GlycoMapsDB: a database of the accessible conformational space of glycosidic linkages

Conformational energy maps of the glycosidic linkages are a valuable resource to gain information about preferred conformations and flexibility of carbohydrates. Here we present GlycoMapsDB, a new database containing more than 2500 calculated conformational maps for a variety of di- to pentasaccharide fragments contained in N- and O-glycans. Oligosaccharides representing branchpoints of N-glycans are included in the set of fragments, thus the influence of neighbouring residues is reflected in the conformational maps. During refinement of new crystal structures, maps contained in GlycoMapsDB can serve as a valuable resource to check whether the torsion values of a glycosidic linkage are located in an ‘allowed’ region similar to the Ramachandran plot analysis for proteins. This might help to improve the structural quality of the glycan data contained in the Protein Data Bank (PDB). A link between GlycoMapsDB and the PDB has been established so that the glycosidic torsions of all glycans contained in the PDB can be retrieved and compared to calculated data. The service is available at

GlycomeDB—a unified database for carbohydrate structures

GlycomeDB integrates the structural and taxonomic data of all major public carbohydrate databases, as well as carbohydrates contained in the Protein Data Bank, which renders the database currently the most comprehensive and unified resource for carbohydrate structures worldwide. GlycomeDB retains the links to the original databases and is updated at weekly intervals with the newest structures available from the source databases. The complete database can be downloaded freely or accessed through a Web-interface (www.glycome-db.org) that provides flexible and powerful search functionalities

Centralized Modularity of N-Linked Glycosylation Pathways in Mammalian Cells

Glycosylation is a highly complex process to produce a diverse repertoire of cellular glycans that are attached to proteins and lipids. Glycans are involved in fundamental biological processes, including protein folding and clearance, cell proliferation and apoptosis, development, immune responses, and pathogenesis. One of the major types of glycans, N-linked glycans, is formed by sequential attachments of monosaccharides to proteins by a limited number of enzymes. Many of these enzymes can accept multiple N-linked glycans as substrates, thereby generating a large number of glycan intermediates and their intermingled pathways. Motivated by the quantitative methods developed in complex network research, we investigated the large-scale organization of such N-linked glycosylation pathways in mammalian cells. The N-linked glycosylation pathways are extremely modular, and are composed of cohesive topological modules that directly branch from a common upstream pathway of glycan synthesis. This unique structural property allows the glycan production between modules to be controlled by the upstream region. Although the enzymes act on multiple glycan substrates, indicating cross-talk between modules, the impact of the cross-talk on the module-specific enhancement of glycan synthesis may be confined within a moderate range by transcription-level control. The findings of the present study provide experimentally-testable predictions for glycosylation processes, and may be applicable to therapeutic glycoprotein engineering

E-government adoption: A cultural comparison

This is the author's accepted manuscript. The final published article is available from the link below. Copyright @ Springer Science + Business Media, LLC 2008.E-government diffusion is an international phenomenon. This study compares e-government adoption in the U.K. to adoption in the U.S. In particular, this study seeks to determine if the same factors are salient in both countries. Several studies have explored citizen acceptance of e-government services in the U.S. However, few studies have explored this phenomenon in the U.K. To identify the similarities and differences between the U.K. and the U.S. a survey is conducted in the U.K. and the findings are compared to the literature that investigates diffusion in the U.S. This study proposes a model of e-government adoption in the U.K. based on salient factors in the U.S. A survey is administered to 260 citizens in London to assess the importance of relative advantage, trust and the digital divide on intention to use e-government. The results of binary logistic regression indicate that there are cultural differences in e-government adoption in the U.K. and the U.S. The results indicate that of the prevailing adoption constructs, relative advantage and trust are pertinent in both the U.S. and the U.K., while ICT adoption barriers such as access and skill may vary by culture. Implications for research and practice are discussed

The phenology of winter rye in Poland: an analysis of long-term experimental data

