esyN: Network Building,Sharing and Publishing

The construction and analysis of networks is increasingly widespread in biological research. We have developed esyN (“easy networks”) as a free and open source tool to facilitate the exchange of biological network models between researchers. esyN acts as a searchable database of user-created networks from any field. We have developed a simple companion web tool that enables users to view and edit networks using data from publicly available databases. Both normal interaction networks (graphs) and Petri nets can be created. In addition to its basic tools, esyN contains a number of logical templates that can be used to create models more easily. The ability to use previously published models as building blocks makes esyN a powerful tool for the construction of models and network graphs. Users are able to save their own projects online and share them either publicly or with a list of collaborators. The latter can be given the ability to edit the network themselves, allowing online collaboration on network construction. esyN is designed to facilitate unrestricted exchange of this increasingly important type of biological information. Ultimately, the aim of esyN is to bring the advantages of Open Source software development to the construction of biological networks.     

A Quick Guide for Building a Successful Bioinformatics Community

“Scientific community” refers to a group of people collaborating together on scientific-research-related activities who also share common goals, interests, and values. Such communities play a key role in many bioinformatics activities. Communities may be linked to a specific location or institute, or involve people working at many different institutions and locations. Education and training is typically an important component of these communities, providing a valuable context in which to develop skills and expertise, while also strengthening links and relationships within the community. Scientific communities facilitate: (i) the exchange and development of ideas and expertise; (ii) career development; (iii) coordinated funding activities; (iv) interactions and engagement with professionals from other fields; and (v) other activities beneficial to individual participants, communities, and the scientific field as a whole. It is thus beneficial at many different levels to understand the general features of successful, high-impact bioinformatics communities; how individual participants can contribute to the success of these communities; and the role of education and training within these communities. We present here a quick guide to building and maintaining a successful, high-impact bioinformatics community, along with an overview of the general benefits of participating in such communities. This article grew out of contributions made by organizers, presenters, panelists, and other participants of the ISMB/ECCB 2013 workshop “The ‘How To Guide’ for Establishing a Successful Bioinformatics Network” at the 21st Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and the 12th European Conference on Computational Biology (ECCB).     

The NIDDK Information Network: A Community Portal for Finding Data,Materials, and Tools for Researchers Studying Diabetes,Digestive, and Kidney Diseases

The NIDDK Information Network (dkNET; http://dknet.org) was launched to serve the needs of basic and clinical investigators in metabolic, digestive and kidney disease by facilitating access to research resources that advance the mission of the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK). By research resources, we mean the multitude of data, software tools, materials, services, projects and organizations available to researchers in the public domain. Most of these are accessed via web-accessible databases or web portals, each developed, designed and maintained by numerous different projects, organizations and individuals. While many of the large government funded databases, maintained by agencies such as European Bioinformatics Institute and the National Center for Biotechnology Information, are well known to researchers, many more that have been developed by and for the biomedical research community are unknown or underutilized. At least part of the problem is the nature of dynamic databases, which are considered part of the “hidden” web, that is, content that is not easily accessed by search engines. dkNET was created specifically to address the challenge of connecting researchers to research resources via these types of community databases and web portals. dkNET functions as a “search engine for data”, searching across millions of database records contained in hundreds of biomedical databases developed and maintained by independent projects around the world. A primary focus of dkNET are centers and projects specifically created to provide high quality data and resources to NIDDK researchers. Through the novel data ingest process used in dkNET, additional data sources can easily be incorporated, allowing it to scale with the growth of digital data and the needs of the dkNET community. Here, we provide an overview of the dkNET portal and its functions. We show how dkNET can be used to address a variety of use cases that involve searching for research resources.     

Mother-infant spatial relationships in domestic goats

This study focused on spatial relationships between female domestic goats and their kids from birth to 15 weeks of age. Results indicate that goat mothers are primarily responsible for the initiation and maintenance of mother-infant contact only during the first week following parturition. A shift to infant responsibility for mother-infant proximity was seen during Week 2, and kids remained primarily responsible throughout all subsequent weeks of observation. Mothers and their young spent most of their time more than 10 mother-lengths from each other during the course of the study; this lack of close physical proximity was particularly evident during the infant's first 6–8 weeks following birth. Thereafter, kids exhibited significant increases in the amount of time spent in close proximity to their dams. This general trend in the development of mother-infant spatial relationships in domestic goats is similar to those reported for other “hider” ungulates, and confirms that the domestic goat has a “hider” rather than a “follower” type of mother-infant relationship.     

