Bioluminescence

© 2016 Elsevier Ltd Kahle and Umbers introduce the ways by which organisms emit light though chemical reactions

Institutional Logics and Community Service-Learning in Higher Education

This paper explores how community service-learning (CSL) participants negotiate competing institutional logics in Canadian higher education. Drawing theoretically from new institutionalism and work on institutional logics, we consider how CSL has developed in Canadian universities and how participants discuss CSL in relation to other dominant institutional logics in higher education. Our analysis suggests participants’ responses to competing community, professional, and market logics vary depending on their positions within the field. We see actors’ use of hybrid logics to validate community-engaged learning as the strategy most likely to effect change in the field.  Cet article s’intéresse aux façons dont les participants à une démarche d’apprentissage par le service communautaire (ASC) s’accommodent des différents courants institutionnels présents dans les institutions d’enseignement postsecondaire au Canada. À partir des théories du nouvel institutionnalisme et des divers courants de pensée sur l’institutionnalisme, nous retraçons l’évolution du concept d’ASC au sein des universités canadiennes, tout en discutant des façons dont les participants à cette recherche comparent l’ASC à d’autres approches sur l’institutionnalisme en vigueur en milieu universitaire. Selon notre analyse, les réactions des participants aux approches communautaires, professionnelles et commerciales des institutions concurrentes varient selon les rôles et postes qu’ils occupent dans le milieu universitaire. Les participants adoptent une approche hybride pour valider l’ASC comme étant une stratégie porteuse de changements.&nbsp

Molecular Characterization of Cold Adaptation of Membrane Proteins in the Vibrionaceae Core-Genome

Cold-adaptation strategies have been studied in multiple psychrophilic organisms, especially for psychrophilic enzymes. Decreased enzyme activity caused by low temperatures as well as a higher viscosity of the aqueous environment require certain adaptations to the metabolic machinery of the cell. In addition to this, low temperature has deleterious effects on the lipid bilayer of bacterial membranes and therefore might also affect the embedded membrane proteins. Little is known about the adaptation of membrane proteins to stresses of the cold. In this study we investigate a set of 66 membrane proteins from the core genome of the bacterial family Vibrionaceae to identify general characteristics that discern psychrophilic and mesophilic membrane proteins. Bioinformatical and statistical methods were used to analyze the alignments of the three temperature groups mesophilic, intermediate and psychrophilic. Surprisingly, our results show little or no adaptation to low temperature for those parts of the proteins that are predicted to be inside the membrane. However, changes in amino acid composition and hydrophobicity are found for complete sequences and sequence parts outside the lipid bilayer. Among others, the results presented here indicate a preference for helix-breaking and destabilizing amino acids Ile, Asp and Thr and an avoidance of the helix-forming amino acid Ala in the amino acid composition of psychrophilic membrane proteins. Furthermore, we identified a lower overall hydrophobicity of psychrophilic membrane proteins in comparison to their mesophilic homologs. These results support the stability-flexibility hypothesis and link the cold-adaptation strategies of membrane proteins to those of loop regions of psychrophilic enzymes. © 2012 Kahlke, Thorvaldsen

Energy landscapes of some matching-problem ensembles

The maximum-weight matching problem and the behavior of its energy landscape is numerically investigated. We apply a perturbation method adapted from the analysis of spin glasses. This gives inside into the complexity of the energy landscape of different ensembles. Erd\"os-Renyi graphs and ring graphs with randomly added edges are considered and two types of distributions for the random edge weighs are used. For maximum-weight matching, fast and scalable algorithms exist, such that we can study large graphs of more than $10^5$ nodes. Our results show that the structure of the energy landscape for standard ensembles of matching is simple, comparable to the energy landscape of a ferromagnet. Nonetheless, for some of the here presented ensembles our results allow for the presence of complex energy landscapes in the spirit of Replica-Symmetry Breaking.Comment: 9 pages, 5 figure

Vibrionaceae core, shell and cloud genes are non-randomly distributed on Chr 1: An hypothesis that links the genomic location of genes with their intracellular placement.

