Characterization of the definitive classical calpain family of vertebrates using phylogenetic, evolutionary and expression analyses

Peer reviewedPublisher PD

Playing with nonuniform grids

Numerical experiments with discretization methods on nonuniform grids are presented for the convection-diffusion equation. These show that the accuracy of the discrete solution is not very well predicted by the local truncation error. The diagonal entries in the discrete coefficient matrix give a better clue: the convective term should not reduce the diagonal. Also, iterative solution of the discrete set of equations is discussed. The same criterion appears to be favourable.

Widespread association between the ericoid mycorrhizal fungus Rhizoscyphus ericae and a leafy liverwort in the maritime and sub-Antarctic

A recent study identified a fungal isolate from the Antarctic leafy liverwort Cephaloziella varians as the ericoid mycorrhizal associate Rhizoscyphus ericae. However, nothing is known about the wider Antarctic distribution of R. ericae in C. varians, and inoculation experiments confirming the ability of the fungus to form coils in the liverwort are lacking. Using direct isolation and baiting with Vaccinium macrocarpon seedlings, fungi were isolated from C. varians sampled from eight sites across a 1875-km transect through sub- and maritime Antarctica. The ability of an isolate to form coils in aseptically grown C. varians was also tested. Fungi with 98–99% sequence identity to R. ericae internal transcribed spacer (ITS) region and partial large subunit ribosomal (r)DNA sequences were frequently isolated from C. varians at all sites sampled. The EF4/Fung5 primer set did not amplify small subunit rDNA from three of five R. ericae isolates, probably accounting for the reported absence of the fungus from C. varians in a previous study. Rhizoscyphus ericae was found to colonize aseptically-grown C. varians intracellularly, forming hyphal coils. This study shows that the association between R. ericae and C. varians is apparently widespread in Antarctica, and confirms that R. ericae is at least in part responsible for the formation of the coils observed in rhizoids of field-collected C. varians

Complex -Glycans Influence the Spatial Arrangement of Voltage Gated Potassium Channels in Membranes of Neuronal-Derived Cells

The intrinsic electrical properties of a neuron depend on expression of voltage gated potassium (Kv) channel isoforms, as well as their distribution and density in the plasma membrane. Recently, we showed that N-glycosylation site occupancy of Kv3.1b modulated its placement in the cell body and neurites of a neuronal-derived cell line, B35 neuroblastoma cells. To extrapolate this mechanism to other N-glycosylated Kv channels, we evaluated the impact of N-glycosylation occupancy of Kv3.1a and Kv1.1 channels. Western blots revealed that wild type Kv3.1a and Kv1.1 α-subunits had complex and oligomannose N-glycans, respectively, and that abolishment of the N-glycosylation site(s) generated Kv proteins without N-glycans. Total internal reflection fluorescence microscopy images revealed that N-glycans of Kv3.1a contributed to its placement in the cell membrane while N-glycans had no effect on the distribution of Kv1.1. Based on particle analysis of EGFP-Kv proteins in the adhered membrane, glycosylated forms of Kv3.1a, Kv1.1, and Kv3.1b had differences in the number, size or density of Kv protein clusters in the cell membrane of neurites and cell body of B35 cells. Differences were also observed between the unglycosylated forms of the Kv proteins. Cell dissociation assays revealed that cell-cell adhesion was increased by the presence of complex N-glycans of Kv3.1a, like Kv3.1b, whereas cell adhesion was similar in the oligomannose and unglycosylated Kv1.1 subunit containing B35 cells. Our findings provide direct evidence that N-glycans of Kv3.1 splice variants contribute to the placement of these glycoproteins in the plasma membrane of neuronal-derived cells while those of Kv1.1 were absent. Further when the cell membrane distribution of the Kv channel was modified by N-glycans then the cell-cell adhesion properties were altered. Our study demonstrates that N-glycosylation of Kv3.1a, like Kv3.1b, provides a mechanism for the distribution of these proteins to the cell body and outgrowths and thereby can generate different voltage-dependent conductances in these membranes

Using Social Media to Promote STEM Education: Matching College Students with Role Models

STEM (Science, Technology, Engineering, and Mathematics) fields have become increasingly central to U.S. economic competitiveness and growth. The shortage in the STEM workforce has brought promoting STEM education upfront. The rapid growth of social media usage provides a unique opportunity to predict users' real-life identities and interests from online texts and photos. In this paper, we propose an innovative approach by leveraging social media to promote STEM education: matching Twitter college student users with diverse LinkedIn STEM professionals using a ranking algorithm based on the similarities of their demographics and interests. We share the belief that increasing STEM presence in the form of introducing career role models who share similar interests and demographics will inspire students to develop interests in STEM related fields and emulate their models. Our evaluation on 2,000 real college students demonstrated the accuracy of our ranking algorithm. We also design a novel implementation that recommends matched role models to the students.Comment: 16 pages, 8 figures, accepted by ECML/PKDD 2016, Industrial Trac

