A network of genes and proteins extends through the scientific literature, touching on phenotypes, pathologies and gene function. We report the development of an information system that provides this network as a natural way of accessing the more than ten million abstracts in PubMed. By using genes and proteins as hyperlinks between sentences and abstracts, we convert the information in PubMed into one navigable resource and bring all the advantages of the internet to scientific literature investigation. Moreover, this literature network can be superimposed on experimental interaction data (e.g., yeasttwo hybrid data from Drosophila melanogaster 1 and Caenorhabditis elegans 2 ) to make possible a simultaneous analysis of new and existing knowledge. The network, called Information Hyperlinked over Proteins (iHOP), contains half a million sentences and 30,000 different genes 3 from humans, mice, D. melanogaster, C. elegans, zebrafish, Arabidopsis thaliana, yeast and Escherichia coli.Whereas conventional keyword and related article searches 4 result in long and not always informative lists of abstracts, navigation along the gene network allows for a stepwise and controlled exploration of the information space. Each step through the network produces information about one single gene and its interactions. Exploration of this geneguided information network is intuitive and follows the associative organization of human memory 5 , in which information is retrieved by connecting similar concepts 6 . The precision of gene name and synonym identification in iHOP ranges between 87% and 99% depending on the organism. Because researchers can move in iHOP between sentences taken directly from source abstracts, however, they always retain control over the reliability and relevance of information. This is an advantage over systems that translate the protein network from the literature into graphical representations 7 , because these representations could give a misleading sense of confidence to the users and cloud the relevance of individual associations.The iHOP system shows that distant medical and biological concepts can be related by surprisingly few intermediate genes; the shortest path between any two genes involves, on average, only four steps. We believe that this highly connected network will make human literature research more intuitive and efficient and also create a theoretical basis for the development of new automatic retrieval algorithms.URL. The iHOP server is publicly accessible at

iHOP is freely accessible at http://www.pdg.cnb.uam.es/UniPub/iHOP/

WikiGenes is the first wiki system to combine the collaborative and largely altruistic possibilities of wikis with explicit authorship. In view of the extraordinary success of Wikipedia there remains no doubt about the potential of collaborative publishing, yet its adoption in science has been limited. Here I discuss a dynamic collaborative knowledge base for the life sciences that provides authors with due credit and that can evolve via continual revision and traditional peer review into a rigorous scientific tool.

Pollen tubes are highly polarized tip-growing cells that depend on cytosolic pH gradients for signaling and growth. Autoinhibited plasma membrane proton (H +) ATPases (AHAs) have been proposed to energize pollen tube growth and underlie cell polarity, however, mechanistic evidence for this is lacking. Here we report that the combined loss of AHA6, AHA8, and AHA9 in Arabidopsis thaliana delays pollen germination and causes pollen tube growth defects, leading to drastically reduced fertility. Pollen tubes of aha mutants had reduced extracellular proton (H +) and anion fluxes, reduced cytosolic pH, reduced tip-toshank proton gradients, and defects in actin organization. Furthermore, mutant pollen tubes had less negative membrane potentials, substantiating a mechanistic role for AHAs in pollen tube growth through plasma membrane hyperpolarization. Our findings define AHAs as energy transducers that sustain the ionic circuit defining the spatial and temporal profiles of cytosolic pH, thereby controlling downstream pH-dependent mechanisms essential for pollen tube elongation, and thus plant fertility.

Background: The application of high throughput approaches to the identification of protein interactions has offered for the first time a glimpse of the global interactome of some model organisms. Until now, however, such genome-wide approaches have not been applied to the human proteome.

iHOP provides fast, accurate, comprehensive, and up-to-date summary information on more than 80 000 biological molecules by automatically extracting key sentences from millions of PubMed documents. Its intuitive user interface and navigation scheme have made iHOP extremely successful among biologists, counting more than 500 000 visits per month (iHOP access statistics: http://www.ihop-net.org/UniPub/iHOP/info/logs/). Here we describe a public programmatic API that enables the integration of main iHOP functionalities in bioinformatic programs and workflows.

Standard-Nutzungsbedingungen:Die Dokumente auf EconStor dürfen zu eigenen wissenschaftlichen Zwecken und zum Privatgebrauch gespeichert und kopiert werden.Sie dürfen die Dokumente nicht für öffentliche oder kommerzielle Zwecke vervielfältigen, öffentlich ausstellen, öffentlich zugänglich machen, vertreiben oder anderweitig nutzen.Sofern die Verfasser die Dokumente unter Open-Content-Lizenzen (insbesondere CC-Lizenzen) zur Verfügung gestellt haben sollten, gelten abweichend von diesen Nutzungsbedingungen die in der dort genannten Lizenz gewährten Nutzungsrechte. Terms of use: Documents in AbstractWe explore the scientific potential of virtual worlds for experimental economists. In particular, we report the results of a series of virtual world experiments designed to examine the suitability of (a) users as subjects and (b) the computer interface as an experimental platform. Formal results and informal observations from the sessions are discussed in terms of the methodological opportunities and challenges of virtual experimentation generally.JEL-Classification: C72; C88; C99; Z13

Insufficient intake of zinc and iron from a cereal-based diet is one of the causes of 'hidden hunger' (micronutrient deficiency), which affects some two billion people(1,2). Identifying a limiting factor in the molecular mechanism of zinc loading into seeds is an important step towards determining the genetic basis for variation of grain micronutrient content and developing breeding strategies to improve this trait(3). Nutrients are translocated to developing seeds at a rate that is regulated by transport processes in source leaves, in the phloem vascular pathway, and at seed sinks. Nutrients are released from a symplasmic maternal seed domain into the seed apoplasm surrounding the endosperm and embryo by poorly understood membrane transport processes(4-6). Plants are unique among eukaryotes in having specific P1B-ATPase pumps for the cellular export of zinc(7). In Arabidopsis, we show that two zinc transporting P1B-ATPases actively export zinc from the mother plant to the filial tissues. Mutant plants that lack both zinc pumps accumulate zinc in the seed coat and consequently have vastly reduced amounts of zinc inside the seed. Blockage of zinc transport was observed at both high and low external zinc supplies. The phenotype was determined by the mother plant and is thus due to a lack of zinc pump activity in the seed coat and not in the filial tissues. The finding that P1B-ATPases are one of the limiting factors controlling the amount of zinc inside a seed is an important step towards combating nutritional zinc deficiency worldwide.