Further improvements to a method for analysing stage-frequency data

An iterative procedure for correcting stage-frequency data is described to allow for situations where the period during which a population is sampled begins after some individuals have entered stage 2 or ends before all individuals are dead. The reason for correcting data in this way is to enableKiritani andNakasuji's method for estimating stage-specific survival rates, with extensions proposed byManly (1976, 1977), to be used to analyse the data. The proposed procedure is illustrated on data obtained by sampling a population of the grasshopper Chorthippus brunneus passing through four instar stages to reach the adult stage.     

The data quality foundation in OMNIITOX information system

Extended Summary Goal and Scope  This paper describes the data quality foundation for the OMNIITOX information system, with regard to data quality requirements and maintenance. Main Features  The data quality concept applied in the OMNIITOX project is based on results that are successfully used in other contexts (Fig. 1). Specific data quality requirements have been developed, which are applied in data acquisition and data review. The data quality requirements and quality maintenance is supported by the OMNIITOX concept model, which supplies a common language for the users from the different disciplines. Results and Discussion  The quality requirements and the concept model have been tested during data acquisition for the information system, and have been found to be a successful framework. The results from practical work demonstrate that it is possible to have a common understanding of the concept model and quality requirements. The user's experience the initial phase of learning the concepts and quality requirements as tedious. Nevertheless, experiences show that the users will benefit from the education during the further work. A considerable amount of data has been acquired based on the data quality foundation. Conclusions  The data quality foundation has been a successful framework for managing data quality in the design and establishment of the OMNIITOX information system. The data quality concept, the concept model, and specific quality requirements are applied as quality management tools to find, acquire, document, and interpret the information. Several quality issues deriving from interdisciplinary differences between the different users have been resolved, which facilitates a common understanding and reduces the risk of misinterpretations and misuse of information. Recommendations and Outlook  An important task for the finalization of the OMNIITOX project is to secure the credibility and long-term stability of the information system. The OMNIITOX information system will somewhat have less potential to support the toxicology related assessments in Europe if any of the involved disciplines chooses to reject or not to apply the concept model and the quality requirements.     

The PSI semantic validator: A framework to check MIAPE compliance of proteomics data

The Human Proteome Organization's Proteomics Standards Initiative (PSI) promotes the development of exchange standards to improve data integration and interoperability. PSI specifies the suitable level of detail required when reporting a proteomics experiment (via the Minimum Information About a Proteomics Experiment), and provides extensible markup language (XML) exchange formats and dedicated controlled vocabularies (CVs) that must be combined to generate a standard compliant document. The framework presented here tackles the issue of checking that experimental data reported using a specific format, CVs and public bio‐ontologies (e.g. Gene Ontology, NCBI taxonomy) are compliant with the Minimum Information About a Proteomics Experiment recommendations. The semantic validator not only checks the XML syntax but it also enforces rules regarding the use of an ontology class or CV terms by checking that the terms exist in the resource and that they are used in the correct location of a document. Moreover, this framework is extremely fast, even on sizable data files, and flexible, as it can be adapted to any standard by customizing the parameters it requires: an XML Schema Definition, one or more CVs or ontologies, and a mapping file describing in a formal way how the semantic resources and the format are interrelated. As such, the validator provides a general solution to the common problem in data exchange: how to validate the correct usage of a data standard beyond simple XML Schema Definition validation. The framework source code and its various applications can be found at http://psidev.info/validator .     

Owner controlled data exchange in nutrigenomic collaborations: the NuGO information network

New ‘omics’ technologies are changing nutritional sciences research. They enable to tackle increasingly complex questions but also increase the need for collaboration between research groups. An important challenge for successful collaboration is the management and structured exchange of information that accompanies data-intense technologies. NuGO, the European Nutrigenomics Organization, the major collaborating network in molecular nutritional sciences, is supporting the application of modern information technologies in this area. We have developed and implemented a concept for data management and computing infrastructure that supports collaboration between nutrigenomics researchers. The system fills the gap between “private” storing with occasional file sharing by email and the use of centralized databases. It provides flexible tools to share data, also during experiments, while preserving ownership. The NuGO Information Network is a decentral, distributed system for data exchange based on standard web technology. Secure access to data, maintained by the individual researcher, is enabled by web services based on the the BioMoby framework. A central directory provides information about available web services. The flexibility of the infrastructure allows a wide variety of services for data processing and integration by combining several web services, including public services. Therefore, this integrated information system is suited for other research collaborations.     

Simple device to monitor aerobic biotransformations by in situ 1H-NMR

A simple device for taking in situ proton NMR measurements in ¹H₂O is described. This allows aeration of reactions in a 10 mm diameter NMR tube without modifying the magnet or the probe head. With this device, aerobic biotransformations can be monitored in the NMR-tube placed in the spectrometer. It allows in situ analyses of the transformations, separating the aeration period temporally from the measurement time, not unlike traditional Warburg respiratory experiments. Two reactions determining kinetic and stoichieometric parameters: (i) a biotransformation by a growing Pseudomonas putida culture and (ii) l-phenylalanine oxidation catalysed by l-amino acid oxidase [E.C. 1.4.3.2]; both incubations were contained in the magnet.     