BackgroundThe genome of Vibrionaceae bacteria, which consists of two circular chromosomes, is replicated in a highly ordered fashion. In fast-growing bacteria, multifork replication results in higher gene copy numbers and increased expression of genes located close to the origin of replication of Chr 1 (ori1). This is believed to be a growth optimization strategy to satisfy the high demand of essential growth factors during fast growth. The relationship between ori1-proximate growth-related genes and gene expression during fast growth has been investigated by many researchers. However, it remains unclear which other gene categories that are present close to ori1 and if expression of all ori1-proximate genes is increased during fast growth, or if expression is selectively elevated for certain gene categories.ResultsWe calculated the pangenome of all complete genomes from the Vibrionaceae family and mapped the four pangene categories, core, softcore, shell and cloud, to their chromosomal positions. This revealed that core and softcore genes were found heavily biased towards ori1, while shell genes were overrepresented at the opposite part of Chr 1 (i.e., close to ter1). RNA-seq of Aliivibrio salmonicida and Vibrio natriegens showed global gene expression patterns that consistently correlated with chromosomal distance to ori1. Despite a biased gene distribution pattern, all pangene categories contributed to a skewed expression pattern at fast-growing conditions, whereas at slow-growing conditions, softcore, shell and cloud genes were responsible for elevated expression.ConclusionThe pangene categories were non-randomly organized on Chr 1, with an overrepresentation of core and softcore genes around ori1, and overrepresentation of shell and cloud genes around ter1. Furthermore, we mapped our gene distribution data on to the intracellular positioning of chromatin described for V. cholerae, and found that core/softcore and shell/cloud genes appear enriched at two spatially separated intracellular regions. Based on these observations, we hypothesize that there is a link between the genomic location of genes and their cellular placement

Vibrionaceae core, shell and cloud genes are non-randomly distributed on Chr 1: An hypothesis that links the genomic location of genes with their intracellular placement

Background - The genome of Vibrionaceae bacteria, which consists of two circular chromosomes, is replicated in a highly ordered fashion. In fast-growing bacteria, multifork replication results in higher gene copy numbers and increased expression of genes located close to the origin of replication of Chr 1 (ori1). This is believed to be a growth optimization strategy to satisfy the high demand of essential growth factors during fast growth. The relationship between ori1-proximate growth-related genes and gene expression during fast growth has been investigated by many researchers. However, it remains unclear which other gene categories that are present close to ori1 and if expression of all ori1-proximate genes is increased during fast growth, or if expression is selectively elevated for certain gene categories. Results - We calculated the pangenome of all complete genomes from the Vibrionaceae family and mapped the four pangene categories, core, softcore, shell and cloud, to their chromosomal positions. This revealed that core and softcore genes were found heavily biased towards ori1, while shell genes were overrepresented at the opposite part of Chr 1 (i.e., close to ter1). RNA-seq of Aliivibrio salmonicida and Vibrio natriegens showed global gene expression patterns that consistently correlated with chromosomal distance to ori1. Despite a biased gene distribution pattern, all pangene categories contributed to a skewed expression pattern at fast-growing conditions, whereas at slow-growing conditions, softcore, shell and cloud genes were responsible for elevated expression. Conclusion - The pangene categories were non-randomly organized on Chr 1, with an overrepresentation of core and softcore genes around ori1, and overrepresentation of shell and cloud genes around ter1. Furthermore, we mapped our gene distribution data on to the intracellular positioning of chromatin described for V. cholerae, and found that core/softcore and shell/cloud genes appear enriched at two spatially separated intracellular regions. Based on these observations, we hypothesize that there is a link between the genomic location of genes and their cellular placement

Dietary variation and overlap in Central and Northwest European Stephanorhinus kirchbergensis and S. hemitoechus (Rhinocerotidae, Mammalia) influenced by habitat diversity

