长过程。该技术在研究微生物被膜形成的理论机制方面存在潜在价值,可以为研究微生物被膜治病性提供理论基础,具有理论指导意义。     

Recurrent Implantation Failure-update overview on etiology,diagnosis, treatment and future directions

Recurrent implantation failure (RIF) refers to cases in which women have had three failed in vitro fertilization (IVF) attempts with good quality embryos. The definition should also take advanced maternal age and embryo stage into consideration. The failure of embryo implantation can be a consequence of uterine, male, or embryo factors, or the specific type of IVF protocol. These cases should be investigated to determine the most likely etiologies of the condition, as this is a complex problem with several variables. There are multiple risk factors for recurrent implantation failure including advanced maternal age, smoking status of both parents, elevated body mass index, and stress levels. Immunological factors such as cytokine levels and presence of specific autoantibodies should be examined, as well as any infectious organisms in the uterus leading to chronic endometritis. Uterine pathologies such as polyps and myomas as well as congenital anatomical anomalies should be ruled out. Sperm analysis, pre-implantation genetic screening and endometrial receptivity should be considered and evaluated, and IVF protocols should be tailored to specific patients or patient populations. Treatment approaches should be directed toward individual patient cases. In addition, we suggest considering a new initial step in approach to patients with RIF, individualized planned activities to activate the brain's reward system in attempt to improve immunological balance in the body.     

Have we overestimated the benefit of human(ized) antibodies?

The infusion of animal-derived antibodies has been known for some time to trigger the generation of antibodies directed at the foreign protein as well as adverse events including cytokine release syndrome. These immunological phenomena drove the development of humanized and fully human monoclonal antibodies. The ability to generate human(ized) antibodies has been both a blessing and a curse. While incremental gains in the clinical efficacy and safety for some agents have been realized, a positive effect has not been observed for all human(ized) antibodies. Many human(ized) antibodies trigger the development of anti-drug antibody responses and infusion reactions. The current belief that antibodies need to be human(ized) to have enhanced therapeutic utility may slow the development of novel animal-derived monoclonal antibody therapeutics for use in clinical indications. In the case of murine antibodies, greater than 20% induce tolerable/negligible immunogenicity, suggesting that in these cases humanization may not offer significant gains in therapeutic utility. Furthermore, humanization of some murine antibodies may reduce their clinical effectiveness. The available data suggest that the utility of human(ized) antibodies needs to be evaluated on a case-by-case basis, taking a cost-benefit approach, taking both biochemical characteristics and the targeted therapeutic indication into account.     

Variation in satellite DNA profiles--causes and effects

Heterochromatic regions of the eukaryotic genome harbour DNA sequences that are repeated many times in tandem, collectively known as satellite DNAs. Different satellite sequences co-exist in the genome, thus forming a set called a satellite DNA library. Within a library, satellite DNAs represent independent evolutionary units. Their evolution can be explained as a result of change in two parameters: copy number and nucleotide sequence, both of them ruled by the same mechanisms of concerted evolution. Individual change in either of these two parameters as well as their simultaneous evolution can lead to the genesis of species-specific satellite profiles. In some cases, changes in satellite DNA profiles can be correlated with chromosomal evolution and could possibly influence the evolution of species.     

High performance liquid chromatographic enantioseparation of chiral bridged polycyclic compounds on chiralcel OD-H and chiralpak OT(+)

The HPLC enantiomeric separation of 29 racemic bridged polycyclic compounds was examined on commercially available Chiralcel OD-H and Chiralpak OT(+) columns. The separations were evaluated under normal-phase mode (hexane containing mobile phase) for Chiralcel OD-H and under normal-phase as well as under reversed-phase mode (pure MeOH, temperature 5 degrees C) for Chiralpak OT(+). Almost all compounds were resolved either on Chiralcel OD-H or on Chiralpak OT(+), in some cases on both. The use of trifluoroacetic acid (TFA), as modifier of the hexanic mobile phase, had a beneficial effect on the enantioseparation of some polar and acidic compounds on Chiralcel OD-H. The influence of small chemical structural modifications of the analytes on the enantioseparation behavior is discussed. A structure-retention relationship has been observed on both stationary phases. This chromatographic evaluation may provide some information about the chiral recognition mechanism: in the case of Chiralcel OD-H, hydrogen bonding, pi-pi and distereoselective repulsive are supposed to be the major analyte-CSP interactions. In the case of Chiralpak OT(+), a reversed-phase enantioseparation could take place through hydrophobic interactions between the aromatic moiety of the analytes and the chiral propeller structure of the CSP. The synthesis of some unknown racemic bromobenzobicyclo[2.2.1] analytes is also described.     