Internal current generation in respiration chambers

A technical device generating a constant and directed current within a sealed respiration chamber is described. It does not involve any external pumps or tubing. This system is easy to handle, and improved the maintenance of rheotactic pelagic species like the Northern krill (Meganyctiphanes norvegica, Crustacea) or small fishes (Gasterosteus aculeatus) under experimental conditions.     

jmzTab: A Java interface to the mzTab data standard

mzTab is the most recent standard format developed by the Proteomics Standards Initiative. mzTab is a flexible tab‐delimited file that can capture identification and quantification results coming from MS‐based proteomics and metabolomics approaches. We here present an open‐source Java application programming interface for mzTab called jmzTab. The software allows the efficient processing of mzTab files, providing read and write capabilities, and is designed to be embedded in other software packages. The second key feature of the jmzTab model is that it provides a flexible framework to maintain the logical integrity between the metadata and the table‐based sections in the mzTab files. In this article, as two example implementations, we also describe two stand‐alone tools that can be used to validate mzTab files and to convert PRIDE XML files to mzTab. The library is freely available at http://mztab.googlecode.com .     

STRUCTURE AND ONTOGENY OF THE STOMATAL COMPLEX IN PINUS STROBUS L. AND PINUS BANKSIANA LAMB.

The morphology of the stomatal complex in Pinus strobus L. and P. banksiana Lamb, is described and it is proposed that the stomatal complex should be considered an eight-celled complex consisting of two guard cells, and two polar, two lateral, and two hypodermal subsidiary cells. An ontogenetic study found these cells closely related developmentally. It was also found that the stomatal complex in these two pines could not readily be classified as haplocheilic because a polar subsidiary cell arises from the same protodermal cell as does the guard cell mother cell. A modification of the classical concept of stomatal development was necessary to describe the stomata as eumesoperigenous.     

Systematics,reproductive isolation and species boundaries in monogonont rotifers

The typological concept of rotifer species and the morphological basis of rotifer systematics is reviewed and alternatives proposed. Occasional sexuality in the cyclical parthenogenetic life cycle of monogononts permits application of the biological species concept to this group. Data from cross-mating experiments with Asplanchna, Brachionus and Epiphanes illustrate the usefulness of reproductive isolation as a criterion for species boundaries. Populations from different geographic regions are often interfertile indicating that rotifer species are genetically integrated over wide areas. The main types of isolating mechanisms operating in monogononts are reviewed. The role of behavioral reproductive isolation in maintaining species boundaries is examined. The use of a mate recognition bioassay which estimates the probability of copulation and quantifies the degree of isolation is described. Recent work of the mechanism of mate recognition is reviewed. It is concluded that the biological species concept is applicable to rotifers and that a more experimental approach to determining species boundaries is both feasible and desirable.     

The fitting of the logistic equation to the rate of increase of population density

Though there are many problems on the usefulness of the logistic curve, it may be necessary to examine before discussing these problems whether or not the actual data fit to the theoretical values. It has been clarified in this paper that the relation between the population density and its rate of increase per individual described by the differential equation (1) is represented by a straight line on a finite difference diagram on which N_i+1−N_i/N_i values are plotted against N_i+1. Utilizing this linear relation we may examine the fittness of the logistic curve to the actual data and when it is fitted we may estimate the parameters of the logistic equation by (5) and (6). The result of the application of this method to the experimental populations of azuki bean weevil indicates that the relation between parent and progeny densities fits well to the logistic type as has been proved byFujita andUtida (1953) who utilized the linear reltion between 1/R+2σ and parent density where R is the apparent rate of reproduction and σ is a constant dependent primarily upon the length of adult life (0≦σ≦1).     

Socio-ecological biotechnology concepts for developing countries

Conclusions The two socio-ecological concepts described will work, of course, also with other microorganisms.Zymomonas mobilis can be replaced by yeast,Rhizopus could be replaced byAspergillus. However, both microorganisms which are presently used can produce by-products that are unsafe for human or animal consumption. It is therefore a microbiological challenge to find further microorganisms to expand the product formation.It should also be realized that the largest renewable resource, cellulose, has not been mentioned in the context of either concept. It is well known that cellulose must eventually be included if research and development can find ways and means to separate lignin from cellulose and convert cellulose to glucose in a similar and as easy a manner as starch (Doelle 1984).In order to be successful, fermentation processes have to be fast and efficient with a low energy input (Doelle 1986a, b; Doelle & Jones 1986). This excludes the traditional microbiological sterilization of substrates, excessive substrate or product inhibitions in any of these processes.A further omission of socio-ecological concepts lies in the fermented food production. It is encouraging to see the realization that fermented foods are mixedculture processes and that it is time to start detailed and extensive investigations into the functioning of such cultures (Doelle 1985; Steinkraus 1987; Okagbu 1988; Odunfa 1988). It is the suggestion of the author to encourage a review on mixed culture with particular emphasis on fermented food production and its waste disposal.     