To trace the dietary evolution of the two abundant Middle to Late Pleistocene rhinoceros species Stephanorhinus kirchbergensis and Stephanorhinus hemitoechus in Europe over several climatic cycles, we examined comprehensive material of stratigraphically well-defined alaeopopulations from different regions and interglacials. Using morphometrics and mesowear analysis, these reconstructions of Stephanorhinus diets indicate that habitat diversity and interspecific competition with closely related rhinoceros species induced variation in feeding behaviour. Although anatomical features of both species suggest significantly higher dietary specializations compared to the Early to early Middle Pleistocene Stephanorhinus hundsheimensis, their mesowear signals are characteristic of a mixed feeder diet, similar to that of extant mammal species in relatively open habitats. Both species retained a degree of dietary flexibility, enabling them to survive in a range of environments. Although each of these rhinoceroses preferred different habitats, species identity alone is not sufficient to establish the real dietary traits of a Stephanorhinus palaeopopulation. As a consequence, their occurrence in a faunal assemblage alone cannot be taken to indicate a specific habitat. S. kirchbergensis and S. hemitoechus were embedded in a dynamic process of temporo-spatial replacements and interspecific differentiation of rhinoceroses in the western Palaearctic. However, dietary specialization in these Middle to Late Pleistocene European rhinoceroses was not the result of a directed time-transgressive evolution. Rather, within the range of each species' ecological tolerance, it was controlled by environmental parameters, with habitat variability as the main factor

Bi-Encoders based Species Normalization -- Pairwise Sentence Learning to Rank

Motivation: Biomedical named-entity normalization involves connecting biomedical entities with distinct database identifiers in order to facilitate data integration across various fields of biology. Existing systems for biomedical named entity normalization heavily rely on dictionaries, manually created rules, and high-quality representative features such as lexical or morphological characteristics. However, recent research has investigated the use of neural network-based models to reduce dependence on dictionaries, manually crafted rules, and features. Despite these advancements, the performance of these models is still limited due to the lack of sufficiently large training datasets. These models have a tendency to overfit small training corpora and exhibit poor generalization when faced with previously unseen entities, necessitating the redesign of rules and features. Contribution: We present a novel deep learning approach for named entity normalization, treating it as a pair-wise learning to rank problem. Our method utilizes the widely-used information retrieval algorithm Best Matching 25 to generate candidate concepts, followed by the application of bi-directional encoder representation from the encoder (BERT) to re-rank the candidate list. Notably, our approach eliminates the need for feature-engineering or rule creation. We conduct experiments on species entity types and evaluate our method against state-of-the-art techniques using LINNAEUS and S800 biomedical corpora. Our proposed approach surpasses existing methods in linking entities to the NCBI taxonomy. To the best of our knowledge, there is no existing neural network-based approach for species normalization in the literature

Der Saiga-Fund von Pahren. Ein Beitrag zur Kenntnis der paläarktischen Verbreitungsgeschichte der Gattung Saiga GRAY 1843 unter besonderer Berücksichtigung des Gebietes der DDR

Ausgehend von einer knappen Darstellung zur Geschichte der Erforschung fossiler Saiga-Reste auf dem Gebiet der DDR wird das bisher vorliegende Fundgut aufgeführt und durch die Beschreibung eines vermutlich letztglazialen Schädelfragmentes von Pahren bei Zeulenroda (Bezirk Gera) ergänzt. Ein Vergleich des Fossils mit entsprechenden Funden Eurasiens führt zur Unterscheidung vorläufiger Formengruppen. Offene taxonomische Probleme werden aufgezeigt. Die regionale Verbreitung fossiler Saiga-Nachweise in der DDR spiegelt den einstigen Verbreitungsraum der Gattung aus taphonomischen und forschungsgeschichtlichen Gründen nicht repräsentativ wider. Die Besiedlung der durch Funde gekennzeichneten Gebiete ist vegetationsgeschichtlich und unter Einbeziehung von Rezentbeobachtungen erklärlich. Es schließt sich ein kurzer Überblick zur bisher bekannten Verbreitungsgeschichte der Gattung Saiga im paläarktischenRaum an.researc