Nematode.net update 2011: addition of data sets and tools featuring next-generation sequencing data

Nematode.net (http://nematode.net) has been a publicly available resource for studying nematodes for over a decade. In the past 3 years, we reorganized Nematode.net to provide more user-friendly navigation through the site, a necessity due to the explosion of data from next-generation sequencing platforms. Organism-centric portals containing dynamically generated data are available for over 56 different nematode species. Next-generation data has been added to the various data-mining portals hosted, including NemaBLAST and NemaBrowse. The NemaPath metabolic pathway viewer builds associations using KOs, rather than ECs to provide more accurate and fine-grained descriptions of proteins. Two new features for data analysis and comparative genomics have been added to the site. NemaSNP enables the user to perform population genetics studies in various nematode populations using next-generation sequencing data. HelmCoP (Helminth Control and Prevention) as an independent component of Nematode.net provides an integrated resource for storage, annotation and comparative genomics of helminth genomes to aid in learning more about nematode genomes, as well as drug, pesticide, vaccine and drug target discovery. With this update, Nematode.net will continue to realize its original goal to disseminate diverse bioinformatic data sets and provide analysis tools to the broad scientific community in a useful and user-friendly manner

Cortical Factor Feedback Model for Cellular Locomotion and Cytofission

Eukaryotic cells can move spontaneously without being guided by external cues. For such spontaneous movements, a variety of different modes have been observed, including the amoeboid-like locomotion with protrusion of multiple pseudopods, the keratocyte-like locomotion with a widely spread lamellipodium, cell division with two daughter cells crawling in opposite directions, and fragmentations of a cell to multiple pieces. Mutagenesis studies have revealed that cells exhibit these modes depending on which genes are deficient, suggesting that seemingly different modes are the manifestation of a common mechanism to regulate cell motion. In this paper, we propose a hypothesis that the positive feedback mechanism working through the inhomogeneous distribution of regulatory proteins underlies this variety of cell locomotion and cytofission. In this hypothesis, a set of regulatory proteins, which we call cortical factors, suppress actin polymerization. These suppressing factors are diluted at the extending front and accumulated at the retracting rear of cell, which establishes a cellular polarity and enhances the cell motility, leading to the further accumulation of cortical factors at the rear. Stochastic simulation of cell movement shows that the positive feedback mechanism of cortical factors stabilizes or destabilizes modes of movement and determines the cell migration pattern. The model predicts that the pattern is selected by changing the rate of formation of the actin-filament network or the threshold to initiate the network formation

The adoption of pottery on Kodiak Island: Insights from organic residue analysis

Pottery technology, originating in Northeast Asia, appeared in Alaska some 2800 years ago. It spread swiftly along Alaska’s coastline but was not adopted on Kodiak Island until around 500 cal BP, as part of the Koniag tradition. While in the southeast pottery was used extensively, people on the northern half of the island did not adopt the technology. What drove these patterns of adoption and non-adoption on Kodiak Island? To better understand the role of ceramic technology in the Koniag tradition we used organic residue analysis to investigate pottery function. Results indicate that pottery was used to process aquatic resources, including anadromous fish, but especially marine species. Based on archaeological and ethnographic data, and spatial analysis of pottery distributions and function, we hypothesize that Koniag pottery was a tool inherent to the rendering of whale oil on the southeast coast of Kodiak Island, supporting previous suggestions by Knecht (1995) and Fitzhugh (2001). When viewed in the broader historical context of major technological and social transformations, we conclude that social identity and cultural boundaries may also have played a role in the delayed and partial adoption of pottery on Kodiak Island

Supply chain management resources, capabilities and execution

This paper identifies inter- and intra-organisational management resources that determine the level of execution of inter-firm alliance supply chain management (SCM). By drawing on network and resource-based view theories, a conceptual model proposes the effects of SCM resources and capabilities as influencing factors on SCM execution. The model was tested using survey data from studies conducted in two European supply chain environments. Variance-based structural equation modelling confirmed the hypothesised hierarchical order of three proposed antecedents: internal SCM resources affect joint SCM resources, which in turn influence collaborative SCM-related processes and finally SCM execution. An importance-performance analysis for both settings shows that providing and investing in internal SCM resources should be a priority when aiming to increase SCM execution. The theoretical contribution of this paper lies in confirming that the improvement of SCM execution follows a clear pathway featuring internal supply chain resources as one of the main drivers. The practical implications of this research include the development of a prioritisation list of measures that elevate SCM execution in the two country settings

Lipoprotein lipase is active as a monomer

Lipoprotein lipase (LPL), the enzyme that hydrolyzes triglycerides in plasma lipoproteins, is assumed to be active only as a homodimer. In support of this idea, several groups have reported that the size of LPL, as measured by density gradient ultracentrifugation, is ∼110 kDa, twice the size of LPL monomers (∼55 kDa). Of note, however, in those studies the LPL had been incubated with heparin, a polyanionic substance that binds and stabilizes LPL. Here we revisited the assumption that LPL is active only as a homodimer. When freshly secreted human LPL (or purified preparations of LPL) was subjected to density gradient ultracentrifugation (in the absence of heparin), LPL mass and activity peaks exhibited the size expected of monomers (near the 66-kDa albumin standard). GPIHBP1-bound LPL also exhibited the size expected for a monomer. In the presence of heparin, LPL size increased, overlapping with a 97.2-kDa standard. We also used density gradient ultracentrifugation to characterize the LPL within the high-salt and low-salt peaks from a heparin-Sepharose column. The catalytically active LPL within the high-salt peak exhibited the size of monomers, whereas most of the inactive LPL in the low-salt peak was at the bottom of the tube (in aggregates). Consistent with those findings, the LPL in the low-salt peak, but not that in the high-salt peak, was easily detectable with single mAb sandwich ELISAs, in which LPL is captured and detected with the same antibody. We conclude that catalytically active LPL can exist in a monomeric state