Biosemiotics, politics and Th.A. Sebeok’s move from linguistics to semiotics

This paper will focus on the political implications for the language sciences of Sebeok’s move from linguistics to a global semiotic perspective, a move that ultimately resulted in biosemiotics. The paper will seek to make more explicit the political bearing of a biosemiotic perspective in the language sciences and the human sciences in general. In particular, it will discuss the definition of language inherent in Sebeok’s project and the fundamental re-drawing of the grounds of linguistic debate heralded by Sebeok’s embrace of the concept of modelling. Thus far, the political co-ordinates of the biosemiotic project have not really been made explicit. This paper will therefore seek to outline 1. how biosemiotics enables us to reconfigure our understanding of the role of language in culture; 2. how exaptation is central to the evolution of language and communication, rather than adaptation; 3. how communication is the key issue in biosphere, rather than language, not just because communication includes language but because the language sciences often refer to language as if it were mere “chatter”, “tropes” and “figures of speech”; 4. how biosemiotics, despite its seeming “neutrality” arising from its transdisciplinarity, is thoroughly political; 5. how the failure to see the implications of the move from linguistics to semiotics arises from the fact that biosemiotics is devoid of old style politics, which is based on representation (devoid of experience) and “construction of [everything] in discourse” (which is grounded in linguistics, not communication study). In contrast to the post-“linguistic turn” idea that the world is “constructed in discourse”, we will argue that biosemiotics entails a reconfiguration of the polis and, in particular, offers the chance to completely reconceptualise ideology

Sources of Sex Information Used by Young British Women Who Have Sex with Women (WSW) and Women Who Have Sex Exclusively with Men (WSEM): Evidence from the National Survey of Sexual Attitudes and Lifestyles

There is little consideration about the provision of information about sex to women who have sex with women (WSW). This study drew on data from the third National Survey of Sexual Attitudes and Lifestyle, a nationally representative survey of people in Great Britain. Logistic regression was undertaken to examine firstly the relationships between WSW and women who have sex exclusively with men (WSEM) and their main source of information about sex, and secondly between WSW/WSEM and unmet need for information about sex. Each source was included as the binary outcome indicating yes this was the main source, or no this was not the main source of information about sex. The results found that WSW had significantly lower odds of reporting lessons at schools as their main source of information, and significantly higher odds of reporting sources defined as ‘other’ (predominantly first girlfriend/boyfriend or sexual partner) as their main source of information. Reported levels of unmet need for information was also higher amongst young WSW compared with WSEM. This study provides new insights into the sex educational needs of young women and highlights the need for sex education in schools in Great Britain to include information on a full-range of sexual practices, including same-sex sexual relationships

A Sparse Stress Model

Force-directed layout methods constitute the most common approach to draw general graphs. Among them, stress minimization produces layouts of comparatively high quality but also imposes comparatively high computational demands. We propose a speed-up method based on the aggregation of terms in the objective function. It is akin to aggregate repulsion from far-away nodes during spring embedding but transfers the idea from the layout space into a preprocessing phase. An initial experimental study informs a method to select representatives, and subsequent more extensive experiments indicate that our method yields better approximations of minimum-stress layouts in less time than related methods.Comment: Appears in the Proceedings of the 24th International Symposium on Graph Drawing and Network Visualization (GD 2016

Challenges of achieving good environmental status in the Northeast Atlantic

The sustainable exploitation of marine ecosystem services is dependent on achieving and maintaining an adequate ecosystem state to prevent undue deterioration. Within the European Union, the Marine Strategy Framework Directive (MSFD) requires member states to achieve Good Environmental Status (GEnS), specified in terms of 11 descriptors. We analyzed the complexity of social-ecological factors to identify common critical issues that are likely to influence the achievement of GEnS in the Northeast Atlantic (NEA) more broadly, using three case studies. A conceptual model developed using a soft systems approach highlights the complexity of social and ecological phenomena that influence, and are likely to continue to influence, the state of ecosystems in the NEA. The development of the conceptual model raised four issues that complicate the implementation of the MSFD, the majority of which arose in the Pressures and State sections of the model: variability in the system, cumulative effects, ecosystem resilience, and conflicting policy targets. The achievement of GEnS targets for the marine environment requires the recognition and negotiation of trade-offs across a broad policy landscape involving a wide variety of stakeholders in the public and private sectors. Furthermore, potential cumulative effects may introduce uncertainty, particularly in selecting appropriate management measures. There also are endogenous pressures that society cannot control. This uncertainty is even more obvious when variability within the system, e.g., climate change, is accounted for. Also, questions related to the resilience of the affected ecosystem to specific pressures must be raised, despite a lack of current knowledge. Achieving good management and reaching GEnS require multidisciplinary assessments. The soft systems approach provides one mechanism for bringing multidisciplinary information together to look at the problems in a different light

Glycan Structures Contain Information for the Spatial Arrangement of Glycoproteins in the Plasma Membrane

Glycoconjugates at the cell surface are crucial for cells to communicate with each other and the extracellular microenvironment. While it is generally accepted that glycans are vectorial biopolymers, their information content is unclear. This report provides evidence that distinct N-glycan structures influence the spatial arrangement of two integral membrane glycoproteins, Kv3.1 and E-cadherin, at the adherent membrane which in turn alter cellular properties. Distinct N-glycan structures were generated by heterologous expression of these glycoproteins in parental and glycosylation mutant Chinese hamster ovary cell lines. Unlike the N-linked glycans, the O-linked glycans of the mutant cell lines are similar to those of the parental cell line. Western and lectin blots of total membranes and GFP immunopurified samples, combined with glycosidase digestion reactions, were employed to verify the glycoproteins had predominantly complex, oligomannose, and bisecting type N-glycans from Pro(-)5, Lec1, and Lec10B cell lines, respectively. Based on total internal reflection fluorescence and differential interference contrast microscopy techniques, and cellular assays of live parental and glycosylation mutant CHO cells, we propose that glycoproteins with complex, oligomannose or bisecting type N-glycans relay information for localization of glycoproteins to various regions of the plasma membrane in both a glycan-specific and protein-specific manner, and furthermore cell-cell interactions are required for deciphering much of this information. These distinct spatial arrangements also impact cell adhesion and migration. Our findings provide direct evidence that N-glycan structures of glycoproteins contribute significantly to the information content of cells