Hydroid nematophores: morphological,structural, and behavioural variety from old knowledge and new data

There is a rich old literature on nematothecae, which have been described from many species of nine families of thecate hydroids, but detailed knowledge of nematophores is from a very few species. Using both old data and new observations, information was gathered on species belonging to the genera Hydrodendron, Zygophylax, Antennella, Plumularia, Monotheca, Macrorhynchia, Gymnangium, and Thecocarpus. Specimens belonging to five families collected on the coral reefs of Réunion Island (SW Indian Ocean) were observed alive and videotaped to gather information on nematophores. Nematophores are classified and named here as belonging to three types. An amoeboid nematophore of the four plumularid families Kirchenpaueriidae, Halopterididae, Plumulariidae, and Aglaopheniidae usually consists of two parts, which are more separate in aglaophenids than in the others. The cnidostyle (or nematostyle) is fixed, is formed of ectoderm and endoderm, and includes a cluster of large nematocysts at its top. It is inferred to serve in defence because nematocysts inside the nematotheca can be fired when stimulated. The sarcostyle is a mobile amoeboid layer of ectoderm capable of considerable extension; those that are bilobed on top can extend in two directions at a time. The sarcostyle can emit small pseudopods on its edges that phagocytose particles at the surface of the perisarc. Its hypothesized function of cleaning the colony and providing nutrition in the form of small detrital particles and bacteria taken up by phagocytosis remains to be confirmed by experimentation. The cnidostyle-like nematophore of the Campanulinidae, Linolariidae, and Clathrozoidae is a fixed structure formed of a bilayered pedicel ending with a cluster of nematocysts able to fire while still inside the nematotheca, like the cnidostyle part of the amoeboid nematophore. It functions in defence as well. The tentacle-like nematophore of the Haleciidae and Lafoeidae, described here for the first time, is a single very extensible process provided with nematocysts that issue from the nematotheca and formed by a file of endodermal chordal cells surrounded by ectoderm. In halecids, nematocysts are not always gathered on the very top, forming what looks like a strongly capitate tentacle, as was previously thought, but can be more scattered, giving the structure a filiform appearance. This type has active movements, being able to twist and bend in all directions. Its prey capture function has not been demonstrated; a sensory function is more probable. Additional data have to be collected for more species to compare the types with more confidence, but they appear to have different origins for their considerably different morphologies, structures, and behaviour.     

Introducing a method for extracting horizontal migration patterns from data storage tags

While data storage tags typically provide information about depth and temperature, the horizontal position of fish is difficult to obtain. The objective of this study is therefore to introduce a method for reconstructing horizontal migration patterns of fish tagged with DSTs. The method works by: establishing a database on bathymetry and environmental information about the target area, moving a large number of virtual fish between the release and recapture positions using a biased random walk procedure, and then terminate trajectories where the information at position is in disagreement with the tag information. For example a trajectory is terminated if the tag depth is greater than the bottom depth. The method is exemplified with two tag recordings from Northeast Arctic cod (Gadus morhua L.) in the Barents Sea. The results show that termination of impossible trajectories limits the number of potential trajectories between release and recapture positions, and in particular the usage of multiple termination criteria (depth and temperature) proved to be effective in reducing the number of possible trajectories. The method is general, simple to use, and can also be used in combination with geolocation methods.     

A new digital field data collection system for dendrochronology

A wide variety of information or ‘metadata’ is required when undertaking dendrochronological sampling. Traditionally, researchers record observations and measurements on field notebooks and/or paper recording forms, and use digital cameras and hand-held GPS devices to capture images and record locations. In the lab, field notes are often manually entered into spreadsheets or personal databases, which are then sometimes linked to images and GPS waypoints. This process is both time consuming and prone to human and instrument error. Specialised hardware technology exists to marry these data sources, but costs can be prohibitive for small scale operations (>$2000 USD). Such systems often include proprietary software that is tailored to very specific needs and might require a high level of expertise to use. We report on the successful testing and deployment of a dendrochronological field data collection system utilising affordable off-the-shelf devices ($100–300 USD). The method builds upon established open source software that has been widely used in developing countries for public health projects as well as to assist in disaster recovery operations. It includes customisable forms for digital data entry in the field, and a marrying of accurate GPS location with geotagged photographs (with possible extensions to other measuring devices via Bluetooth) into structured data fields that are easy to learn and operate. Digital data collection is less prone to human error and efficiently captures a range of important metadata. In our experience, the hardware proved field worthy in terms of size, ruggedness, and dependability (e.g., battery life). The system integrates directly with the Tellervo software to both create forms and populate the database, providing end users with the ability to tailor the solution to their particular field data collection needs.