中国梅花草属植物的叶表皮特征及其系统学意义

利用光学显微镜和扫描电镜对梅花草属Parnassia 30种植物的叶表皮进行了观察。结果表明:气孔器普遍存在于叶的下表皮,少数种的上表皮也有分布,均为无规则型。叶表皮细胞形状为多边形或不规则形;垂周壁式样可区分为近平直、浅波状和波状。在扫描电镜下,叶表皮气孔器外拱盖内缘为近平滑、浅波状或波状;一些种的保卫细胞两端有加厚;角质膜条纹状,有的条纹隆起,有的条纹上附有颗粒或小孔穴。气孔器类型及下表皮细胞形状的一致性表明梅花草属是一个自然分类群;sect. Saxifragastrum叶表皮特征具有多样性显示该组可能是一个复合群;突隔梅花草P. delavayi属于subsect. Xiphosandra,其气孔下陷,与其细胞学特征相似,支持独立为一组;此外,气孔器的分布、保卫细胞两端加厚、气孔器外拱盖内缘形态以及角质膜等特征对该属部分种的区分有一定的参考价值。     

Spore diffusate isolated from some strains of Aspergillus fumigatus inhibits phagocytosis by murine alveolar macrophages

Aspergillus fumigatus is a ubiquitous fungus that grows in decaying organic matter. It can cause disease in both immunodeficient and immunocompetent patients by using virulence factors to escape the host defenses. Some of these factors, such as a diffusate, released from the spores of A. fumigatus, have previously been described. This diffusate was demonstrated to inhibit oxidative burst and phagocytosis of coated red blood cells. The present study has shown that this substance can inhibit the phagocytosis of A. fumigatus spores by murine alveolar macrophages (MALU) and evaluated the action of this substance. We quantified phagocytosis by MALU cells with and without diffusate and evaluated the inhibition of phagocytosis by testing diffusates from different strains. We conclude that the spore diffusate of some strains of A. fumigatus can reversibly decrease the ability of alveolar macrophages to ingest A. fumigatus spores.     

Drug resistance in the sexually transmitted protozoan Trichomonas vaginalis

Trichomoniasis is the most common, sexually transmitted infection.It is caused by the flagellated protozoan parasite Trichomonas vagina/is. Symptoms include vaginitis and infections have been associatedwith preterm delivery, low birth weight and increased infant mortality, as well as predisposing to HIV/AIDSand cervical cancer. Trichomoniasis has the highest prevalence and incidence of any sexually transmitted infection. The 5-nitroimidazole drugs, of which metronidazole is the most prescribed, are the only approved,effective drugs to treat trichomoniasis. Resistance against metronidazole is frequently reported and cross-resistance among the family of 5-nitroimidazole drugs is common, leaving no alternative for treatment, withsome cases remaining unresolved. The mechanism of metronidazole resistance in T. Vagina/is from treatment failures is not well understood, unlike resistance which is developed in the laboratory under increasingmet ronidazole pressure. In the latter situation, hydrog enosomal function which is involved in activationof the prodrug, metronidazole, is down-regulated. Reversion to sensitivity is incomplete after removal ofdrug pressure in the highly resistant parasites while clinically resistant strains, so far analysed, maintaintheir resistance levels in the absence of drug pressure. Although anaerobic resistance has been regarded asa laboratory induced phenomenon, it clearly has been demonstrated in clinical isolates. Pursuit of both approaches will allow dissection of the underlying mechanisms. Many alternative drugs and treatments have been tested in vivo in cases of refractory trichomoniasis, as well as in vitro with some successes including the broad spectrum anti-parasitic drug nitazoxanide. Drug resistance incidence in T. Vagina/is appears to be on the increase and improved surveillance of treatment failures is urged.     

Determination of kinetic parameters from chemical relaxation data discrimination between coupled two-step binding reactions differing in stoichiometry

The chemical relaxation times of two different two-step equilibrium reactions, characterized by a 1:1 binding process followed by a subsequent rearrangement step and a stepwise 1:2 binding reaction, are analyzed for the purpose of qualitative model discrimination and quantitative determination of kinetic parameters. The equations describing the dependences of the two reciprocal relaxation times on suitable concentrations are given for both models in the general case as well as for four different limiting situations which are characterized by well separated relaxation times. The conditions corresponding to the limiting cases are expressed in terms of strong, weak and no coupling between the two partial equilibrium steps involved in both models. The coupling strength depends on the rate constants as well as on the total concentrations of the reactants. Criteria to discriminate between these two reaction models under defined limiting conditions are developed. In the general case, the product of both reciprocal relaxation times can be used to distinguish both models. If only one relaxation time can be resolved experimentally, it is possible under conditions described to determine only a reduced set of individual rate constants for most of the limiting cases considered. If both relaxation times are observed, all rate constants are determinable in the general case as well as in most of the limiting cases discussed.     