The study of the phenology of crops, although quite popular, has limitations, mainly because of frequent changes to crop varieties and management practices. Here, we present data on the phenology and yield of winter rye in western Poland collected between 1957 and 2012 from a long-term field experiment. Data were examined for trends through time and compared to climatological factors using regression analysis. Both annual air temperature and precipitation increased during the study period, equivalent to 2 °C and 186 mm, respectively, over the 52-year period for which met data were available. We detected significant delays in sowing date and recently in emergence, but significant advances were apparent in full flowering date equivalent to 4 days/decade. Yield and plant density experienced a step like change in 1986; yield increasing by ca. 70 % and plant density increasing by ca. 50 %, almost coinciding with a similar change in annual mean temperature, but most likely caused by a changed seed rate and use of herbicides. Future climate change is expected to have a greater impact on this crop, but farmers may be able to adapt to these changes by modifying water regimes, using new machinery and sowing new rye varieties

Seasonality of Leaf and Fig Production in Ficus squamosa, a Fig Tree with Seeds Dispersed by Water

The phenology of plants reflects selection generated by seasonal climatic factors and interactions with other plants and animals, within constraints imposed by their phylogenetic history. Fig trees (Ficus) need to produce figs year-round to support their short-lived fig wasp pollinators, but this requirement is partially de-coupled in dioecious species, where female trees only develop seeds, not pollinator offspring. This allows female trees to concentrate seed production at more favorable times of the year. Ficus squamosa is a riparian species whose dispersal is mainly by water, rather than animals. Seeds can float and travel in long distances. We recorded the leaf and reproductive phenology of 174 individuals for three years in Chiang Mai, Northern Thailand. New leaves were produced throughout the year. Fig production occurred year-round, but with large seasonal variations that correlated with temperature and rainfall. Female and male trees initiated maximal fig crops at different times, with production in female trees confined mainly to the rainy season and male figs concentrating fig production in the preceding months, but also often bearing figs continually. Ficus squamosa concentrates seed production by female plants at times when water levels are high, favouring dispersal by water, and asynchronous flowering within male trees allow fig wasps to cycle there, providing them with potential benefits by maintaining pollinators for times when female figs become available to pollinate

Concept drift over geological times : predictive modeling baselines for analyzing the mammalian fossil record

Fossils are the remains organisms from earlier geological periods preserved in sedimentary rock. The global fossil record documents and characterizes the evidence about organisms that existed at different times and places during the Earth's history. One of the major directions in computational analysis of such data is to reconstruct environmental conditions and track climate changes over millions of years. Distribution of fossil animals in space and time make informative features for such modeling, yet concept drift presents one of the main computational challenges. As species continuously go extinct and new species originate, animal communities today are different from the communities of the past, and the communities at different times in the past are different from each other. The fossil record is continuously increasing as new fossils and localities are being discovered, but it is not possible to observe or measure their environmental contexts directly, because the time is gone. Labeled data linking organisms to climate is available only for the present day, where climatic conditions can be measured. The approach is to train models on the present day and use them to predict climatic conditions over the past. But since species representation is continuously changing, transfer learning approaches are needed to make models applicable and climate estimates to be comparable across geological times. Here we discuss predictive modeling settings for such paleoclimate reconstruction from the fossil record. We compare and experimentally analyze three baseline approaches for predictive paleoclimate reconstruction: (1) averaging over habitats of species, (2) using presence-absence of species as features, and (3) using functional characteristics of species communities as features. Our experiments on the present day African data and a case study on the fossil data from the Turkana Basin over the last 7 million of years suggest that presence-absence approaches are the most accurate over short time horizons, while species community approaches, also known as ecometrics, are the most informative over longer time horizons when, due to ongoing evolution, taxonomic relations between the present day and fossil species become more and more uncertain.Peer reviewe

Bioinformatics and molecular modeling in glycobiology

The field of glycobiology is concerned with the study of the structure, properties, and biological functions of the family of biomolecules called carbohydrates. Bioinformatics for glycobiology is a particularly challenging field, because carbohydrates exhibit a high structural diversity and their chains are often branched. Significant improvements in experimental analytical methods over recent years have led to a tremendous increase in the amount of carbohydrate structure data generated. Consequently, the availability of databases and tools to store, retrieve and analyze these data in an efficient way is of fundamental importance to progress in glycobiology. In this review, the various graphical representations and sequence formats of carbohydrates are introduced, and an overview of newly developed databases, the latest developments in sequence alignment and data mining, and tools to support experimental glycan analysis are presented. Finally, the field of structural glycoinformatics and molecular modeling of carbohydrates, glycoproteins, and protein–carbohydrate interaction are reviewed