Growth control in HeLa cells by serum and anchorage

HeLa-S3 cells in suspension cultures arrest in the G1(G0) phase of the cell cycle because DNA synthesis is controlled by serum factor(s). In monolayer cultures of identical cells DNA synthesis is constitutive, i.e. independent of external signals, and cells grow without restraint. These cells reversibly display “normal” or “transformed” properties depending on the culture conditions.     

Base Compositional Bias and Phylogenetic Analyses: A Test of the “Flying DNA” Hypothesis

Phylogenetic methods can produce biased estimates of phylogeny when base composition varies along different lineages. Pettigrew (1994,Curr. Biol.4:277–280) has suggested that base composition bias is responsible for the apparent support for the monophyly of bats (Chiroptera: megabats and microbats) from several different nuclear and mitochondrial genes. Pettigrew's “flying DNA” hypothesis makes several predictions: (1) that metabolic constraints associated with flying result in elevated levels of adenine and thymine throughout the genome of both megabats and microbats, (2) that the resulting base compositional bias in bats is sufficient to mislead phylogenetic methods and account for the support for bat monophyly from several nuclear and mitochondrial genes, and (3) that phylogenetic analysis using pairwise distances corrected for compositional bias should eliminate the support for bat monophyly. We tested these predictions by analyzing DNA sequences from two nuclear and three mitochondrial genes. The predicted base compositional bias does not appear to exist in some of the genes, and in other genes the differences in AT content are very small. Analyses under a wide diversity of criteria and models of evolution, including analyses that take base composition into account (using log-determinant distances), all strongly support bat monophyly. Moreover, simulation analyses indicate that even extreme bias toward AT-base composition in bats would be insufficient to explain the observed levels of support for bat monophyly. These analyses provide no support for the “flying DNA” hypothesis, whereas the monophyly of bats appears to be well supported by the DNA sequence data.     

Electrochemistry of some substituted pteridines

Some substituted 4(3H)-pteridones have been investigated by classical polarography, cyclic voltammetry, and controlled potential electrolysis; based on these results, the following reaction path for substituted 2-amino-4(3H)-pteridones seems likely. In neutral and slightly alkaline solution the first step is a reversible two-electron reduction to the unreducible 5,8-dihydro derivative, which tautomerizes into a reducible 7,8-dihydropteridone at a rate depending on the substituents. At a more negative potential the 7,8-dihydro derivative is reduced in a two-electron reaction to the unreducible 5,6,7,8-tetrahydropteridone. This compound can be oxidized in a reversible reaction to a 6,7-dihydropteridone, a “quinonoid” form, which tautomerizes into the 7,8-dihydropteridone. The data from cyclic voltammetry favour the formulation of the “quinonoid” form as the 6,7-dihydropteridone, an “o-quinonoid” structure.     

Comparison of the Antimicrobial Adhesion Potential of Human Body Fluid Glycoconjugates Using Fucose-Binding Lectin (PA-IIL) of Pseudomonas aeruginosa and Ulex europaeus Lectin (UEA-I)

Pseudomonas aeruginosa produces a fucose-binding lectin (PA-IIL) which strongly binds to human cells. This lectin was shown to be highly sensitive to inhibition by fucose-bearing human milk glycoproteins. Since the glycans of these glycoproteins mimic human cell receptors, they may function as decoys in blocking lectin-dependent pathogen adhesion to the host cells. Human saliva and seminal fluid also contain such compounds, and body fluids of individuals who are “secretors” express additional fucosylated (alpha 1,2) residues. The latter are selectively detected by Ulex europaeus lectin UEA-I. The aim of the present research was to compare the PA-IIL and UEA-I interactions with human salivas and seminal fluids of “secretors” and “nonsecretors” with those obtained with the respective milks. Using hemagglutination inhibition and Western blot analyses, we showed that PA-IIL interactions with the saliva and seminal fluid glycoproteins were somewhat weaker than those obtained with the milk and that “nonsecretor” body fluids were not less efficient than those of “secretors” in PA-IIL blocking. UEA-I, which interacted only with the “secretors” glycoproteins, was most sensitive to those of the seminal fluids.     

Tainted Blood and Vengeful Spirits: The Legacy of Japan’s Yakugai Eizu (AIDS) Trial

Medical anthropologists often point to the importance of “illness narratives” as emergent or incipient forms in which patients attempt to make sense of the moral dimensions of illness and suffering (Kleinman 1988; Mattingly 1998). In this article I draw upon published accounts, newspapers, and legal documents, supplemented by ethnographic interviews carried out from 1999 to 2001, to show how plaintiffs in the yakugai AIDS trials brought by HIV-infected hemophiliacs against the Japanese government and the pharmaceutical industries that sold them tainted blood products appropriated powerful cultural themes in producing narrative accounts of their suffering. These narratives resonate with themes of lost trust, filial piety, and the desire for a “good death.” In contrast, I show how the neat and tidy narrative that emerged in the course of the yakugai AIDS trial served to impose meaning upon the plaintiffs’ unruly experiences such that, when it was over, the Japanese public was convinced that the “AIDS problem” had been “solved.”     

