Bioconversion of arachidonic acid in the human gastrointestinal tract

The data presented demonstrate that the bioconversion of [14C]arachidonic acid in homogenates like these is very easily influenced by protein (enzyme) and substrate concentration as well as exogenous cofactors. This is not unexpected but variations will lead to artifactual differences. Neither quantitative nor qualitative differences could be detected between biopsies taken from healthy as compared to diseased individuals. No products other than PGE2, PGF2 alpha, TxB2, and 6-keto-PGF1 alpha (and metabolites thereof) could be demonstrated although special efforts were undertaken to determine whether there was any detectable lipoxygenase activity. Therefore it seems that future studies on the possible roles of prostaglandins in gastrointestinal physiology should be restricted to those compounds identified, primarily PGE2 and PGF2 alpha. The monotony in the pattern of products formed in homogenates from different tissues also suggests that in order to be able to detect possible differences between various conditions such studies should involve a minimum of tissue manipulation.     

On the mechanism of amylose branching by potato Q-enzyme.

1. When potato Q-enzyme converts amylose into an amylopectin-like molecule, the action is by a random, endo-type transglycosylation of the substrate chains. 2. Inter-chain transfer takes place during the formation of the amylopectin branch linkage. This is seen in experiments in which radioactive label was transferred between substrates of disparate molecular weight. Intra-chain transfer, leading to the formation of a branch linkage, is not excluded by these experiments. 3. The minimum length of amylose chain that can act as an acceptor in the transglycosylation reaction, under the experimental conditions described, is greater than 40 glucose units. 4. The requirement of Q-enzyme for substrate chains at least 40 glucose units in length is interpreted as meaning that a stabilized secondary and tertiary structure must be established in the substrate before it can be utilized by Q-enzyme, and that the forces that provide such conformation are sufficiently strong only when the chains are longer than the minimum. Inter-chain transfer is seen as taking place by one of two mechanisms. The first involved the reaction of the enzyme with a chain that has a stabilized (helical?) conformation. An enzyme-donor chain intermediate is formed, that then reacts with an acceptor chain to complete the transglycosylation. The second mechanism envisages the substrate for the enzyme as being a complex formed between two chains (a double helix?). The enzyme encounters the complex and carries out an inter-chain transglycosylation reactions.     

A note on the false discovery rate and inconsistent comparisons between experiments

MOTIVATION: The false discovery rate (FDR) has been widely adopted to address the multiple comparisons issue in high-throughput experiments such as microarray gene-expression studies. However, while the FDR is quite useful as an approach to limit false discoveries within a single experiment, like other multiple comparison corrections it may be an inappropriate way to compare results across experiments. This article uses several examples based on gene-expression data to demonstrate the potential misinterpretations that can arise from using FDR to compare across experiments. Researchers should be aware of these pitfalls and wary of using FDR to compare experimental results. FDR should be augmented with other measures such as p-values and expression ratios. It is worth including standard error and variance information for meta-analyses and, if possible, the raw data for re-analyses. This is especially important for high-throughput studies because data are often re-used for different objectives, including comparing common elements across many experiments. No single error rate or data summary may be appropriate for all of the different objectives.     

Heat inactivation data for Mycobacterium avium subsp. paratuberculosis: implications for interpretation

AIMS: We discuss several factors that are critical for heat inactivation experiments and which should be taken into account for future research. METHODS AND RESULTS: On the basis of examples from the literature we discuss critical factors influencing the calculated heat inactivation of Mycobacterium avium subsp. paratuberculosis (MAP). Furthermore, using a modelling approach, we show that tailing of the inactivation curve of MAP is caused by the presence of cell clumps and not by a more heat-resistant cell fraction. CONCLUSIONS: The experimental conditions of the MAP heat inactivation studies of different research groups vary significantly and lead to considerable differences in results and conclusions. Therefore, a more consensual approach should be employed in future studies. In addition, our model on clumping of MAP can be used to predict the decimal reduction of MAP during heat treatment and to study the effect of clumping on other lethal effects. SIGNIFICANCE AND IMPACT OF THE STUDY: We discuss several factors that should be carefully considered in heat resistance experiments. This is essential for a thorough interpretation of results from experiments and should be given proper attention in future experiments and publications on this topic.     