A comparison of direct infusion MS and GC-MS for metabolic footprinting of yeast mutants

Recent technical advances in mass spectrometry (MS) have propelled this technology to the forefront of methods employed in metabolome analysis. Here, we compare two distinct analytical approaches based on MS for their potential in revealing specific metabolic footprints of yeast single-deletion mutants. Filtered fermentation broth samples were analyzed by GC-MS and direct infusion ESI-MS. The potential of both methods in producing specific and, therefore, discriminant metabolite profiles was evaluated using samples from several yeast deletion mutants grown in batch-culture conditions with glucose as the carbon source. The mutants evaluated were cat8, gln3, ino2, opi1, and nil1, all with deletion of genes involved in nutrient sensing and regulation. From the analysis, we found that both methods can be used to classify mutants, but the classification depends on which metabolites are measured. Thus, the GC-MS method is good for classification of mutants with altered nitrogen regulation as it primarily measures amino acids, whereas this method cannot classify mutants involved in regulation of phospholipids metabolism as well as the direct infusion MS (DI-MS) method. From the analysis, we find that it is possible to discriminate the mutants in both the exponential and stationary growth phase, but the data from the exponential growth phase provide more physiological relevant information. Based on the data, we identified metabolites that are primarily involved in discrimination of the different mutants, and hereby providing a link between high-throughput metabolome analysis, strain classification, and physiology.     

Experimental design issues for the early detection of disease: novel designs

This paper investigates two experimental designs which have been used to evaluate the benefit of the early detection of breast cancer. They have some advantages over a classical design (the screening program versus usual medical care) in that subjects in a control group may benefit by participating in the study. We refer to the two experimental designs as the up-front (UFD) and close-out (COD) designs. The UFD consists of offering an initial exam to all participants. Then they can be randomized to a usual care group or a screening group receiving one or more special examinations. If the outcome of the initial examination is included in the analysis, then the study can answer the question of the benefit of an additional screening program after an initial examination. If the analysis excludes all the cases diagnosed at the initial examination, then the analysis evaluates the benefit of a screening program after elimination of the prevalent cases. These prevalent cases are most likely to be affected by length bias sampling and consequently will tend to have less aggressive disease and live longer. As a result, the UFD can answer two scientific questions. The COD consists of randomizing subjects to a usual care group and a screened group. However, the usual care group receives an examination which coincides at the time of the last exam in the study group. In this paper the power of these two designs have been evaluated. In both cases the power is severely reduced compared to the usual control group receiving no special exams. The power is a function of the sensitivity of the exam, the number and spacings of the exams given to the screened group as well as the sample size, disease incidence of the population and the survival distribution. The theoretical results on power are applied to the Canadian National Breast Cancer Study (ages 40-49) which used an UFD and the Stockholm Mammography Breast Cancer Screening Trial which utilized a COD.     

Have we overestimated the benefit of human(ized) antibodies?

The infusion of animal-derived antibodies has been known for some time to trigger the generation of antibodies directed at the foreign protein as well as adverse events including cytokine release syndrome. These immunological phenomena drove the development of humanized and fully human monoclonal antibodies. The ability to generate human(ized) antibodies has been both a blessing and a curse. While incremental gains in the clinical efficacy and safety for some agents have been realized, a positive effect has not been observed for all human(ized) antibodies. Many human(ized) antibodies trigger the development of anti-drug antibody responses and infusion reactions. The current belief that antibodies need to be human(ized) to have enhanced therapeutic utility may slow the development of novel animal-derived monoclonal antibody therapeutics for use in clinical indications. In the case of murine antibodies, greater than 20% induce tolerable/negligible immunogenicity, suggesting that in these cases humanization may not offer significant gains in therapeutic utility. Furthermore, humanization of some murine antibodies may reduce their clinical effectiveness. The available data suggest that the utility of human(ized) antibodies needs to be evaluated on a case-by-case basis, taking a cost-benefit approach, taking both biochemical characteristics and the targeted therapeutic indication into account.Key words: immunogenicity, human anti-mouse antibody, cytokine release syndrome