Privacy Risks from Genomic Data-Sharing Beacons

The human genetics community needs robust protocols that enable secure sharing of genomic data from participants in genetic research. Beacons are web servers that answer allele-presence queries—such as “Do you have a genome that has a specific nucleotide (e.g., A) at a specific genomic position (e.g., position 11,272 on chromosome 1)?”—with either “yes” or “no.” Here, we show that individuals in a beacon are susceptible to re-identification even if the only data shared include presence or absence information about alleles in a beacon. Specifically, we propose a likelihood-ratio test of whether a given individual is present in a given genetic beacon. Our test is not dependent on allele frequencies and is the most powerful test for a specified false-positive rate. Through simulations, we showed that in a beacon with 1,000 individuals, re-identification is possible with just 5,000 queries. Relatives can also be identified in the beacon. Re-identification is possible even in the presence of sequencing errors and variant-calling differences. In a beacon constructed with 65 European individuals from the 1000 Genomes Project, we demonstrated that it is possible to detect membership in the beacon with just 250 SNPs. With just 1,000 SNP queries, we were able to detect the presence of an individual genome from the Personal Genome Project in an existing beacon. Our results show that beacons can disclose membership and implied phenotypic information about participants and do not protect privacy a priori. We discuss risk mitigation through policies and standards such as not allowing anonymous pings of genetic beacons and requiring minimum beacon sizes.     

Impact of herbal medicines on physical impairment

The usefulness of recording physical impairment during intervention studies in chronic low back patients has been questioned. A re-analysis of all of our studies investigating aqueous extracts of Harpagophytum procumbens and a proprietary ethanolic Salix extract for chronic non-specific low back pain revealed that the “physical impairment” component of the Arhus low back pain index changed very little during treatment despite appreciable changes in the other two components, “pain” and “disability”, over time. For comparison, we also extracted data from the literature on the topical use of capsaicin, which showed the same thing. There may be little to lose from omitting the time-consuming assessments of “physical impairment” in studies of the (primarily analgesic) effectiveness of herbal preparations.     

The use of precision dendrometers in research on daily stem size and wood property variation: A review

Dendrometers are instruments which are used to measure the diameters of trees. This review considers the use of dendrometers with high spatial and temporal precision in past and present research, the value of which is increasingly being realised. Various insights into tree growth and physiology can be obtained using high-resolution dendrometers, including the assessment of stem daily water status and the understanding of short-term growth responses to changing environmental conditions. This kind of data is useful for irrigation scheduling, assessing site quality, and developing models of the main drivers of tree growth at sub-diurnal resolution. A third, more novel application is the potential these instruments provide as a “template” that relates temporal measurement of growth to spatial measurements of wood properties. Accordingly, this kind of “re-scaled” data is useful in linking environmental conditions which prevailed as the wood formed to varying wood properties along a pith-to-bark wood profile of the sort generated by systems like CSIRO's SilviScan™. This can provide valuable insights into how tree ring structure and radially varying wood properties represent past climates. The development of dendrometers, their use in these three main areas, and a systematic approach to growth-wood property rescaling is discussed in this review.     

Evolution of eye development in arthropods: phylogenetic aspects

The architecture of the adult arthropod visual system for many decades has contributed important character sets that are useful for reconstructing the phylogenetic relationships within this group. In the current paper we explore whether aspects of eye development can also contribute new arguments to the discussion of arthropod phylogeny. We review the current knowledge on eye formation in Trilobita, Xiphosura, Myriapoda, Hexapoda, and Crustacea. All euarthropod taxa share the motif of a proliferation zone at the side of the developing eye field that contributes new eye elements. Two major variations of this common motif can be distinguished: 1. The “row by row type” of Trilobita, Xiphosura, and Diplopoda. In this type, the proliferation zone at the side of the eye field generates new single, large elements with a high and variable cell number, which are added to the side of the eye and extend rows of existing eye elements. Cell proliferation, differentiation and ommatidial assembly seem to be separated in time but spatially confined within the precursors of the optic units which grow continuously once they are formed (intercalary growth). 2. The “morphogenetic front type” of eye formation in Crustacea + Hexapoda (Tetraconata). In this type, there is a clear temporal and spatial separation of the formation and differentiation processes. Proliferation and the initial steps of pattern formation take place in linear and parallel mitotic and morphogenetic fronts (the mitotic waves and the morphogenetic furrow/transition zone) and numerous but small new elements with a strictly fixed set of cells are added to the eye field. In Tetraconata, once formed, the individual ommatidia do not grow any more. Scutigeromorph chilopods take an intermediate position between these two major types. We suggest that the “row by row type” as seen in Trilobita, Xiphosura and Diplopoda represents the plesiomorphic developmental mode of eye formation from the euarthropod ground pattern whereas the “morphogenetic front type” is apomorphic for the Tetraconata. Our data are discussed with regard to two competing hypotheses on arthropod phylogeny, the “Tracheata” versus “Tetraconata” concept. The modes of eye development in Myriapoda is more parsimonious to explain in the Tetraconata hypothesis so that our data raise the possibility that myriapod eyes may not be secondarily reconstructed insect eyes as the prevailing hypothesis suggests.     