古代DNA研究实验技术

现代分子生物技术的发展,使从古代样品中获取微量DNA成为现实。在过去的十多年里,古DNA研究取得了重大进展,但实验方案还需要加以改进,其结果的分析与推论也需要多方面的验证。本综述着重介绍了古DNA研究的实验技术及可靠性分析。 Experimental Techniques for Ancient DNA Research YANG Shu-juan1,LAI Xu-long1,2,TANG Xian-hua1,SHENG Gui-lian1,2 1.Faculty of Earth Sciences,China University of Geosciences,Wuhan,430074,China; 2.Institute of Life Sciences,China University of Geosciences,Wuhan,430074,China Abstract:The development of modern molecular biological techniques makes it possible to study minimum DNA from ancient materials.During past decade,a lot of significant achievements on ancient DNA research have been made in many fields especially in molecular evolutionary biology.The nature of degradation and contamination of ancient DNA from ancient biological materials pose a dominating problem in ancient DNA research.Therefore,the experiments should be modified based on the modern molecular techniques and more factors should be considered when the results are analyzed.In this paper,authors review the general experimental protocols on sampling,extraction and amplification as well as authenticity of ancient DNA. Key words：ancient DNA;authenticity;ancient DNA techniques     

Controlled One-on-One Encounters between Immune Cells and Microbes Reveal Mechanisms of Phagocytosis

Among many challenges facing the battle against infectious disease, one quandary stands out. On the one hand, it is often unclear how well animal models and cell lines mimic human immune behavior. On the other hand, many core methods of cell and molecular biology cannot be applied to human subjects. For example, the profound susceptibility of neutropenic patients to infection marks neutrophils (the most abundant white blood cells in humans) as vital immune defenders. Yet because these cells cannot be cultured or genetically manipulated, there are gaps in our understanding of the behavior of human neutrophils. Here, we discuss an alternative, interdisciplinary strategy to dissect fundamental mechanisms of immune-cell interactions with bacteria and fungi. We show how biophysical analyses of single-live-cell/single-target encounters are revealing universal principles of immune-cell phagocytosis, while also dispelling misconceptions about the minimum required mechanistic determinants of this process.     

A Role for Ultrasonic Vocalisation in Social Communication and Divergence of Natural Populations of the House Mouse (Mus musculus domesticus)

It has long been known that rodents emit signals in the ultrasonic range, but their role in social communication and mating is still under active exploration. While inbred strains of house mice have emerged as a favourite model to study ultrasonic vocalisation (USV) patterns, studies in wild animals and natural situations are still rare. We focus here on two wild derived mouse populations. We recorded them in dyadic encounters for extended periods of time to assess possible roles of USVs and their divergence between allopatric populations. We have analysed song frequency and duration, as well as spectral features of songs and syllables. We show that the populations have indeed diverged in several of these aspects and that USV patterns emitted in a mating context differ from those emitted in same sex encounters. We find that females vocalize not less, in encounters with another female even more than males. This implies that the current focus of USVs being emitted mainly by males within the mating context needs to be reconsidered. Using a statistical syntax analysis we find complex temporal sequencing patterns that could suggest that the syntax conveys meaningful information to the receivers. We conclude that wild mice use USV for complex social interactions and that USV patterns can diverge fast between populations.     

A double classification tree search algorithm for index SNP selection

Background  

In population-based studies, it is generally recognized that single nucleotide polymorphism (SNP) markers are not independent. Rather, they are carried by haplotypes, groups of SNPs that tend to be coinherited. It is thus possible to choose a much smaller number of SNPs to use as indices for identifying haplotypes or haplotype blocks in genetic association studies. We refer to these characteristic SNPs as index SNPs. In order to reduce costs and work, a minimum number of index SNPs that can distinguish all SNP and haplotype patterns should be chosen. Unfortunately, this is an NP-complete problem, requiring brute force algorithms that are not feasible for large data sets.     

PREDAEA LUCESCENS SP. NOV., A NEW COOL-TEMPERATE AUSTRALIAN SPECIES WITH UNIQUE, UNDIFFERENTIATED NUTRITIVE FILAMENTS

Classical ecological theory predicts that whenever growing individuals share a common and limiting resource, such as substratum in mid-intertidal and shallow subtidal habitats, preemptive competition will occur determining species abundance and distribution patterns. However, conspecificity of several ecologically dominant Rhodophyta may coalesce when grown in laboratory cultures. The extent at which intraspecific coalescence occurs in the field and whether the process may also happens during interspecific encounters remain to be determined. If intra- and interspecific coalescence effectively occurs, then coexistence through coalescence rises as an alternative to competition among red-algal dominated intertidal and shallow subtidal communities. Populations of Mazzaella laminarioides and Nothogenia fastigiata living in mid-intertidal, semi-exposed rocky habitats in Central Chile are being used to test the above ideas. Intra- and interspecific encounters occur in the field throughout the year. Coalescence does occur among conspecific partners but it has not been detected in interspecific encounters. Rather, a thick interface of compressed cells, necrotic tissues and cyanobacterial nodules is formed between the two contacting partners. In addition, observations of laboratory cultures indicate that spore germination, germling survival and differentiation of erect axes in bispecific cultures may be reduced when compared to single-species controls. Interspecific differences in growth and differentiation rates appear as the mechanisms explaining a lack of coalescence and negative effects during interspecific contacts. On the other hand, the existence of conspecific coalescence in the field suggests this process should be considered as a real alternative to intraspecific competition among coalescing Rhodophyta.     

Reduced resource defence in an uncertain world: an experimental test using captive nutmeg mannikins

Recent models of economic defence in a group-foraging context predict that the frequency of aggressive interactions should decline as resource density increases, but empirical studies have provided only equivocal support for this prediction. We suggest that whether or not foragers have information concerning the location of patches will influence both the intensity of aggressive encounters and the effect that changes in food density will have on aggression. The intensity of aggression should be greatest when patch locations are known to all, making resources spatially predictable and the availability of alternatives more certain. When food is hidden, increasing the density of patches should have little effect on aggression levels, mostly as a result of the greater uncertainty about the availability of replacement food patches. To test these predictions, we investigated the effect of patch density on the use of aggressive behaviour in nutmeg mannikins, Lonchura punctulata, when food patches were either visible (signalled patch location) or hidden (unsignalled patch location) to all foragers. As predicted, we found that the intensity of aggressive encounters was higher when patch location was signalled than when it was not. Moreover, the effect of patch density on aggression depended on whether patch location was signalled or not. When patch location was unknown, the number of aggressive encounters was unaffected by changes in patch density, but when food location was signalled, increasing patch density resulted in the expected decline in the frequency of aggression.     

COALESCENCE VERSUS COMPETITION: FIELD AND LABORATORY STUDIES OF INTRA‐ AND INTERSPECIFIC ENCOUNTERS AMONG COALESCING SEAWEEDS

Classical ecological theory predicts that whenever growing individuals share a common and limiting resource, such as substratum in mid‐intertidal and shallow subtidal habitats, preemptive competition will occur determining species abundance and distribution patterns. However, conspecificity of several ecologically dominant Rhodophyta may coalesce when grown in laboratory cultures. The extent at which intraspecific coalescence occurs in the field and whether the process may also happens during interspecific encounters remain to be determined. If intra‐ and interspecific coalescence effectively occurs, then coexistence through coalescence rises as an alternative to competition among red‐algal dominated intertidal and shallow subtidal communities. Populations of Mazzaella laminarioides and Nothogenia fastigiata living in mid‐intertidal, semi‐exposed rocky habitats in Central Chile are being used to test the above ideas. Intra‐ and interspecific encounters occur in the field throughout the year. Coalescence does occur among conspecific partners but it has not been detected in interspecific encounters. Rather, a thick interface of compressed cells, necrotic tissues and cyanobacterial nodules is formed between the two contacting partners. In addition, observations of laboratory cultures indicate that spore germination, germling survival and differentiation of erect axes in bispecific cultures may be reduced when compared to single‐species controls. Interspecific differences in growth and differentiation rates appear as the mechanisms explaining a lack of coalescence and negative effects during interspecific contacts. On the other hand, the existence of conspecific coalescence in the field suggests this process should be considered as a real alternative to intraspecific competition among coalescing Rhodophyta.     

Finding the one: optimal choosiness under sequential mate choice

When mates are encountered sequentially, each encounter involves a decision whether to reject the current suitor and risk not finding a better mate, or to accept them despite their flaws. I provide a flexible framework for modelling optimal choosiness when mate encounters occur unpredictably in time. The model allows for temporal variation in the fitness benefits of mating, including seasonal breeding conditions, accrual of mate search costs, survival of the choosing individual or senescence of gametes. The basic optimality framework can be applied iteratively to obtain mate choice equilibria in dynamically evolving populations. My model predicts that individuals should be choosier when the average rate of mate encounters is high, but that choosiness should decline over time as the likelihood of future mate encounters decreases. When mate encounters are uncertain, there is a trade‐off between reproductive timing and mate choice (the ‘when’ and the ‘who’). Mate choice may be selected against when reproductive timing is highly important (e.g. when breeding conditions show a narrow peak in time). This can even lead to step‐shaped mate choice functions, where individuals abruptly switch from rejecting to accepting all suitors as peak breeding conditions approach. The model contributes to our understanding of why individuals may not express mate preferences, even when there is substantial variation in mate quality.     