Crystalline inclusions in hepatocytes and associated interhepatocytic macrophages from female Ohrid trout (Salmo letnica Kar.)

When characterizing the liver ultrastructure in Ohrid trout, we noticed that cells often displayed unusual cytoplasmic crystalline inclusions. Their morphology varied much, concerning the size, shape and electron density, showing aspects never reported in fish liver. In hepatocytes, the inclusions existed in close topographical relationship with dense bodies (often within them). Such “crystals” inclusions also existed in macrophages and in biliary passages lumina. Data revealed seasonal/breeding-related changes of the dense bodies and crystalline inclusions within hepatocytes; decreasing from the earliest to the more advanced ovary maturation stages. Additionally, based on the negative correlations between the amounts of dense bodies and of “crystals” and the ovary somatic ratio, we suggested there might be connections between the sex steroids status and the inclusions formation. A positive correlation between the quantities of “crystals” and of dense bodies further suggested that the inclusions might derive from normal processes, e.g., the females’ cyclic liver changes, that involves dense bodies’ turnover. However, a toxicological aetiology cannot be excluded. Additionally, multiple mechanisms can contribute to the “crystals” genesis. Facing literature reports and because the inclusions content seemed washed out during tissue processing, they are likely lipid in nature, but their exact composition and genesis require further analyses.     

Ecological communities: conceptual problems and definitions

Three major problems with respect to ecological communities are tackled. The first is the problem of ambiguity, i.e. the fact that the term “community” is being used for various kinds of objects at different levels of organisation. We argue that this problem can be resolved by restricting use of the term “community” to sets of co-occurring organisms belonging to a single taxonomic phylum or class (plants, birds, insects, etc.) and by using the term “biocoenosis” for sets of organisms belonging to multiple phyla or classes and comprising the biotic components of ecosystems. We also argue that interaction between organisms is neither a necessary nor a sufficient condition for community membership, or, in other words, that communities may consist of both interacting and non-interacting organisms. The second and third problems are the boundary problem and the problem of heterogeneity, i.e. the fact that communities, as currently defined, most often do not have discrete boundaries and are quite heterogeneous with respect to species composition. We argue that both problems result from the fact that communities are seen as groups of co-occurring populations of species, whereas actually populations of different species rarely if ever co-occur in exactly the same area. These problems can be resolved by redefining communities as particular sets of individuals occurring in the intersection of the areas occupied by different populations of species. In the final section we defend our definition against some potential objections, viz. (1) that it would lead to an excessive number of small communities, especially in species-rich situations, and (2) that, because population boundaries may change all the time, such communities would be very unstable.     