Tabulation and assessment of 113 human surveillance cytogenetic studies conducted between 1965 and 1984

There is an increasing tendency to monitor human exposure to genotoxic chemicals by the assessment of chromosomal aberrations or sister-chromatid exchanges (SCEs) in peripheral blood lymphocytes. In order to assess the sensitivity of these techniques, and to discern minimal criteria for their conduct, a survey of 113 human lymphocyte cytogenetic surveillance studies conducted between 1965 and 1984 has been undertaken. The present survey indicates the urgent need for standardization of study protocols. It is suggested that a common method of reporting chromosomal aberrations should be adopted, and that this should be based on the system described by Scott et al. It is also suggested that a minimum acceptable size of control and exposed populations should be agreed, and that potentially important factors such as the gender, the period and extent of exposure and individual smoking habits be defined in advance of the commission of future surveillance studies. As general awareness of the possible hazard presented by exposure of man to genotoxic chemicals increases, so appropriate preventative industrial hygiene measures will be instituted. This implies that future human cytogenetic surveillance studies may yield either weakly positive or negative data. This emphasizes the current need for agreement on appropriate study protocols. The formation of a central repository for control databases, and its subsequent updating and use by those involved in human cytogenetic surveillance studies, is recommended. Minimal experimental criteria for the design of future studies are also outlined.     

Discontinuous or semi‐discontinuous DNA replication in Escherichia coli?

The postulate that a stalled/collapsed replication fork will be generated when the replication complex encounters a UV-induced lesion in the template for leading-strand DNA synthesis is based on the model of semi-discontinuous DNA replication. A review of existing data indicates that the semi-discontinuous DNA replication model is supported by data from in vitro studies, while the discontinuous DNA replication model is supported by in vivo studies in Escherichia coli. Until the question of whether DNA replicates discontinuously in one or both strands is clearly resolved, any model building based on either one of the two DNA replication models should be treated with caution.     

How superdiffusion gets arrested: ecological encounters explain shift from Lévy to Brownian movement

Ecological theory uses Brownian motion as a default template for describing ecological movement, despite limited mechanistic underpinning. The generality of Brownian motion has recently been challenged by empirical studies that highlight alternative movement patterns of animals, especially when foraging in resource-poor environments. Yet, empirical studies reveal animals moving in a Brownian fashion when resources are abundant. We demonstrate that Einstein''s original theory of collision-induced Brownian motion in physics provides a parsimonious, mechanistic explanation for these observations. Here, Brownian motion results from frequent encounters between organisms in dense environments. In density-controlled experiments, movement patterns of mussels shifted from Lévy towards Brownian motion with increasing density. When the analysis was restricted to moves not truncated by encounters, this shift did not occur. Using a theoretical argument, we explain that any movement pattern approximates Brownian motion at high-resource densities, provided that movement is interrupted upon encounters. Hence, the observed shift to Brownian motion does not indicate a density-dependent change in movement strategy but rather results from frequent collisions. Our results emphasize the need for a more mechanistic use of Brownian motion in ecology, highlighting that especially in rich environments, Brownian motion emerges from ecological interactions, rather than being a default movement pattern.     

A DIRECT-SPRAY TECHNIQUE FOR THE BIOLOGICAL EVALUATION OF PYRETHRUM-IN-OIL INSECTICIDES FOR USE AGAINST STORED PRODUCT INSECTS IN WAREHOUSES

A direct-spray technique for the biological assay of pyrethrins in Shell oil P31 is described, together with the experiments leading to its adoption. The technique is such that film effects are reduced to the minimum practicable, but it is otherwise as similar as possible to the film technique described by Parkin & Green (1943). Methods for statistical analysis of the results are discussed. For the biological assay of pyrethrins in Shell oil P31, the direct-spray method is slightly superior to Parkin & Green's film method, but both techniques should have their uses in general experimental work.     

The relationship between vegetation density and its protective value depends on the densities and traits of prey and predators

Densities of submerged vegetation and those of associated animals tend to co‐vary. This relationship is often attributed to the positive correlation between the density of vegetation and its protective value against predators. However, two counteracting basic elements underlying this paradigm limit its generality. That is, increasing vegetation density should result in decreased predator–prey encounters, whilst at the same time predator–prey encounters should increase as animal densities increase. These two mechanisms should thus counteract each other when the densities of vegetation and associated animals, including both prey and predators, co‐vary. Experimental designs that expose fixed densities of prey and predators to varying densities of vegetation assess only the former mechanism and may thus not properly evaluate the protective value of vegetation in such conditions. By contrast, designs that mimic the naturally co‐varying organism densities test both mechanisms and thus their counteractive impacts on predator–prey encounters. We compared the outcomes of the two alternative designs and carried out additional experiments to explain the putative discrepancy. Increasing vegetation density (mimics of Potamogeton pectinatus) enhanced prey (Daphnia magna) survival only when fixed densities of prey and predators (Perca fluviatilis or Rutilus rutilus) were used. When the animal densities were allowed to co‐vary with vegetation density, vegetation had no impact on prey survival. Instead, prey survival was determined by the aggregate density of prey and predators, shaped by the species‐specific traits of the latter. Thus, the impact of the increased animal densities overrode the impact of the increased vegetation density on predator–prey encounters. It may be insufficient to attribute the co‐variation of vegetation, prey and predator densities simply to the association between vegetation density and its protective value. Increased food resources and reduced competition within vegetation may promote prey and thereby also predator abundance to a greater extent than previously thought.     

Developmental plasticity and maternal effects of reproductive characteristics in the frog,Bombina orientalis

Summary Life history theory suggests that reproductive characteristics such as ovum size and clutch size should be well buffered against vararies of the environment. However, studies which demonstrate environmental sensitivity of reproductive characteristics are increasing in number, as are studies which find that maternal effects are responsible for much of the variation in developmental and growth rates in embryonic and larval fish and amphibians. The data reported here demonstrate that the environment, in terms of temperature and food availability that a specific individual encounters during vitellogenesis, exerts a strong influence on both egg size and number. Warmer temperatures and less food decrease ovum size, while colder temperatures and less food decrease clutch size. The variation in ovum size that is induced by the environment can exert a strong influence on variation in offspring development and growth and serve as an excellent model for studies on the evolution of developmental plasticity.     

Eye colour and aggression in juvenile guppies, Poecilia reticulata peters (Pisces: Poeciliidae)

A series of four related experiments on guppy, Poecilia reticulata, juveniles indicates that eye colour is related to motivational state. In juveniles of this species two distinct eye colour states are easily discernible, with a transient intermediate state infrequently seen. These states are dark, light, and intermediate. In aggressive interactions involving both both dark- and light-eyed fish, dark-eyed fish won 98.6% of the encounters (N=222 encounters). Eye colours are significantly correlated with bout lengths of certain behaviours (aggressive encounters, swimming, substrate biting); total time spent in certain behaviours (swimming, aggressive encounters); and type and intensity of aggressive encounters. Eye colour appears to be related to motivational state and may serve a signal function.     

Anti-Predator Signals as Advertisements: Evidence in White-Throated Magpie-Jays

Calls and displays elicited by predators usually function as alarms or to inform predators of their detection. However, predator encounters may afford some individuals the opportunity to demonstrate quality or signal their availability. Here, I report on a class of vocal signals produced in predator-elicited displays that share many characteristics with sexually selected song. White-throated magpie-jays ( Calocitta formosa ) display at low-threat predators while producing 'loud display calls' (LDCs). I use this term because the calls occur primarily in two display contexts (see below) though occasionally in other contexts as well. Such calls and displays are primarily produced by males, and also occur in one other context, at dawn. Playback experiments showed that despite being elicited by predators, males were more likely than females to respond to LDCs, and more likely to respond when their mate was fertile. Over 134 different call types were produced in over 200 displays by 34 males; the largest minimum repertoire size was 67. Presentations of taxidermic raptor mounts elicited some LDCs, but fewer calls and lower diversity than at dawn or in predator approach displays. The male bias and high diversity suggest that LDCs are an outcome of intersexual selection, while their elicitation by predators suggests an alarm function. I propose that male magpie-jays use predator encounters as opportunities to advertise their presence and availability as mates; they use LDCs as songs. Such a communication system seems to have been favored by the unusual social system of magpie-jays, in which female groups defend territories and males have little opportunity to defend resources for mate attraction, forcing them to advertise when females are paying the most attention, during predator encounters.