Preface

Since the recent growth of molecular and genetic methods, and their implementation into organismic biology, zoology has been slowly regaining the importance it enjoyed until the late 1970's. Biologists are becoming increasingly aware that dynamic processes between molecules and proteins, the products of expressed genes, are relevant in the context of the whole organism's physiological status and behaviour. This modernization of organismic biology, however, has also resulted in more differentiation and diversity of methods within the disciplines that apply to the animal sciences. This increasing diversity within zoological disciplines was highlighted in the series of lectures held at our annual meeting in Halle in 2002.The highlight of the Halle meeting was undoubtedly the awarding of the Karl von Frisch Prize to F. G. Barth from Vienna University. Since Karl von Frisch's work few have so successfully exemplified the wealth of knowledge and insights that may be gained by applying modern methods, and convergent approaches from different disciplines to one single species. Barth's work focused on the wandering spiders Cupiennius. His lecture, “spider senses – technical perfection and biology” demonstrated to us the scientific power of a holistic approach.In the context of the behavioural studies of our colleagues at Halle University, Charlotte Helfrich-Förster presented a survey of “The circadian system of Drosphila melanogaster and its light input pattern”. Behavioural research on rhythms has its roots in Germany and enjoys a long tradition in zoology. As in many other disciplines, modern genetics opened up new and very fruitful insights into the subject.A greater understanding of the mechanisms of learning and memory is another field of research that has benefitted greatly from molecular biology. It has become a flourishing and expanding area of research, especially in invertebrate zoology. The current state of research, from a neurobiological and molecular point of view, was presented in three lectures, including one by Uli Müller, of the Berlin School. Cognition in audition, a still emerging field, was introduced to us in Bernhard Gaese's lecture on “Precognitive and cognitive elements in sound localization”. In the future, auditory cognition will surely become a Dorado for neurobiologists and acoustic psychologists. Susan D. Healy connected cognition with ecological constraints in her talk “Animal learning and memory: an integration of cognition and ecology”. She argued that cognitive performances can only be explained in the context of species-specific behaviours and ecology. “Cognitive ecology”, as it may be termed, is an emerging and genuinely zoological field of research that will have an important impact on our understanding of evolution. It's challenges will require highly motivated young zoologists.Research on species diversity takes a different approach to the subject of evolution and diversity, investigating the preconditions for speciation processes, and evolutionary trends and mechanisms. Unfortunately the fauna of soils is rarely considered, in spite of its great importance to ecological conditions. Richard Bagdett made up for this neglect in his lecture on the “Causes and consequences of biological diversity in soil”, and Bernhard Misof reported on speciation processes in Anisoptera.“Classical” physiology is still the backbone of organismic research. Modern versions of two very different topics were presented in Halle. Stephan Huber reported on the “Development of renal function”, and Fritz-Olaf Lehmann presented a new and convincing concept of aerodynamics and energetics in insect flight. His research continues the worthwhile tradition of flight analysis founded by Werner Nachtigall.The topics of our annual meeting in Halle could hardly have been more diverse. However, it is this the very diversity of modern and productive research field in zoology that characterizes a promising and fascinating future. In zoology, more than in any other biological discipline, exciting problems relevant to the understanding of evolution and its mechanisms are waiting to be solved by young scientists. Zoology has again become a start-up enterprise with promising rewards.     

Protein analysis of dwarfed transgenic rice plants overexpressing GA2-oxidase gene

Using 2-D electrophoresis, we analyzed proteins from transgenic rice overexpressing gibberellin acid (GA) catabolic enzyme, GA2-oxidase. These results indicate eight specific proteins differentially expressed in the transformed rice stems of T₁ generation, but non in case of T₂ generation. Proteins isolated from different stages of leaves of T₁ generation showed no significant differences, except one-month-old leaf, where five differentially expressed proteins are visible.This work was supported in part by a research project of an Identification and Analysis of Proteins for Gene Discovery and Elucidation of Functions of Useful Genes in Rice Genome from Ministry of Agriculture, Forestry and Fisheries, and also supported by a part of grant from the Program of Basic Research Activities for Innovative Biosciences. Martin Hajduch was supported by European Commission’s specific research and technological development program “Confirming the International Role of Community Research” 1998-2002 (EU Fellowship to Japan). The authors are solely responsible for the content of this paper and it does not represent the opinion of the Community, and the Community is not responsible for any of use that might be made of date appearing herein.     

The stochastic community and the logistic-J distribution

A new formal model called the multispecies logistical (MSL) system produces species/abundance distributions that are compared statistically with those found in natural communities. The system, which is able to handle thousands of individuals from hundreds of species, iteratively selects random pairs of individuals and transfers a unit of biomass (or energy) between the respective species. Several elaborations of the model, including those with trophic compartments, appear to produce the same distribution. The theoretical distribution underlying the MSL system is a hyperbolic section, here called the logistic-J distribution. In the study reported here, the logistic-J distribution has been fitted to the species-abundance histograms of 125 randomly selected taxocoenoses. Since the overall chi square score of the logistic-J achieved near-optimality in this study, it cannot be distinguished statistically from the J-curves observed by field biologists. For comparison, the log-series distribution was given the same test and scored significantly higher (more poorly) than the mean logistic-J score. If there is a single, major distribution underlying natural communities, it is not the log-series distribution. Nor, owing to a mathematical error in its formulation, can it be the lognormal distribution. In the MSL system each species follows a “stochastic orbit” about the mean abundance producing, in consequence, the logistic-J distribution. Such orbits are produced by any system in which the probabilities of reproduction and death are approximately equal. Accordingly, the “stochastic communities hypothesis” is proposed here as the overall mechanism governing abundances in all natural communities. It is not a single mechanism, per se, but the net effect of all environmental influences.